Setup: Environment and Data
This file starts from the astrocyte object generated in Step 11.5 .
The input object should already contain:
Fernando-defined astrocyte cells
astrocyte subclusters
reactive / inflammatory / stress / ECM module scores
condition informationThe main biological goal is to identify lncRNAs associated with a cluster-defined astrocyte state transition:
Homeostatic-like astrocytes
→ reactive / stress-like PD-enriched astrocytesThis is an astrocyte state analysis , not a broad cell-type discovery analysis.
library (Seurat)library (tidyverse)library (patchwork)library (AnnotationDbi)library (org.Hs.eg.db)set.seed (1234 )<- "/Users/yoshimurasouhei/Downloads/010_school/4年生/bioinfomaticsリサーチクラークシップ/PD_2026" <- file.path ("results" ,"Step11_5_fernando_astrocyte_reclustering" ,"SO_astro_step11_5_fernando_reclustered_scored.rds" <- file.path ("results" ,"Step12_5_fernando_astrocyte_lncRNA_analysis" dir.create (results_dir, recursive = TRUE , showWarnings = FALSE )<- readRDS (input_path)DefaultAssay (SO_astro) <- "RNA" if ("Assay5" %in% class (SO_astro[["RNA" ]])) {<- JoinLayers (SO_astro, assay = "RNA" )
An object of class Seurat
87674 features across 5259 samples within 2 assays
Active assay: RNA (47773 features, 2000 variable features)
3 layers present: counts, data, scale.data
1 other assay present: SCT
4 dimensional reductions calculated: pca, umap, harmony, umap_astro
colnames (SO_astro@ meta.data)
[1] "orig.ident" "nCount_RNA"
[3] "nFeature_RNA" "percent_mt"
[5] "percent_rib" "Damage_score"
[7] "scDblFinder.score" "scDblFinder.class"
[9] "sparsity" "Subject"
[11] "Sample" "condition"
[13] "APOE_e4" "age"
[15] "Sex" "PMI"
[17] "Braak" "MMSE"
[19] "DRS" "snRNA.seq"
[21] "snRNA.seq_Batch_visto" "cond_sex"
[23] "nCount_SCT" "nFeature_SCT"
[25] "SCT_snn_res.1" "seurat_clusters"
[27] "S.Score" "G2M.Score"
[29] "Phase" "preint_clusters1"
[31] "unintegrated_clusters" "SCT_snn_res.0.5"
[33] "Cell_types" "fernando_celltype_annotation"
[35] "condition_use" "astro_original_identity"
[37] "RNA_snn_res.0.3" "Astro_identity_score1"
[39] "Reactive_astro_score1" "Inflammatory_score1"
[41] "Stress_score1" "ECM_score1"
table (SO_astro$ seurat_clusters)
0 1 2 3 4 5 6 7 8 9 10 11
921 806 706 516 443 432 431 423 249 210 62 60
table (SO_astro$ condition)<- c ("Astro_identity_score1" ,"Reactive_astro_score1" ,"Inflammatory_score1" ,"Stress_score1" ,"ECM_score1" <- setdiff (score_cols, colnames (SO_astro@ meta.data))if (length (missing_score_cols) > 0 ) {stop (paste ("Missing score columns from Step 11.5:" ,paste (missing_score_cols, collapse = ", " )
Step 12.1: Refine Astrocyte State Annotation
Here, the main state definition is cluster-based , not quartile-based.
Based on Step 11.5 cluster summaries, the main groups are:
Reactive_stress_like_PD:
clusters 0, 6, 8
Homeostatic_like_C:
clusters 2, 4, 5
Excluded from main binary DE:
clusters 1, 3, 7, 9, 10, 11Cluster 10 is kept out of the main homeostatic group because it is small, mixed by condition, and has weaker astrocyte identity compared with cluster 2.
The combined reactivity score is calculated only for visualization and summary. It is not used to define the main DE groups.
$ astro_cluster <- as.character (SO_astro$ seurat_clusters)<- c ("0" , "6" , "8" )<- c ("2" , "4" , "5" )<- c ("9" , "10" , "11" )$ astro_state_refined <- case_when ($ astro_cluster %in% reactive_stress_clusters ~ "Reactive_stress_like_PD" ,$ astro_cluster %in% homeostatic_clusters ~ "Homeostatic_like_C" ,$ astro_cluster == "3" ~ "PD_enriched_low_reactivity" ,$ astro_cluster == "1" ~ "Mixed_PD_biased" ,$ astro_cluster == "7" ~ "Mixed_balanced" ,$ astro_cluster %in% minor_or_intermediate_clusters ~ "Minor_or_intermediate" ,TRUE ~ "Unassigned" $ astro_state_refined <- factor ($ astro_state_refined,levels = c ("Homeostatic_like_C" ,"Reactive_stress_like_PD" ,"PD_enriched_low_reactivity" ,"Mixed_PD_biased" ,"Mixed_balanced" ,"Minor_or_intermediate" ,"Unassigned" table (SO_astro$ astro_cluster, SO_astro$ astro_state_refined)
Homeostatic_like_C Reactive_stress_like_PD PD_enriched_low_reactivity
0 0 921 0
1 0 0 0
10 0 0 0
11 0 0 0
2 706 0 0
3 0 0 516
4 443 0 0
5 432 0 0
6 0 431 0
7 0 0 0
8 0 249 0
9 0 0 0
Mixed_PD_biased Mixed_balanced Minor_or_intermediate Unassigned
0 0 0 0 0
1 806 0 0 0
10 0 0 62 0
11 0 0 60 0
2 0 0 0 0
3 0 0 0 0
4 0 0 0 0
5 0 0 0 0
6 0 0 0 0
7 0 423 0 0
8 0 0 0 0
9 0 0 210 0
table (SO_astro$ astro_state_refined, SO_astro$ condition)
C PD
Homeostatic_like_C 1578 3
Reactive_stress_like_PD 8 1593
PD_enriched_low_reactivity 12 504
Mixed_PD_biased 303 503
Mixed_balanced 211 212
Minor_or_intermediate 224 108
Unassigned 0 0
<- SO_astro@ meta.data[, c ("Reactive_astro_score1" ,"Inflammatory_score1" ,"Stress_score1" ,"ECM_score1" $ combined_reactivity_score_z <- rowMeans (scale (reactivity_score_matrix),na.rm = TRUE summary (SO_astro$ combined_reactivity_score_z)
Min. 1st Qu. Median Mean 3rd Qu. Max.
-1.2683 -0.5273 -0.1045 0.0000 0.4100 3.7505
<- SO_astro@ meta.data %>% mutate (astro_cluster = as.character (seurat_clusters),astro_state_refined = as.character (astro_state_refined)%>% group_by (astro_cluster, astro_state_refined) %>% summarise (n_cells = n (),mean_astro_identity = mean (Astro_identity_score1, na.rm = TRUE ),mean_combined_reactivity_z = mean (combined_reactivity_score_z, na.rm = TRUE ),mean_reactive = mean (Reactive_astro_score1, na.rm = TRUE ),mean_inflammatory = mean (Inflammatory_score1, na.rm = TRUE ),mean_stress = mean (Stress_score1, na.rm = TRUE ),mean_ecm = mean (ECM_score1, na.rm = TRUE ),percent_PD = mean (condition == "PD" , na.rm = TRUE ),percent_C = mean (condition == "C" , na.rm = TRUE ),.groups = "drop" %>% arrange (desc (mean_combined_reactivity_z))
# A tibble: 12 × 11
astro_cluster astro_state_refined n_cells mean_astro_identity
<chr> <chr> <int> <dbl>
1 0 Reactive_stress_like_PD 921 1.05
2 8 Reactive_stress_like_PD 249 0.510
3 6 Reactive_stress_like_PD 431 0.463
4 4 Homeostatic_like_C 443 1.08
5 5 Homeostatic_like_C 432 1.21
6 1 Mixed_PD_biased 806 0.636
7 11 Minor_or_intermediate 60 0.775
8 9 Minor_or_intermediate 210 0.581
9 3 PD_enriched_low_reactivity 516 0.706
10 2 Homeostatic_like_C 706 0.903
11 7 Mixed_balanced 423 0.472
12 10 Minor_or_intermediate 62 0.691
# ℹ 7 more variables: mean_combined_reactivity_z <dbl>, mean_reactive <dbl>,
# mean_inflammatory <dbl>, mean_stress <dbl>, mean_ecm <dbl>,
# percent_PD <dbl>, percent_C <dbl>
<- SO_astro@ meta.data %>% mutate (astro_cluster = as.character (seurat_clusters),astro_state_refined = as.character (astro_state_refined)%>% group_by (astro_state_refined) %>% summarise (n_cells = n (),mean_astro_identity = mean (Astro_identity_score1, na.rm = TRUE ),mean_combined_reactivity_z = mean (combined_reactivity_score_z, na.rm = TRUE ),mean_reactive = mean (Reactive_astro_score1, na.rm = TRUE ),mean_inflammatory = mean (Inflammatory_score1, na.rm = TRUE ),mean_stress = mean (Stress_score1, na.rm = TRUE ),mean_ecm = mean (ECM_score1, na.rm = TRUE ),percent_PD = mean (condition == "PD" , na.rm = TRUE ),percent_C = mean (condition == "C" , na.rm = TRUE ),clusters_included = paste (sort (unique (astro_cluster)), collapse = ", " ),.groups = "drop" %>% arrange (desc (mean_combined_reactivity_z))
# A tibble: 6 × 11
astro_state_refined n_cells mean_astro_identity mean_combined_reactiv…¹
<chr> <int> <dbl> <dbl>
1 Reactive_stress_like_PD 1601 0.807 0.513
2 Mixed_PD_biased 806 0.636 -0.0523
3 Homeostatic_like_C 1581 1.04 -0.167
4 PD_enriched_low_reactivity 516 0.706 -0.348
5 Minor_or_intermediate 332 0.637 -0.363
6 Mixed_balanced 423 0.472 -0.508
# ℹ abbreviated name: ¹mean_combined_reactivity_z
# ℹ 7 more variables: mean_reactive <dbl>, mean_inflammatory <dbl>,
# mean_stress <dbl>, mean_ecm <dbl>, percent_PD <dbl>, percent_C <dbl>,
# clusters_included <chr>
<- DimPlot (reduction = "umap_astro" ,group.by = "astro_state_refined" ,label = TRUE ,repel = TRUE ,pt.size = 0.5 + labs (title = "Cluster-Based Refined Astrocyte State Annotation" )<- FeaturePlot (features = "combined_reactivity_score_z" ,reduction = "umap_astro" ,pt.size = 0.5 + labs (title = "Z-scored Combined Astrocyte Reactivity Score" )| p_score
$ astro_DE_group <- case_when ($ astro_state_refined == "Reactive_stress_like_PD" ~ "Reactive_stress_like_PD" ,$ astro_state_refined == "Homeostatic_like_C" ~ "Homeostatic_like_C" ,TRUE ~ NA_character_ $ astro_DE_group <- factor ($ astro_DE_group,levels = c ("Homeostatic_like_C" , "Reactive_stress_like_PD" )table (SO_astro$ astro_DE_group, useNA = "ifany" )
Homeostatic_like_C Reactive_stress_like_PD <NA>
1581 1601 2077
table (SO_astro$ astro_DE_group, SO_astro$ condition, useNA = "ifany" )
C PD
Homeostatic_like_C 1578 3
Reactive_stress_like_PD 8 1593
<NA> 750 1327
write.csv (file.path (results_dir, "Step12_1_refined_astrocyte_state_cluster_summary.csv" ),row.names = FALSE write.csv (file.path (results_dir, "Step12_1_refined_astrocyte_state_group_summary.csv" ),row.names = FALSE write.csv (as.data.frame.matrix (table (SO_astro$ astro_state_refined, SO_astro$ condition)),file.path (results_dir, "Step12_1_refined_astrocyte_state_condition_table.csv" )write.csv (as.data.frame.matrix (table (SO_astro$ astro_cluster, SO_astro$ astro_state_refined)),file.path (results_dir, "Step12_1_cluster_to_refined_state_table.csv" )
Step 12.2: Define Comparison Groups for Differential Expression
We define two main comparisons:
1. Reactive_stress_like_PD vs Homeostatic_like_C
2. PD vs C within Fernando-defined astrocytesThe first comparison prioritizes cluster-defined astrocyte state-associated genes.
<- subset (subset = ! is.na (astro_DE_group)$ astro_DE_group <- droplevels (SO_astro_main_DE$ astro_DE_group)table (SO_astro_main_DE$ astro_DE_group)
Homeostatic_like_C Reactive_stress_like_PD
1581 1601
table (SO_astro_main_DE$ astro_DE_group, SO_astro_main_DE$ condition)
C PD
Homeostatic_like_C 1578 3
Reactive_stress_like_PD 8 1593
<- 0.05 <- 0.10 <- 0.05 <- 0.25
Step 12.3: Differential Expression Analysis
We run DE for:
Reactive_stress_like_PD vs Homeostatic_like_C
PD vs C
Idents (SO_astro_main_DE) <- SO_astro_main_DE$ astro_DE_group<- FindMarkers (ident.1 = "Reactive_stress_like_PD" ,ident.2 = "Homeostatic_like_C" ,min.pct = min_pct_use,logfc.threshold = logfc_threshold_use,test.use = "wilcox" %>% rownames_to_column ("gene" ) %>% arrange (p_val_adj, desc (avg_log2FC))%>% head (20 )
gene p_val avg_log2FC pct.1 pct.2 p_val_adj
1 MACF1 4.911134e-218 1.3377014 0.978 0.944 2.346196e-213
2 CTNNA3 6.268922e-193 -2.9109371 0.179 0.664 2.994852e-188
3 SAMD4A 1.188064e-190 1.8055224 0.893 0.698 5.675737e-186
4 CHI3L1 4.366689e-185 3.9070337 0.590 0.132 2.086099e-180
5 SHROOM3 3.717934e-172 -2.2315482 0.247 0.716 1.776169e-167
6 LAMA2 1.114688e-169 -3.3695726 0.083 0.533 5.325197e-165
7 MDGA2 3.974630e-158 -3.7057221 0.064 0.479 1.898800e-153
8 MALAT1 1.576425e-154 -1.0845420 0.999 0.999 7.531054e-150
9 SORBS1 1.026837e-147 0.9546918 0.964 0.932 4.905508e-143
10 NEAT1 6.735259e-147 1.3745627 0.982 0.973 3.217635e-142
11 SLC14A1 1.246036e-144 -2.1177526 0.463 0.815 5.952688e-140
12 MIR3171HG.1 1.104515e-140 -5.9661639 0.011 0.357 5.276599e-136
13 SPARCL1 7.560531e-140 -1.2279617 0.775 0.950 3.611892e-135
14 MEIS2 6.270658e-139 -1.8654372 0.251 0.685 2.995682e-134
15 ENSG00000299261 1.274055e-136 -3.9455646 0.035 0.397 6.086541e-132
16 TMTC2 8.230734e-136 2.8653109 0.618 0.249 3.932068e-131
17 PRKCA 2.090744e-127 1.1960313 0.908 0.835 9.988109e-123
18 NTRK2 4.556233e-125 -1.1765710 0.681 0.911 2.176649e-120
19 SLC4A4 3.863073e-124 -1.2609661 0.600 0.884 1.845506e-119
20 HSPH1 9.417259e-122 4.1160810 0.443 0.096 4.498907e-117
Idents (SO_astro) <- SO_astro$ condition<- FindMarkers (ident.1 = "PD" ,ident.2 = "C" ,min.pct = min_pct_use,logfc.threshold = logfc_threshold_use,test.use = "wilcox" %>% rownames_to_column ("gene" ) %>% arrange (p_val_adj, desc (avg_log2FC))%>% head (20 )
gene p_val avg_log2FC pct.1 pct.2 p_val_adj
1 MALAT1 3.904114e-208 -1.0785343 0.999 0.999 1.865112e-203
2 CTNNA3 8.235943e-169 -2.2641051 0.266 0.575 3.934557e-164
3 SHROOM3 5.544921e-167 -1.6831448 0.313 0.653 2.648975e-162
4 MIR3171HG.1 1.078193e-163 -5.3019563 0.013 0.261 5.150851e-159
5 MDGA2 1.934560e-160 -2.7634112 0.109 0.416 9.241972e-156
6 MACF1 5.147090e-160 0.9162958 0.953 0.929 2.458920e-155
7 SORBS1 3.055967e-153 0.7907757 0.949 0.905 1.459927e-148
8 LAMA2 1.413994e-120 -2.0908767 0.171 0.449 6.755073e-116
9 CHI3L1 2.793107e-118 2.9560471 0.409 0.143 1.334351e-113
10 NEAT1 6.966431e-117 0.8786913 0.978 0.969 3.328073e-112
11 MT-ND3 4.478098e-113 0.9905999 0.900 0.743 2.139322e-108
12 DGKB 2.051512e-112 -1.5855716 0.249 0.522 9.800688e-108
13 SLC4A4 5.277187e-111 -0.9956392 0.620 0.821 2.521071e-106
14 SAMD4A 3.252936e-110 1.2140910 0.811 0.673 1.554025e-105
15 TMTC2 2.705426e-104 1.6778367 0.571 0.301 1.292463e-99
16 HSP90AA1 9.360653e-103 1.3043607 0.741 0.561 4.471865e-98
17 HSPH1 7.423274e-102 3.2857209 0.342 0.103 3.546321e-97
18 PAMR1 2.030730e-101 -1.0918818 0.431 0.686 9.701405e-97
19 DST 5.265388e-101 0.8461550 0.934 0.923 2.515434e-96
20 SPARCL1 1.010250e-99 -0.9123379 0.796 0.905 4.826269e-95
Step 12.4: Cluster-Specific DE Analysis
Here we extract markers for each astrocyte subcluster.
These are subcluster/state markers , not broad astrocyte identity markers.
Idents (SO_astro) <- SO_astro$ seurat_clusters<- FindAllMarkers (only.pos = TRUE ,min.pct = min_pct_use,logfc.threshold = logfc_threshold_use,test.use = "wilcox" %>% arrange (cluster, p_val_adj, desc (avg_log2FC))%>% head (30 )
p_val avg_log2FC pct.1 pct.2 p_val_adj cluster
MACF1 8.379025e-304 1.449995 0.991 0.932 4.002912e-299 0
TPST1 2.641441e-292 2.635258 0.822 0.318 1.261896e-287 0
ARHGEF3 3.696520e-271 2.862048 0.724 0.223 1.765939e-266 0
CD44 1.474182e-265 1.972104 0.924 0.519 7.042612e-261 0
CHI3L1 1.562677e-233 2.730023 0.680 0.209 7.465376e-229 0
COLEC12 2.766009e-230 2.613918 0.775 0.342 1.321405e-225 0
SULF1 9.542085e-214 3.711245 0.434 0.066 4.558540e-209 0
ENSG00000297939 7.032475e-212 3.087899 0.488 0.090 3.359624e-207 0
SLC44A3-AS1 8.742003e-209 2.631803 0.685 0.251 4.176317e-204 0
ENSG00000228408 1.257367e-207 3.066317 0.579 0.156 6.006821e-203 0
DST 4.170632e-201 1.484174 0.965 0.921 1.992436e-196 0
ACTN1 1.419066e-193 3.143134 0.507 0.119 6.779304e-189 0
SAMD4A 3.786126e-183 1.600419 0.912 0.715 1.808746e-178 0
CRISPLD1 6.660049e-183 3.007689 0.507 0.129 3.181705e-178 0
MAP3K14 7.300518e-181 2.831615 0.549 0.157 3.487676e-176 0
SLC39A14 7.773643e-176 2.528831 0.570 0.174 3.713702e-171 0
ZFYVE28 2.131224e-175 2.314126 0.609 0.210 1.018149e-170 0
ANO6 5.297830e-167 2.368319 0.634 0.253 2.530932e-162 0
ENSG00000304278 2.961324e-163 4.388264 0.277 0.027 1.414713e-158 0
NAV2 1.914969e-157 1.089004 0.958 0.894 9.148382e-153 0
TMTC2 5.414732e-157 2.314413 0.730 0.392 2.586780e-152 0
TNC 7.635786e-155 2.255025 0.736 0.405 3.647844e-150 0
FN1 1.502225e-151 3.976176 0.368 0.072 7.176581e-147 0
F3 6.836960e-151 2.291800 0.610 0.245 3.266221e-146 0
ETV6 1.957076e-150 1.908684 0.746 0.429 9.349541e-146 0
GNA14 6.091452e-147 2.893224 0.529 0.181 2.910069e-142 0
GFRA2 2.364266e-146 3.444080 0.313 0.047 1.129481e-141 0
GFAP 1.338196e-144 1.119851 0.940 0.784 6.392966e-140 0
PMP2 9.984503e-141 2.277491 0.628 0.287 4.769896e-136 0
CPNE8 2.382086e-139 2.434396 0.549 0.205 1.137994e-134 0
gene
MACF1 MACF1
TPST1 TPST1
ARHGEF3 ARHGEF3
CD44 CD44
CHI3L1 CHI3L1
COLEC12 COLEC12
SULF1 SULF1
ENSG00000297939 ENSG00000297939
SLC44A3-AS1 SLC44A3-AS1
ENSG00000228408 ENSG00000228408
DST DST
ACTN1 ACTN1
SAMD4A SAMD4A
CRISPLD1 CRISPLD1
MAP3K14 MAP3K14
SLC39A14 SLC39A14
ZFYVE28 ZFYVE28
ANO6 ANO6
ENSG00000304278 ENSG00000304278
NAV2 NAV2
TMTC2 TMTC2
TNC TNC
FN1 FN1
F3 F3
ETV6 ETV6
GNA14 GNA14
GFRA2 GFRA2
GFAP GFAP
PMP2 PMP2
CPNE8 CPNE8
<- astro_cluster_markers %>% group_by (cluster) %>% slice_min (order_by = p_val_adj, n = 20 , with_ties = FALSE ) %>% ungroup ()
# A tibble: 240 × 7
p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene
<dbl> <dbl> <dbl> <dbl> <dbl> <fct> <chr>
1 8.38e-304 1.45 0.991 0.932 4.00e-299 0 MACF1
2 2.64e-292 2.64 0.822 0.318 1.26e-287 0 TPST1
3 3.70e-271 2.86 0.724 0.223 1.77e-266 0 ARHGEF3
4 1.47e-265 1.97 0.924 0.519 7.04e-261 0 CD44
5 1.56e-233 2.73 0.68 0.209 7.47e-229 0 CHI3L1
6 2.77e-230 2.61 0.775 0.342 1.32e-225 0 COLEC12
7 9.54e-214 3.71 0.434 0.066 4.56e-209 0 SULF1
8 7.03e-212 3.09 0.488 0.09 3.36e-207 0 ENSG00000297939
9 8.74e-209 2.63 0.685 0.251 4.18e-204 0 SLC44A3-AS1
10 1.26e-207 3.07 0.579 0.156 6.01e-203 0 ENSG00000228408
# ℹ 230 more rows
Step 12.5: Identify lncRNA Candidates
We define lncRNA candidates using gene symbols and available gene annotation.
This step uses two complementary approaches:
1. Symbol-based detection for common lncRNA-style names
2. AnnotationDbi / org.Hs.eg.db annotation where available
<- paste (c ("^LINC" ,"-AS[0-9]*$" ,"^AC[0-9]" ,"^AL[0-9]" ,"^AP[0-9]" ,"^MIR[0-9].*HG$" ,"^SNHG" ,"^NEAT1$" ,"^MALAT1$" ,"^XIST$" ,"^KCNQ1OT1$" ,"^MEG3$" ,"^H19$" collapse = "|"
[1] "^LINC|-AS[0-9]*$|^AC[0-9]|^AL[0-9]|^AP[0-9]|^MIR[0-9].*HG$|^SNHG|^NEAT1$|^MALAT1$|^XIST$|^KCNQ1OT1$|^MEG3$|^H19$"
<- function (de_table) {%>% mutate (lncRNA_symbol_like = str_detect (regex (lncRNA_symbol_pattern, ignore_case = FALSE )<- add_lncRNA_symbol_flag (astro_reactive_vs_homeostatic_DE)<- add_lncRNA_symbol_flag (astro_PD_vs_C_DE)<- add_lncRNA_symbol_flag (astro_cluster_markers)
Step 12.6: Add Gene Annotation for Ensembl IDs
If row names are gene symbols, this step adds available Entrez/Ensembl annotation from org.Hs.eg.db.
If some genes are already Ensembl IDs, this step also tries to map them to symbols.
<- unique (c ($ gene,$ gene,$ gene<- all_genes[! str_detect (all_genes, "^ENSG" )]<- all_genes[str_detect (all_genes, "^ENSG" )]if (length (symbol_genes) > 0 ) {<- AnnotationDbi:: select (keys = symbol_genes,keytype = "SYMBOL" ,columns = c ("SYMBOL" , "ENTREZID" , "ENSEMBL" , "GENENAME" )%>% as_tibble () %>% distinct (SYMBOL, .keep_all = TRUE ) %>% mutate (gene = SYMBOL) %>% :: select (gene, SYMBOL, ENTREZID, ENSEMBL, GENENAME)else {<- tibble (gene = character (),SYMBOL = character (),ENTREZID = character (),ENSEMBL = character (),GENENAME = character ()if (length (ensembl_like_genes) > 0 ) {<- AnnotationDbi:: select (keys = ensembl_like_genes,keytype = "ENSEMBL" ,columns = c ("SYMBOL" , "ENTREZID" , "ENSEMBL" , "GENENAME" )%>% as_tibble () %>% distinct (ENSEMBL, .keep_all = TRUE ) %>% mutate (gene = ENSEMBL) %>% :: select (gene, SYMBOL, ENTREZID, ENSEMBL, GENENAME)else {<- tibble (gene = character (),SYMBOL = character (),ENTREZID = character (),ENSEMBL = character (),GENENAME = character ()<- bind_rows (%>% distinct (gene, .keep_all = TRUE )%>% head (20 )
# A tibble: 20 × 5
gene SYMBOL ENTREZID ENSEMBL GENENAME
<chr> <chr> <chr> <chr> <chr>
1 MACF1 MACF1 23499 ENSG00000127603 microtubule actin crosslink…
2 CTNNA3 CTNNA3 29119 ENSG00000183230 catenin alpha 3
3 SAMD4A SAMD4A 23034 ENSG00000020577 sterile alpha motif domain …
4 CHI3L1 CHI3L1 1116 ENSG00000133048 chitinase 3 like 1
5 SHROOM3 SHROOM3 57619 ENSG00000138771 shroom family member 3
6 LAMA2 LAMA2 3908 ENSG00000196569 laminin subunit alpha 2
7 MDGA2 MDGA2 161357 ENSG00000139915 MAM domain containing glyco…
8 MALAT1 MALAT1 378938 ENSG00000251562 metastasis associated lung …
9 SORBS1 SORBS1 10580 ENSG00000095637 sorbin and SH3 domain conta…
10 NEAT1 NEAT1 283131 ENSG00000245532 nuclear paraspeckle assembl…
11 SLC14A1 SLC14A1 6563 ENSG00000141469 solute carrier family 14 me…
12 MIR3171HG.1 MIR3171HG.1 <NA> <NA> <NA>
13 SPARCL1 SPARCL1 8404 ENSG00000152583 SPARC like 1
14 MEIS2 MEIS2 4212 ENSG00000134138 Meis homeobox 2
15 TMTC2 TMTC2 160335 ENSG00000179104 transmembrane O-mannosyltra…
16 PRKCA PRKCA 5578 ENSG00000154229 protein kinase C alpha
17 NTRK2 NTRK2 4915 ENSG00000148053 neurotrophic receptor tyros…
18 SLC4A4 SLC4A4 8671 ENSG00000080493 solute carrier family 4 mem…
19 HSPH1 HSPH1 10808 ENSG00000120694 heat shock protein family H…
20 CNTN1 CNTN1 1272 ENSG00000018236 contactin 1
<- function (de_table) {%>% left_join (gene_annotation, by = "gene" ) %>% mutate (gene_symbol_for_plot = case_when (! is.na (SYMBOL) ~ SYMBOL,TRUE ~ genelncRNA_annotated_like = case_when (~ TRUE ,str_detect (gene_symbol_for_plot, regex (lncRNA_symbol_pattern)) ~ TRUE ,TRUE ~ FALSE <- annotate_de_table (astro_reactive_vs_homeostatic_DE)<- annotate_de_table (astro_PD_vs_C_DE)<- annotate_de_table (astro_cluster_markers)
Step 12.7: Extract Annotated lncRNA Candidates
We extract lncRNA-like candidates from each comparison.
<- astro_reactive_vs_homeostatic_annotated %>% filter (< p_adj_cutoff,abs (avg_log2FC) >= lncRNA_logfc_cutoff%>% arrange (p_val_adj, desc (abs (avg_log2FC)))<- astro_PD_vs_C_annotated %>% filter (< p_adj_cutoff,abs (avg_log2FC) >= lncRNA_logfc_cutoff%>% arrange (p_val_adj, desc (abs (avg_log2FC)))<- astro_cluster_markers_annotated %>% filter (< p_adj_cutoff,abs (avg_log2FC) >= lncRNA_logfc_cutoff%>% arrange (cluster, p_val_adj, desc (avg_log2FC))%>% head (30 )
gene p_val avg_log2FC pct.1 pct.2 p_val_adj
1 MALAT1 1.576425e-154 -1.0845420 0.999 0.999 7.531054e-150
2 NEAT1 6.735259e-147 1.3745627 0.982 0.973 3.217635e-142
3 MIR9-1HG 2.324876e-101 -1.1546672 0.490 0.805 1.110663e-96
4 SLC44A3-AS1 1.186607e-78 2.1948605 0.508 0.236 5.668776e-74
5 OBI1-AS1 4.877087e-76 -0.7804023 0.778 0.929 2.329931e-71
6 MIR9-2HG 8.063893e-68 -0.9675675 0.465 0.742 3.852364e-63
7 MIR4300HG 1.738300e-56 -1.3761905 0.319 0.567 8.304380e-52
8 POT1-AS1 1.060027e-52 -1.5792964 0.169 0.406 5.064069e-48
9 UFL1-AS1 5.625404e-50 -2.2780168 0.048 0.230 2.687424e-45
10 PARD6G-AS1 6.780393e-48 3.7422278 0.162 0.015 3.239197e-43
11 SNHG14 2.763769e-47 -0.7431429 0.643 0.837 1.320335e-42
12 ZBTB47-AS1 2.382862e-44 -2.3180731 0.055 0.226 1.138365e-39
13 GNG12-AS1 5.376493e-44 -2.1136746 0.064 0.239 2.568512e-39
14 PCDH9-AS2 1.054542e-41 -1.9696666 0.061 0.229 5.037861e-37
15 LINC03122 6.274795e-39 -1.8833119 0.067 0.232 2.997658e-34
16 SLC38A4-AS1 3.089697e-37 -1.0271390 0.162 0.369 1.476041e-32
17 LINC00412 3.122074e-36 -1.6541773 0.063 0.219 1.491509e-31
18 LINC-PINT 4.700455e-34 0.6813181 0.836 0.818 2.245548e-29
19 XIST 8.160380e-34 1.0386112 0.506 0.307 3.898459e-29
20 PTCHD1-AS 1.040683e-33 0.8249788 0.711 0.625 4.971655e-29
21 MIR99AHG 1.379086e-33 -0.3390699 0.807 0.929 6.588306e-29
22 LINC01376 1.428940e-31 -1.5774871 0.076 0.225 6.826476e-27
23 PAX8-AS1 4.718901e-31 -2.4511875 0.019 0.125 2.254361e-26
24 LINC02232 5.067363e-31 -3.5482579 0.010 0.106 2.420831e-26
25 HEY2-AS1 6.328208e-28 -2.6337186 0.021 0.120 3.023175e-23
26 ENSG00000257545 4.963220e-27 -1.5686148 0.095 0.234 2.371079e-22
27 HOXB-AS1 9.671189e-27 -4.5063008 0.003 0.078 4.620217e-22
28 DBX2-AS1 3.096548e-26 -1.7286998 0.061 0.183 1.479314e-21
29 HECTD2-AS1 7.314350e-26 -1.3889513 0.055 0.175 3.494285e-21
30 LMCD1-AS1 1.167732e-25 -0.5235736 0.525 0.708 5.578605e-21
lncRNA_symbol_like SYMBOL ENTREZID ENSEMBL
1 TRUE MALAT1 378938 ENSG00000251562
2 TRUE NEAT1 283131 ENSG00000245532
3 TRUE MIR9-1HG 10485 ENSG00000125462
4 TRUE SLC44A3-AS1 101928079 ENSG00000293271
5 TRUE OBI1-AS1 100874222 ENSG00000234377
6 TRUE MIR9-2HG 645323 ENSG00000245526
7 TRUE MIR4300HG 101928989 ENSG00000245832
8 TRUE POT1-AS1 401398 ENSG00000224897
9 TRUE UFL1-AS1 100861530 <NA>
10 TRUE PARD6G-AS1 100130522 ENSG00000267270
11 TRUE SNHG14 104472715 <NA>
12 TRUE ZBTB47-AS1 101928323 <NA>
13 TRUE GNG12-AS1 100289178 ENSG00000232284
14 TRUE PCDH9-AS2 100874064 ENSG00000228842
15 TRUE LINC03122 285668 ENSG00000178722
16 TRUE SLC38A4-AS1 100288798 ENSG00000257261
17 TRUE LINC00412 102723332 <NA>
18 TRUE LINC-PINT 378805 ENSG00000231721
19 TRUE XIST 7503 ENSG00000229807
20 TRUE PTCHD1-AS 100873065 <NA>
21 TRUE MIR99AHG 388815 ENSG00000215386
22 TRUE LINC01376 400945 ENSG00000236204
23 TRUE PAX8-AS1 654433 ENSG00000189223
24 TRUE LINC02232 401134 ENSG00000250125
25 TRUE HEY2-AS1 105377986 ENSG00000237742
26 FALSE RFX4-AS1 100287944 ENSG00000257545
27 TRUE HOXB-AS1 100874362 ENSG00000230148
28 TRUE DBX2-AS1 120766145 <NA>
29 TRUE HECTD2-AS1 100188947 ENSG00000289228
30 TRUE LMCD1-AS1 100288428 ENSG00000227110
GENENAME
1 metastasis associated lung adenocarcinoma transcript 1
2 nuclear paraspeckle assembly transcript 1
3 MIR9-1 host gene
4 SLC44A3 antisense RNA 1
5 OBI1 antisense RNA 1
6 MIR9-2 host gene
7 MIR4300 host gene
8 POT1 antisense RNA 1
9 UFL1 antisense RNA 1
10 PARD6G antisense RNA 1
11 small nucleolar RNA host gene 14
12 ZBTB47 and NKTR antisense RNA 1
13 GNG12, DIRAS3 and WLS antisense RNA 1
14 PCDH9 antisense RNA 2
15 long intergenic non-protein coding RNA 3122
16 SLC38A4 antisense RNA 1
17 long intergenic non-protein coding RNA 412
18 long intergenic non-protein coding RNA, p53 induced transcript
19 X inactive specific transcript
20 PTCHD1 and PHEX antisense RNA
21 mir-99a-let-7c cluster host gene
22 long intergenic non-protein coding RNA 1376
23 PAX8 antisense RNA 1
24 long intergenic non-protein coding RNA 2232
25 HEY2 antisense RNA 1
26 RFX4 antisense RNA 1
27 HOXB cluster antisense RNA 1
28 DBX2 antisense RNA 1
29 HECTD2 antisense RNA 1
30 LMCD1 antisense RNA 1
gene_symbol_for_plot lncRNA_annotated_like
1 MALAT1 TRUE
2 NEAT1 TRUE
3 MIR9-1HG TRUE
4 SLC44A3-AS1 TRUE
5 OBI1-AS1 TRUE
6 MIR9-2HG TRUE
7 MIR4300HG TRUE
8 POT1-AS1 TRUE
9 UFL1-AS1 TRUE
10 PARD6G-AS1 TRUE
11 SNHG14 TRUE
12 ZBTB47-AS1 TRUE
13 GNG12-AS1 TRUE
14 PCDH9-AS2 TRUE
15 LINC03122 TRUE
16 SLC38A4-AS1 TRUE
17 LINC00412 TRUE
18 LINC-PINT TRUE
19 XIST TRUE
20 PTCHD1-AS TRUE
21 MIR99AHG TRUE
22 LINC01376 TRUE
23 PAX8-AS1 TRUE
24 LINC02232 TRUE
25 HEY2-AS1 TRUE
26 RFX4-AS1 TRUE
27 HOXB-AS1 TRUE
28 DBX2-AS1 TRUE
29 HECTD2-AS1 TRUE
30 LMCD1-AS1 TRUE
%>% head (30 )
gene p_val avg_log2FC pct.1 pct.2 p_val_adj
1 MALAT1 3.904114e-208 -1.0785343 0.999 0.999 1.865112e-203
2 NEAT1 6.966431e-117 0.8786913 0.978 0.969 3.328073e-112
3 XIST 3.557471e-87 1.2858607 0.563 0.321 1.699511e-82
4 OBI1-AS1 8.957876e-78 -0.6859095 0.753 0.874 4.279446e-73
5 MIR9-1HG 1.668211e-54 -0.6348170 0.559 0.729 7.969543e-50
6 SLC44A3-AS1 1.123083e-53 1.6386193 0.406 0.229 5.365303e-49
7 LINC00609 7.080087e-52 2.2084204 0.325 0.158 3.382370e-47
8 LINC-PINT 7.873246e-47 0.5638433 0.856 0.811 3.761286e-42
9 LINC02232 1.191495e-40 -3.3450042 0.009 0.084 5.692130e-36
10 PARD6G-AS1 6.513569e-39 2.7031355 0.118 0.022 3.111727e-34
11 PCDH9-AS2 4.253215e-38 -1.7008230 0.071 0.185 2.031888e-33
12 LINC02608 1.878389e-37 3.3371588 0.092 0.011 8.973627e-33
13 POT1-AS1 2.435508e-37 -1.1404088 0.208 0.354 1.163515e-32
14 MIR9-2HG 6.986588e-37 -0.5590838 0.541 0.682 3.337703e-32
15 SNHG14 3.191637e-33 -0.5304722 0.684 0.788 1.524741e-28
16 HOXB-AS1 1.901957e-32 -4.0556306 0.005 0.062 9.086220e-28
17 PAX8-AS1 8.063820e-31 -2.0379081 0.023 0.096 3.852329e-26
18 UFL1-AS1 2.535847e-29 -1.4241608 0.100 0.206 1.211450e-24
19 LINC03082 6.022537e-28 1.4480734 0.177 0.075 2.877146e-23
20 GNG12-AS1 1.910602e-27 -1.2630328 0.087 0.185 9.127518e-23
21 LMCD1-AS1 3.354721e-27 -0.4804939 0.553 0.682 1.602651e-22
22 LINC02649 2.582638e-26 -0.4312792 0.374 0.525 1.233804e-21
23 A2ML1-AS1 5.438267e-25 -2.2663428 0.015 0.071 2.598023e-20
24 ENSG00000257545 5.209622e-24 -1.4020254 0.095 0.188 2.488793e-19
25 LINC00499 4.027478e-23 -1.4627475 0.145 0.241 1.924047e-18
26 GBX2-AS1 4.130220e-23 -0.8578170 0.140 0.247 1.973130e-18
27 LINC01748 4.385189e-23 -0.5107564 0.365 0.491 2.094936e-18
28 AP1S2 1.558181e-22 1.2481882 0.215 0.116 7.443896e-18
29 LINC01727 7.708870e-21 -2.1462329 0.022 0.076 3.682758e-16
30 ENTPD1-AS1 8.047007e-21 -0.6912777 0.270 0.382 3.844297e-16
lncRNA_symbol_like SYMBOL ENTREZID ENSEMBL
1 TRUE MALAT1 378938 ENSG00000251562
2 TRUE NEAT1 283131 ENSG00000245532
3 TRUE XIST 7503 ENSG00000229807
4 TRUE OBI1-AS1 100874222 ENSG00000234377
5 TRUE MIR9-1HG 10485 ENSG00000125462
6 TRUE SLC44A3-AS1 101928079 ENSG00000293271
7 TRUE LINC00609 101101773 ENSG00000257585
8 TRUE LINC-PINT 378805 ENSG00000231721
9 TRUE LINC02232 401134 ENSG00000250125
10 TRUE PARD6G-AS1 100130522 ENSG00000267270
11 TRUE PCDH9-AS2 100874064 ENSG00000228842
12 TRUE LINC02608 101929541 ENSG00000226251
13 TRUE POT1-AS1 401398 ENSG00000224897
14 TRUE MIR9-2HG 645323 ENSG00000245526
15 TRUE SNHG14 104472715 <NA>
16 TRUE HOXB-AS1 100874362 ENSG00000230148
17 TRUE PAX8-AS1 654433 ENSG00000189223
18 TRUE UFL1-AS1 100861530 <NA>
19 TRUE LINC03082 101927646 ENSG00000275830
20 TRUE GNG12-AS1 100289178 ENSG00000232284
21 TRUE LMCD1-AS1 100288428 ENSG00000227110
22 TRUE LINC02649 399715 ENSG00000215244
23 TRUE A2ML1-AS1 100874108 <NA>
24 FALSE RFX4-AS1 100287944 ENSG00000257545
25 TRUE LINC00499 100874047 ENSG00000251372
26 TRUE GBX2-AS1 121853074 ENSG00000233611
27 TRUE LINC01748 105378763 ENSG00000226476
28 TRUE AP1S2 8905 ENSG00000182287
29 TRUE LINC01727 101929625 <NA>
30 TRUE ENTPD1-AS1 728558 ENSG00000226688
GENENAME
1 metastasis associated lung adenocarcinoma transcript 1
2 nuclear paraspeckle assembly transcript 1
3 X inactive specific transcript
4 OBI1 antisense RNA 1
5 MIR9-1 host gene
6 SLC44A3 antisense RNA 1
7 long intergenic non-protein coding RNA 609
8 long intergenic non-protein coding RNA, p53 induced transcript
9 long intergenic non-protein coding RNA 2232
10 PARD6G antisense RNA 1
11 PCDH9 antisense RNA 2
12 long intergenic non-protein coding RNA 2608
13 POT1 antisense RNA 1
14 MIR9-2 host gene
15 small nucleolar RNA host gene 14
16 HOXB cluster antisense RNA 1
17 PAX8 antisense RNA 1
18 UFL1 antisense RNA 1
19 long intergenic non-protein coding RNA 3082
20 GNG12, DIRAS3 and WLS antisense RNA 1
21 LMCD1 antisense RNA 1
22 long intergenic non-protein coding RNA 2649
23 A2ML1 antisense RNA 1
24 RFX4 antisense RNA 1
25 long intergenic non-protein coding RNA 499
26 GBX2 and ASB18 antisense RNA 1
27 long intergenic non-protein coding RNA 1748
28 adaptor related protein complex 1 subunit sigma 2
29 long intergenic non-protein coding RNA 1727
30 ENTPD1 antisense RNA 1
gene_symbol_for_plot lncRNA_annotated_like
1 MALAT1 TRUE
2 NEAT1 TRUE
3 XIST TRUE
4 OBI1-AS1 TRUE
5 MIR9-1HG TRUE
6 SLC44A3-AS1 TRUE
7 LINC00609 TRUE
8 LINC-PINT TRUE
9 LINC02232 TRUE
10 PARD6G-AS1 TRUE
11 PCDH9-AS2 TRUE
12 LINC02608 TRUE
13 POT1-AS1 TRUE
14 MIR9-2HG TRUE
15 SNHG14 TRUE
16 HOXB-AS1 TRUE
17 PAX8-AS1 TRUE
18 UFL1-AS1 TRUE
19 LINC03082 TRUE
20 GNG12-AS1 TRUE
21 LMCD1-AS1 TRUE
22 LINC02649 TRUE
23 A2ML1-AS1 TRUE
24 RFX4-AS1 TRUE
25 LINC00499 TRUE
26 GBX2-AS1 TRUE
27 LINC01748 TRUE
28 AP1S2 TRUE
29 LINC01727 TRUE
30 ENTPD1-AS1 TRUE
%>% head (30 )
p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene
1 8.742003e-209 2.6318030 0.685 0.251 4.176317e-204 0 SLC44A3-AS1
2 6.324121e-130 1.1923412 0.826 0.377 3.021222e-125 0 XIST
3 2.512517e-83 2.7566790 0.355 0.117 1.200305e-78 0 BAALC-AS1
4 1.451409e-82 2.7640326 0.279 0.071 6.933817e-78 0 ENSG00000225339
5 3.727745e-74 5.5093739 0.091 0.003 1.780856e-69 0 LINC01141
6 8.762268e-34 3.2402029 0.086 0.015 4.185998e-29 0 LINC02149
7 8.474345e-32 2.2878437 0.156 0.051 4.048449e-27 0 SNHG31
8 1.696937e-31 2.8286122 0.107 0.026 8.106778e-27 0 SOCS2-AS1
9 2.133988e-29 1.5687449 0.284 0.147 1.019470e-24 0 AP1S2
10 1.935949e-26 0.9473323 0.545 0.419 9.248607e-22 0 LINC02649
11 2.016538e-25 1.4668162 0.227 0.106 9.633606e-21 0 MIR646HG
12 4.288853e-24 3.0928547 0.054 0.008 2.048914e-19 0 LINC01507
13 8.100093e-19 0.5715078 0.686 0.620 3.869657e-14 0 PTCHD1-AS
14 4.538572e-12 1.7310517 0.090 0.038 2.168212e-07 0 ENSG00000258926
15 6.267751e-12 2.0678675 0.077 0.030 2.994293e-07 0 LINC01982
16 1.769349e-11 0.8133984 0.403 0.325 8.452712e-07 0 GABPB1-AS1
17 1.689691e-10 1.5084002 0.077 0.032 8.072163e-06 0 LINC00378
18 3.195055e-10 2.0993945 0.061 0.023 1.526374e-05 0 GNA14-AS1
19 4.161150e-09 1.3188744 0.142 0.084 1.987906e-04 0 LINC02930
20 8.626027e-09 1.8119770 0.068 0.030 4.120912e-04 0 SCN1A-AS1
21 2.022796e-08 1.2628007 0.177 0.117 9.663503e-04 0 TSC22D1-AS1
22 1.044957e-07 1.3530253 0.055 0.023 4.992074e-03 0 MIR325HG
23 1.190234e-07 1.4343420 0.111 0.063 5.686105e-03 0 SAMD4A-AS1
24 2.434808e-07 1.0018066 0.093 0.050 1.163181e-02 0 LINC02177
25 2.470816e-07 1.6585276 0.062 0.028 1.180383e-02 0 MMP25-AS1
26 8.992759e-07 1.5792062 0.051 0.022 4.296111e-02 0 SNHG12
27 3.112877e-46 0.8556845 0.968 0.976 1.487115e-41 1 NEAT1
28 5.441906e-32 0.8602506 0.775 0.702 2.599762e-27 1 LINC01088
29 2.977688e-27 2.3731592 0.105 0.026 1.422531e-22 1 LINC00906
30 1.732202e-18 1.1937929 0.341 0.222 8.275247e-14 1 LINC00836
lncRNA_symbol_like SYMBOL ENTREZID ENSEMBL
1 TRUE SLC44A3-AS1 101928079 ENSG00000293271
2 TRUE XIST 7503 ENSG00000229807
3 TRUE BAALC-AS1 100499183 <NA>
4 FALSE SMIM29-AS1 139281638 ENSG00000225339
5 TRUE LINC01141 339505 <NA>
6 TRUE LINC02149 101929454 <NA>
7 TRUE SNHG31 101928103 ENSG00000229267
8 TRUE SOCS2-AS1 144481 ENSG00000246985
9 TRUE AP1S2 8905 ENSG00000182287
10 TRUE LINC02649 399715 ENSG00000215244
11 TRUE MIR646HG 284757 ENSG00000228340
12 TRUE LINC01507 101927477 <NA>
13 TRUE PTCHD1-AS 100873065 <NA>
14 FALSE PRKCH-AS2 105370525 ENSG00000258926
15 TRUE LINC01982 105371830 ENSG00000263317
16 TRUE GABPB1-AS1 100129387 <NA>
17 TRUE LINC00378 101926930 <NA>
18 TRUE GNA14-AS1 101927422 ENSG00000231373
19 TRUE LINC02930 105378516 ENSG00000274461
20 TRUE SCN1A-AS1 101929680 ENSG00000236107
21 TRUE TSC22D1-AS1 641467 ENSG00000278156
22 TRUE MIR325HG 101928469 ENSG00000280870
23 TRUE SAMD4A-AS1 729451 <NA>
24 TRUE LINC02177 101927009 ENSG00000261617
25 TRUE MMP25-AS1 100507419 <NA>
26 TRUE SNHG12 85028 ENSG00000197989
27 TRUE NEAT1 283131 ENSG00000245532
28 TRUE LINC01088 100505875 <NA>
29 TRUE LINC00906 148145 ENSG00000267339
30 TRUE LINC00836 101929052 ENSG00000280809
GENENAME gene_symbol_for_plot
1 SLC44A3 antisense RNA 1 SLC44A3-AS1
2 X inactive specific transcript XIST
3 BAALC antisense RNA 1 BAALC-AS1
4 SMIM29 antisense RNA 1 SMIM29-AS1
5 long intergenic non-protein coding RNA 1141 LINC01141
6 long intergenic non-protein coding RNA 2149 LINC02149
7 small nucleolar RNA host gene 31 SNHG31
8 SOCS2 antisense RNA 1 SOCS2-AS1
9 adaptor related protein complex 1 subunit sigma 2 AP1S2
10 long intergenic non-protein coding RNA 2649 LINC02649
11 MIR646 host gene MIR646HG
12 long intergenic non-protein coding RNA 1507 LINC01507
13 PTCHD1 and PHEX antisense RNA PTCHD1-AS
14 PRKCH antisense RNA 2 PRKCH-AS2
15 long intergenic non-protein coding RNA 1982 LINC01982
16 GABPB1 antisense RNA 1 GABPB1-AS1
17 long intergenic non-protein coding RNA 378 LINC00378
18 GNA14 antisense RNA 1 GNA14-AS1
19 long intergenic non-protein coding RNA 2930 LINC02930
20 SCN1A and SCN9A antisense RNA 1 SCN1A-AS1
21 TSC22D1 antisense RNA 1 TSC22D1-AS1
22 MIR325 host gene MIR325HG
23 SAMD4A antisense RNA 1 SAMD4A-AS1
24 long intergenic non-protein coding RNA 2177 LINC02177
25 MMP25 antisense RNA 1 MMP25-AS1
26 small nucleolar RNA host gene 12 SNHG12
27 nuclear paraspeckle assembly transcript 1 NEAT1
28 long intergenic non-protein coding RNA 1088 LINC01088
29 long intergenic non-protein coding RNA 906 LINC00906
30 long intergenic non-protein coding RNA 836 LINC00836
lncRNA_annotated_like
1 TRUE
2 TRUE
3 TRUE
4 TRUE
5 TRUE
6 TRUE
7 TRUE
8 TRUE
9 TRUE
10 TRUE
11 TRUE
12 TRUE
13 TRUE
14 TRUE
15 TRUE
16 TRUE
17 TRUE
18 TRUE
19 TRUE
20 TRUE
21 TRUE
22 TRUE
23 TRUE
24 TRUE
25 TRUE
26 TRUE
27 TRUE
28 TRUE
29 TRUE
30 TRUE
Step 12.8: Prioritize lncRNAs Shared Across Comparisons
The strongest candidates are lncRNAs associated with both the reactive/stress-like astrocyte state and PD status.
<- reactive_lncRNA_candidates %>% :: select (avg_log2FC_reactive_vs_homeostatic = avg_log2FC,p_val_adj_reactive_vs_homeostatic = p_val_adj,pct.1_reactive = pct.1 ,pct.2_homeostatic = pct.2 ,%>% inner_join (%>% :: select (avg_log2FC_PD_vs_C = avg_log2FC,p_val_adj_PD_vs_C = p_val_adj,pct.1_PD = pct.1 ,pct.2_C = pct.2 by = "gene" %>% mutate (same_direction = sign (avg_log2FC_reactive_vs_homeostatic) == sign (avg_log2FC_PD_vs_C),priority_score = - log10 (p_val_adj_reactive_vs_homeostatic + 1e-300 ) + - log10 (p_val_adj_PD_vs_C + 1e-300 ) + abs (avg_log2FC_reactive_vs_homeostatic) + abs (avg_log2FC_PD_vs_C)%>% arrange (desc (same_direction), desc (priority_score))
gene gene_symbol_for_plot avg_log2FC_reactive_vs_homeostatic
1 MALAT1 MALAT1 -1.0845420
2 NEAT1 NEAT1 1.3745627
3 MIR9-1HG MIR9-1HG -1.1546672
4 OBI1-AS1 OBI1-AS1 -0.7804023
5 SLC44A3-AS1 SLC44A3-AS1 2.1948605
6 XIST XIST 1.0386112
7 MIR9-2HG MIR9-2HG -0.9675675
8 PARD6G-AS1 PARD6G-AS1 3.7422278
9 POT1-AS1 POT1-AS1 -1.5792964
10 PCDH9-AS2 PCDH9-AS2 -1.9696666
11 UFL1-AS1 UFL1-AS1 -2.2780168
12 LINC-PINT LINC-PINT 0.6813181
13 SNHG14 SNHG14 -0.7431429
14 LINC02232 LINC02232 -3.5482579
15 GNG12-AS1 GNG12-AS1 -2.1136746
16 MIR4300HG MIR4300HG -1.3761905
17 HOXB-AS1 HOXB-AS1 -4.5063008
18 PAX8-AS1 PAX8-AS1 -2.4511875
19 ZBTB47-AS1 ZBTB47-AS1 -2.3180731
20 LINC00412 LINC00412 -1.6541773
21 LINC03122 LINC03122 -1.8833119
22 A2ML1-AS1 A2ML1-AS1 -2.8471687
23 ENSG00000257545 RFX4-AS1 -1.5686148
24 LMCD1-AS1 LMCD1-AS1 -0.5235736
25 LINC02608 LINC02608 2.4331917
26 LINC01376 LINC01376 -1.5774871
27 LINC01727 LINC01727 -4.1531683
28 SLC38A4-AS1 SLC38A4-AS1 -1.0271390
29 LINC01748 LINC01748 -0.5289954
30 HECTD2-AS1 HECTD2-AS1 -1.3889513
31 HEY2-AS1 HEY2-AS1 -2.6337186
32 PTCHD1-AS PTCHD1-AS 0.8249788
33 LRP4-AS1 LRP4-AS1 -3.2142539
34 LINC01572 LINC01572 -1.4602397
35 ANK2-AS1 ANK2-AS1 -2.6043069
36 PKIA-AS1 PKIA-AS1 -2.9101779
37 DBX2-AS1 DBX2-AS1 -1.7286998
38 ENTPD1-AS1 ENTPD1-AS1 -0.6786507
39 GBX2-AS1 GBX2-AS1 -0.7910011
40 LINC00173 LINC00173 -1.2509725
41 RAP2C-AS1 RAP2C-AS1 -1.7403309
42 RASSF8-AS1 RASSF8-AS1 -1.0654679
43 TET2-AS1 TET2-AS1 1.5461079
44 LIFR-AS1 LIFR-AS1 -2.3646125
45 BAALC-AS1 BAALC-AS1 1.9699019
46 SOCS2-AS1 SOCS2-AS1 2.9038008
47 AP1S2 AP1S2 1.3954165
48 GASK1B-AS1 GASK1B-AS1 -0.7620764
49 LINC00960 LINC00960 -1.8085364
50 ATP13A4-AS1 ATP13A4-AS1 -2.0601332
51 LINC01414 LINC01414 -2.4219273
52 SLC28A2-AS1 SLC28A2-AS1 -1.2546195
53 MIR4500HG MIR4500HG -2.4564245
54 LINC00499 LINC00499 -1.2669032
55 MIDEAS-AS1 MIDEAS-AS1 -2.1047880
56 SNED1-AS1 SNED1-AS1 -2.0433184
57 MEF2C-AS1 MEF2C-AS1 -0.7341850
58 HEXIM2-AS1 HEXIM2-AS1 -0.9379578
59 ZKSCAN7-AS1 ZKSCAN7-AS1 -1.1009480
60 LINC03062 LINC03062 -2.5855973
61 CALCRL-AS1 CALCRL-AS1 -1.4599570
62 FSIP2-AS1 FSIP2-AS1 -0.7595069
63 USP3-AS1 USP3-AS1 -1.7767793
64 LINC00378 LINC00378 2.1267031
65 NECTIN3-AS1 NECTIN3-AS1 -2.9074828
66 WEE2-AS1 WEE2-AS1 -2.3028693
67 PDE7B-AS1 PDE7B-AS1 -1.1195818
68 ZNF337-AS1 ZNF337-AS1 -0.9198971
69 MIR219A2HG MIR219A2HG -1.8896088
70 LINC01117 LINC01117 -1.7541741
71 IPO9-AS1 IPO9-AS1 -1.3286924
72 LINC02580 LINC02580 -1.3816355
73 OTX2-AS1 OTX2-AS1 2.9017871
74 LIX1-AS1 LIX1-AS1 -1.2574453
75 SYNPO2L-AS1 SYNPO2L-AS1 -1.2648196
76 ENSG00000303699 ANKRD17-AS1 -1.5284179
77 LINC00240 LINC00240 -1.5438983
78 BDNF-AS BDNF-AS -0.7941867
79 LINC00862 LINC00862 1.5586712
80 BCL10-AS1 BCL10-AS1 -2.1383304
81 NR2F1-AS1 NR2F1-AS1 -0.5012591
82 LINC02614 LINC02614 -0.9224436
83 PDK4-AS1 PDK4-AS1 -1.0305083
84 TMEM72-AS1 TMEM72-AS1 -1.0091249
85 UBE2D3-AS1 UBE2D3-AS1 1.6360227
86 EIF1B-AS1 EIF1B-AS1 -0.5186210
87 DAAM2-AS1 DAAM2-AS1 -1.7214142
88 MIR9-3HG MIR9-3HG -1.0149620
89 LSAMP-AS1 LSAMP-AS1 -1.4696069
90 ENSG00000225339 SMIM29-AS1 1.5609970
91 LINC00472 LINC00472 0.9223688
92 ITGA9-AS1 ITGA9-AS1 -0.5956222
93 ZFPM2-AS1 ZFPM2-AS1 -1.9082963
94 LINC00467 LINC00467 -1.3848838
95 LINC00844 LINC00844 -0.8087702
96 ZFHX3-AS1 ZFHX3-AS1 -1.6656193
97 ENSG00000287158 LINC03214 -1.4928563
98 LINC01994 LINC01994 -0.8380970
99 ENSG00000258162 PPFIA2-AS2 -1.5247043
100 MIR3659HG MIR3659HG 1.5856483
101 JAKMIP2-AS1 JAKMIP2-AS1 -1.3164264
102 RHOQ-AS1 RHOQ-AS1 -1.7468010
103 LINC02796 LINC02796 -0.6065784
104 LINC02934 LINC02934 -0.4288249
105 PRKCA-AS1 PRKCA-AS1 -0.8366604
106 DPP10-AS3 DPP10-AS3 -1.3361915
107 RBMS3-AS3 RBMS3-AS3 -1.5543115
108 AP1AR AP1AR 1.4325981
109 LINC03051 LINC03051 0.4705735
110 LINC02895 LINC02895 -0.6752028
p_val_adj_reactive_vs_homeostatic pct.1_reactive pct.2_homeostatic
1 7.531054e-150 0.999 0.999
2 3.217635e-142 0.982 0.973
3 1.110663e-96 0.490 0.805
4 2.329931e-71 0.778 0.929
5 5.668776e-74 0.508 0.236
6 3.898459e-29 0.506 0.307
7 3.852364e-63 0.465 0.742
8 3.239197e-43 0.162 0.015
9 5.064069e-48 0.169 0.406
10 5.037861e-37 0.061 0.229
11 2.687424e-45 0.048 0.230
12 2.245548e-29 0.836 0.818
13 1.320335e-42 0.643 0.837
14 2.420831e-26 0.010 0.106
15 2.568512e-39 0.064 0.239
16 8.304380e-52 0.319 0.567
17 4.620217e-22 0.003 0.078
18 2.254361e-26 0.019 0.125
19 1.138365e-39 0.055 0.226
20 1.491509e-31 0.063 0.219
21 2.997658e-34 0.067 0.232
22 6.510260e-20 0.013 0.095
23 2.371079e-22 0.095 0.234
24 5.578605e-21 0.525 0.708
25 1.251068e-05 0.051 0.012
26 6.826476e-27 0.076 0.225
27 3.420788e-20 0.006 0.080
28 1.476041e-32 0.162 0.369
29 2.343689e-19 0.359 0.552
30 3.494285e-21 0.055 0.175
31 3.023175e-23 0.021 0.120
32 4.971655e-29 0.711 0.625
33 3.112172e-17 0.007 0.075
34 3.222778e-19 0.052 0.163
35 9.870437e-17 0.020 0.099
36 2.104432e-19 0.016 0.100
37 1.479314e-21 0.061 0.183
38 3.463486e-15 0.254 0.408
39 1.372355e-12 0.152 0.279
40 1.277363e-19 0.060 0.178
41 1.698291e-16 0.031 0.119
42 9.932642e-18 0.104 0.234
43 2.567255e-11 0.177 0.083
44 8.193928e-18 0.023 0.109
45 4.533165e-17 0.247 0.126
46 8.319323e-10 0.072 0.016
47 1.104988e-07 0.207 0.123
48 1.490042e-10 0.150 0.263
49 1.165603e-13 0.034 0.115
50 8.703296e-12 0.026 0.094
51 5.590474e-10 0.014 0.068
52 4.050410e-15 0.048 0.144
53 1.642947e-11 0.014 0.073
54 2.308796e-04 0.187 0.254
55 6.921594e-11 0.011 0.065
56 4.400615e-11 0.017 0.078
57 3.655561e-19 0.241 0.413
58 3.007789e-14 0.073 0.181
59 4.258019e-16 0.064 0.173
60 2.123997e-11 0.012 0.068
61 2.003744e-08 0.033 0.096
62 4.434546e-15 0.169 0.312
63 1.663182e-11 0.017 0.080
64 1.042241e-05 0.054 0.013
65 1.767182e-13 0.012 0.075
66 2.808869e-11 0.015 0.074
67 8.706967e-10 0.053 0.132
68 1.408456e-11 0.059 0.150
69 2.947967e-06 0.020 0.067
70 3.181638e-07 0.019 0.068
71 5.277608e-12 0.037 0.116
72 6.212818e-12 0.045 0.127
73 2.448193e-09 0.081 0.023
74 1.435700e-11 0.065 0.156
75 3.363365e-13 0.041 0.127
76 5.706931e-07 0.041 0.103
77 4.163614e-07 0.021 0.072
78 3.282729e-10 0.121 0.228
79 1.107380e-06 0.091 0.034
80 4.561151e-09 0.019 0.074
81 6.773300e-12 0.330 0.475
82 4.979919e-12 0.129 0.242
83 2.349247e-11 0.067 0.158
84 1.666430e-11 0.080 0.178
85 1.691957e-06 0.112 0.049
86 2.362974e-09 0.236 0.362
87 1.194161e-09 0.029 0.093
88 1.303006e-09 0.081 0.171
89 8.009277e-07 0.032 0.089
90 1.352302e-08 0.179 0.096
91 8.015808e-06 0.458 0.421
92 5.918311e-11 0.154 0.275
93 1.982926e-05 0.019 0.063
94 1.892471e-07 0.031 0.089
95 1.232605e-09 0.101 0.200
96 1.276877e-07 0.028 0.085
97 3.588883e-07 0.037 0.098
98 1.670540e-05 0.072 0.142
99 7.016993e-05 0.024 0.070
100 5.929153e-04 0.087 0.039
101 1.995836e-04 0.031 0.078
102 3.953795e-04 0.024 0.066
103 2.010877e-06 0.120 0.209
104 3.256543e-07 0.264 0.388
105 7.953078e-03 0.070 0.125
106 4.968059e-05 0.025 0.071
107 6.315568e-04 0.024 0.065
108 2.143264e-02 0.074 0.034
109 6.502419e-05 0.736 0.746
110 6.031012e-03 0.073 0.130
GENENAME
1 metastasis associated lung adenocarcinoma transcript 1
2 nuclear paraspeckle assembly transcript 1
3 MIR9-1 host gene
4 OBI1 antisense RNA 1
5 SLC44A3 antisense RNA 1
6 X inactive specific transcript
7 MIR9-2 host gene
8 PARD6G antisense RNA 1
9 POT1 antisense RNA 1
10 PCDH9 antisense RNA 2
11 UFL1 antisense RNA 1
12 long intergenic non-protein coding RNA, p53 induced transcript
13 small nucleolar RNA host gene 14
14 long intergenic non-protein coding RNA 2232
15 GNG12, DIRAS3 and WLS antisense RNA 1
16 MIR4300 host gene
17 HOXB cluster antisense RNA 1
18 PAX8 antisense RNA 1
19 ZBTB47 and NKTR antisense RNA 1
20 long intergenic non-protein coding RNA 412
21 long intergenic non-protein coding RNA 3122
22 A2ML1 antisense RNA 1
23 RFX4 antisense RNA 1
24 LMCD1 antisense RNA 1
25 long intergenic non-protein coding RNA 2608
26 long intergenic non-protein coding RNA 1376
27 long intergenic non-protein coding RNA 1727
28 SLC38A4 antisense RNA 1
29 long intergenic non-protein coding RNA 1748
30 HECTD2 antisense RNA 1
31 HEY2 antisense RNA 1
32 PTCHD1 and PHEX antisense RNA
33 LRP4 antisense RNA 1
34 long intergenic non-protein coding RNA 1572
35 ANK2 antisense RNA 1
36 PKIA antisense RNA 1
37 DBX2 antisense RNA 1
38 ENTPD1 antisense RNA 1
39 GBX2 and ASB18 antisense RNA 1
40 long intergenic non-protein coding RNA 173
41 RAP2C antisense RNA 1
42 RASSF8 antisense RNA 1
43 TET2 antisense RNA 1
44 LIFR antisense RNA 1
45 BAALC antisense RNA 1
46 SOCS2 antisense RNA 1
47 adaptor related protein complex 1 subunit sigma 2
48 GASK1B antisense RNA 1
49 long intergenic non-protein coding RNA 960
50 ATP13A4 antisense RNA 1
51 long intergenic non-protein coding RNA 1414
52 SLC28A2 antisense RNA 1
53 MIR4500 host gene
54 long intergenic non-protein coding RNA 499
55 MIDEAS antisense RNA 1
56 SNED1 antisense RNA 1
57 MEF2C antisense RNA 1
58 HEXIM2 antisense RNA 1
59 ZKSCAN7 ZNF cluster antisense RNA 1
60 long intergenic non-protein coding RNA 3062
61 CALCRL and TFPI antisense RNA 1
62 FSIP2 antisense RNA 1
63 USP3 antisense RNA 1
64 long intergenic non-protein coding RNA 378
65 NECTIN3 antisense RNA 1
66 WEE2 antisense RNA 1
67 PDE7B antisense RNA 1
68 ZNF337 antisense RNA 1
69 MIR219A2 host gene
70 long intergenic non-protein coding RNA 1117
71 IPO9 antisense RNA 1
72 long intergenic non-protein coding RNA 2580
73 OTX2 antisense RNA 1
74 LIX1 and RIOK2 antisense RNA 1
75 SYNPO2L antisense RNA 1
76 ANKRD17 antisense RNA1
77 long intergenic non-protein coding RNA 240
78 BDNF antisense RNA
79 long intergenic non-protein coding RNA 862
80 BCL10 antisense RNA 1
81 NR2F1 regulatory antisense RNA 1
82 long intergenic non-protein coding RNA 2614
83 PDK4 antisense RNA 1
84 TMEM72 antisense RNA 1
85 UBE2D3 antisense RNA 1
86 EIF1B antisense RNA 1
87 DAAM2 antisense RNA 1
88 MIR9-3 host gene
89 LSAMP antisense RNA 1
90 SMIM29 antisense RNA 1
91 long intergenic non-protein coding RNA 472
92 ITGA9 antisense RNA 1
93 ZFPM2 antisense RNA 1
94 long intergenic non-protein coding RNA 467
95 long intergenic non-protein coding RNA 844
96 ZFHX3 antisense RNA 1
97 long intergenic non-protein coding RNA 3214
98 long intergenic non-protein coding RNA 1994
99 PPFIA2 antisense RNA 2
100 MIR3659 host gene
101 JAKMIP2 antisense RNA 1
102 RHOQ antisense RNA 1
103 long intergenic non-protein coding RNA 2796
104 long intergenic non-protein coding RNA 2934
105 PRKCA antisense RNA 1
106 DPP10 antisense RNA 3
107 RBMS3 antisense RNA 3
108 adaptor related protein complex 1 associated regulatory protein
109 long intergenic non-protein coding RNA 3051
110 long intergenic non-protein coding RNA 2895
avg_log2FC_PD_vs_C p_val_adj_PD_vs_C pct.1_PD pct.2_C same_direction
1 -1.0785343 1.865112e-203 0.999 0.999 TRUE
2 0.8786913 3.328073e-112 0.978 0.969 TRUE
3 -0.6348170 7.969543e-50 0.559 0.729 TRUE
4 -0.6859095 4.279446e-73 0.753 0.874 TRUE
5 1.6386193 5.365303e-49 0.406 0.229 TRUE
6 1.2858607 1.699511e-82 0.563 0.321 TRUE
7 -0.5590838 3.337703e-32 0.541 0.682 TRUE
8 2.7031355 3.111727e-34 0.118 0.022 TRUE
9 -1.1404088 1.163515e-32 0.208 0.354 TRUE
10 -1.7008230 2.031888e-33 0.071 0.185 TRUE
11 -1.4241608 1.211450e-24 0.100 0.206 TRUE
12 0.5638433 3.761286e-42 0.856 0.811 TRUE
13 -0.5304722 1.524741e-28 0.684 0.788 TRUE
14 -3.3450042 5.692130e-36 0.009 0.084 TRUE
15 -1.2630328 9.127518e-23 0.087 0.185 TRUE
16 -0.3826847 3.402057e-06 0.402 0.481 TRUE
17 -4.0556306 9.086220e-28 0.005 0.062 TRUE
18 -2.0379081 3.852329e-26 0.023 0.096 TRUE
19 -1.1977744 1.730185e-13 0.121 0.203 TRUE
20 -1.0041436 1.908970e-14 0.108 0.192 TRUE
21 -0.7953887 2.527353e-11 0.132 0.213 TRUE
22 -2.2663428 2.598023e-20 0.015 0.071 TRUE
23 -1.4020254 2.488793e-19 0.095 0.188 TRUE
24 -0.4804939 1.602651e-22 0.553 0.682 TRUE
25 3.3371588 8.973627e-33 0.092 0.011 TRUE
26 -0.9334588 2.621275e-13 0.120 0.205 TRUE
27 -2.1462329 3.682758e-16 0.022 0.076 TRUE
28 -0.5356175 6.442011e-08 0.227 0.311 TRUE
29 -0.5107564 2.094936e-18 0.365 0.491 TRUE
30 -1.0857890 2.722708e-14 0.077 0.153 TRUE
31 -1.4310725 3.328734e-10 0.044 0.098 TRUE
32 0.3840640 3.855021e-07 0.652 0.606 TRUE
33 -2.4653985 2.536101e-13 0.014 0.057 TRUE
34 -1.2175268 7.039090e-14 0.066 0.137 TRUE
35 -2.0617487 7.873702e-13 0.027 0.077 TRUE
36 -1.7806304 5.116827e-10 0.032 0.080 TRUE
37 -1.0621147 9.223505e-10 0.082 0.147 TRUE
38 -0.6912777 3.844297e-16 0.270 0.382 TRUE
39 -0.8578170 1.973130e-18 0.140 0.247 TRUE
40 -0.8934571 7.264393e-11 0.069 0.135 TRUE
41 -1.2403898 7.949843e-12 0.053 0.114 TRUE
42 -0.8599095 4.999190e-10 0.125 0.200 TRUE
43 1.1735145 2.246857e-15 0.173 0.086 TRUE
44 -1.3251389 9.795100e-08 0.051 0.100 TRUE
45 1.2507027 1.965654e-08 0.190 0.119 TRUE
46 2.5328871 3.205104e-13 0.061 0.014 TRUE
47 1.2481882 7.443896e-18 0.215 0.116 TRUE
48 -0.9390244 7.411156e-16 0.138 0.233 TRUE
49 -1.4989419 6.298500e-10 0.038 0.087 TRUE
50 -1.8837620 6.789299e-11 0.026 0.072 TRUE
51 -2.2000756 1.084779e-11 0.019 0.062 TRUE
52 -1.0324631 2.030816e-08 0.072 0.131 TRUE
53 -1.8622106 1.004560e-09 0.020 0.060 TRUE
54 -1.4627475 1.924047e-18 0.145 0.241 TRUE
55 -1.7928889 3.561712e-10 0.014 0.051 TRUE
56 -1.6182813 8.616760e-10 0.022 0.064 TRUE
57 -0.3033979 1.693342e-03 0.323 0.398 TRUE
58 -0.6881924 1.129753e-07 0.100 0.164 TRUE
59 -0.7325966 1.846123e-05 0.094 0.149 TRUE
60 -1.7315357 2.687633e-07 0.019 0.054 TRUE
61 -1.6336982 2.237494e-11 0.033 0.083 TRUE
62 -0.5366656 4.912220e-06 0.207 0.278 TRUE
63 -1.4075043 1.038754e-07 0.026 0.066 TRUE
64 1.9176396 1.354137e-12 0.061 0.015 TRUE
65 -1.5334647 2.083619e-04 0.028 0.061 TRUE
66 -1.5212145 3.770219e-07 0.023 0.060 TRUE
67 -1.2077131 1.396314e-09 0.048 0.101 TRUE
68 -0.8570729 8.650509e-08 0.076 0.134 TRUE
69 -1.9527912 1.067118e-10 0.024 0.068 TRUE
70 -1.6799383 5.811928e-10 0.015 0.053 TRUE
71 -1.0080648 6.225659e-05 0.050 0.092 TRUE
72 -0.9498066 7.167198e-05 0.066 0.111 TRUE
73 1.4726849 2.411075e-05 0.066 0.029 TRUE
74 -0.8830735 3.146696e-05 0.087 0.139 TRUE
75 -0.8009231 1.895176e-03 0.064 0.106 TRUE
76 -1.5731402 1.310611e-08 0.032 0.076 TRUE
77 -1.6760204 3.061914e-08 0.026 0.066 TRUE
78 -0.6863693 9.725967e-07 0.139 0.206 TRUE
79 1.0898264 6.905976e-09 0.096 0.043 TRUE
80 -1.5546684 4.077856e-05 0.027 0.061 TRUE
81 -0.3255635 8.698939e-05 0.385 0.458 TRUE
82 -0.6547661 9.459607e-04 0.168 0.223 TRUE
83 -0.7743301 2.033560e-03 0.090 0.135 TRUE
84 -0.5999107 2.813741e-03 0.114 0.164 TRUE
85 1.1927386 9.762336e-07 0.100 0.051 TRUE
86 -0.4332346 8.009286e-05 0.293 0.360 TRUE
87 -1.2034929 1.563902e-02 0.039 0.069 TRUE
88 -0.7669306 1.351762e-03 0.100 0.148 TRUE
89 -1.3777549 3.701280e-05 0.040 0.078 TRUE
90 1.1038821 1.475434e-03 0.128 0.082 TRUE
91 0.5760819 3.018961e-07 0.482 0.420 TRUE
92 -0.3769998 1.344479e-02 0.211 0.268 TRUE
93 -1.5876122 5.350543e-05 0.020 0.051 TRUE
94 -1.0521023 1.956912e-03 0.043 0.079 TRUE
95 -0.5279199 4.012277e-02 0.120 0.166 TRUE
96 -1.1075559 1.683174e-02 0.042 0.074 TRUE
97 -1.1679230 8.163301e-03 0.047 0.081 TRUE
98 -0.8802699 2.367852e-05 0.072 0.121 TRUE
99 -1.3962449 2.191334e-04 0.027 0.060 TRUE
100 1.1126372 1.843104e-05 0.090 0.046 TRUE
101 -1.3442059 3.803868e-04 0.029 0.061 TRUE
102 -1.6176164 1.415566e-03 0.026 0.055 TRUE
103 -0.5799762 4.504183e-03 0.128 0.179 TRUE
104 -0.3467941 1.448512e-02 0.300 0.366 TRUE
105 -1.0205611 8.579029e-06 0.054 0.100 TRUE
106 -1.1193793 9.337767e-03 0.026 0.054 TRUE
107 -1.3326728 2.169708e-03 0.024 0.052 TRUE
108 1.0889663 8.213554e-04 0.070 0.034 TRUE
109 0.2826169 5.626406e-03 0.730 0.721 TRUE
110 -0.8321417 9.758364e-04 0.074 0.118 TRUE
priority_score
1 354.015516
2 255.223524
3 146.842468
4 144.467581
5 125.350396
6 112.503255
7 95.417476
8 82.441924
9 81.949433
10 72.660344
11 72.189536
12 71.318503
13 70.969735
14 67.754023
15 64.006673
16 58.307826
17 56.938886
18 55.550349
19 55.221473
20 47.203896
21 46.799253
22 43.885270
23 43.199705
24 43.052703
25 42.720101
26 41.258237
27 41.199102
28 40.584637
29 37.348681
30 36.496381
31 36.062049
32 35.926515
33 34.782422
34 34.322020
35 32.775540
36 32.658673
37 32.655858
38 31.245598
39 31.216196
40 31.176916
41 29.850350
42 28.229413
43 27.958578
44 27.785250
45 27.270696
46 27.010758
47 26.728447
48 26.658016
49 25.441690
50 25.172387
51 24.839213
52 24.371913
53 24.101035
54 24.082050
55 23.505812
56 23.082742
57 22.245884
58 22.094919
59 21.938076
60 21.560609
61 21.442051
62 20.958046
63 20.946831
64 20.894712
65 20.874848
66 20.799186
67 20.242445
68 19.691185
69 19.344665
70 19.167141
71 17.820135
72 17.682804
73 17.603416
74 17.485600
75 17.261319
76 17.227682
77 17.114455
78 16.976388
79 16.764976
80 16.423492
81 16.056556
82 15.904114
83 15.125653
84 14.937964
85 14.610818
86 13.674803
87 13.653635
88 13.536046
89 13.375417
90 13.364886
91 13.114646
92 13.071870
93 12.470204
94 11.868386
95 11.642475
96 11.440897
97 11.193954
98 11.121155
99 10.734090
100 10.659743
101 9.780282
102 9.616473
103 9.229553
104 9.101940
105 9.023248
106 8.789141
107 8.750171
108 7.275958
109 7.189884
110 6.737577
<- cluster_lncRNA_candidates %>% group_by (gene) %>% summarise (cluster_support = paste (sort (unique (cluster)), collapse = ";" ),max_cluster_log2FC = max (avg_log2FC, na.rm = TRUE ),min_cluster_p_val_adj = min (p_val_adj, na.rm = TRUE ),.groups = "drop" <- priority_astro_lncRNAs %>% left_join (cluster_lncRNA_support, by = "gene" ) %>% arrange (desc (same_direction), desc (priority_score))
gene gene_symbol_for_plot avg_log2FC_reactive_vs_homeostatic
1 MALAT1 MALAT1 -1.0845420
2 NEAT1 NEAT1 1.3745627
3 MIR9-1HG MIR9-1HG -1.1546672
4 OBI1-AS1 OBI1-AS1 -0.7804023
5 SLC44A3-AS1 SLC44A3-AS1 2.1948605
6 XIST XIST 1.0386112
7 MIR9-2HG MIR9-2HG -0.9675675
8 PARD6G-AS1 PARD6G-AS1 3.7422278
9 POT1-AS1 POT1-AS1 -1.5792964
10 PCDH9-AS2 PCDH9-AS2 -1.9696666
11 UFL1-AS1 UFL1-AS1 -2.2780168
12 LINC-PINT LINC-PINT 0.6813181
13 SNHG14 SNHG14 -0.7431429
14 LINC02232 LINC02232 -3.5482579
15 GNG12-AS1 GNG12-AS1 -2.1136746
16 MIR4300HG MIR4300HG -1.3761905
17 HOXB-AS1 HOXB-AS1 -4.5063008
18 PAX8-AS1 PAX8-AS1 -2.4511875
19 ZBTB47-AS1 ZBTB47-AS1 -2.3180731
20 LINC00412 LINC00412 -1.6541773
21 LINC03122 LINC03122 -1.8833119
22 A2ML1-AS1 A2ML1-AS1 -2.8471687
23 ENSG00000257545 RFX4-AS1 -1.5686148
24 LMCD1-AS1 LMCD1-AS1 -0.5235736
25 LINC02608 LINC02608 2.4331917
26 LINC01376 LINC01376 -1.5774871
27 LINC01727 LINC01727 -4.1531683
28 SLC38A4-AS1 SLC38A4-AS1 -1.0271390
29 LINC01748 LINC01748 -0.5289954
30 HECTD2-AS1 HECTD2-AS1 -1.3889513
31 HEY2-AS1 HEY2-AS1 -2.6337186
32 PTCHD1-AS PTCHD1-AS 0.8249788
33 LRP4-AS1 LRP4-AS1 -3.2142539
34 LINC01572 LINC01572 -1.4602397
35 ANK2-AS1 ANK2-AS1 -2.6043069
36 PKIA-AS1 PKIA-AS1 -2.9101779
37 DBX2-AS1 DBX2-AS1 -1.7286998
38 ENTPD1-AS1 ENTPD1-AS1 -0.6786507
39 GBX2-AS1 GBX2-AS1 -0.7910011
40 LINC00173 LINC00173 -1.2509725
41 RAP2C-AS1 RAP2C-AS1 -1.7403309
42 RASSF8-AS1 RASSF8-AS1 -1.0654679
43 TET2-AS1 TET2-AS1 1.5461079
44 LIFR-AS1 LIFR-AS1 -2.3646125
45 BAALC-AS1 BAALC-AS1 1.9699019
46 SOCS2-AS1 SOCS2-AS1 2.9038008
47 AP1S2 AP1S2 1.3954165
48 GASK1B-AS1 GASK1B-AS1 -0.7620764
49 LINC00960 LINC00960 -1.8085364
50 ATP13A4-AS1 ATP13A4-AS1 -2.0601332
51 LINC01414 LINC01414 -2.4219273
52 SLC28A2-AS1 SLC28A2-AS1 -1.2546195
53 MIR4500HG MIR4500HG -2.4564245
54 LINC00499 LINC00499 -1.2669032
55 MIDEAS-AS1 MIDEAS-AS1 -2.1047880
56 SNED1-AS1 SNED1-AS1 -2.0433184
57 MEF2C-AS1 MEF2C-AS1 -0.7341850
58 HEXIM2-AS1 HEXIM2-AS1 -0.9379578
59 ZKSCAN7-AS1 ZKSCAN7-AS1 -1.1009480
60 LINC03062 LINC03062 -2.5855973
61 CALCRL-AS1 CALCRL-AS1 -1.4599570
62 FSIP2-AS1 FSIP2-AS1 -0.7595069
63 USP3-AS1 USP3-AS1 -1.7767793
64 LINC00378 LINC00378 2.1267031
65 NECTIN3-AS1 NECTIN3-AS1 -2.9074828
66 WEE2-AS1 WEE2-AS1 -2.3028693
67 PDE7B-AS1 PDE7B-AS1 -1.1195818
68 ZNF337-AS1 ZNF337-AS1 -0.9198971
69 MIR219A2HG MIR219A2HG -1.8896088
70 LINC01117 LINC01117 -1.7541741
71 IPO9-AS1 IPO9-AS1 -1.3286924
72 LINC02580 LINC02580 -1.3816355
73 OTX2-AS1 OTX2-AS1 2.9017871
74 LIX1-AS1 LIX1-AS1 -1.2574453
75 SYNPO2L-AS1 SYNPO2L-AS1 -1.2648196
76 ENSG00000303699 ANKRD17-AS1 -1.5284179
77 LINC00240 LINC00240 -1.5438983
78 BDNF-AS BDNF-AS -0.7941867
79 LINC00862 LINC00862 1.5586712
80 BCL10-AS1 BCL10-AS1 -2.1383304
81 NR2F1-AS1 NR2F1-AS1 -0.5012591
82 LINC02614 LINC02614 -0.9224436
83 PDK4-AS1 PDK4-AS1 -1.0305083
84 TMEM72-AS1 TMEM72-AS1 -1.0091249
85 UBE2D3-AS1 UBE2D3-AS1 1.6360227
86 EIF1B-AS1 EIF1B-AS1 -0.5186210
87 DAAM2-AS1 DAAM2-AS1 -1.7214142
88 MIR9-3HG MIR9-3HG -1.0149620
89 LSAMP-AS1 LSAMP-AS1 -1.4696069
90 ENSG00000225339 SMIM29-AS1 1.5609970
91 LINC00472 LINC00472 0.9223688
92 ITGA9-AS1 ITGA9-AS1 -0.5956222
93 ZFPM2-AS1 ZFPM2-AS1 -1.9082963
94 LINC00467 LINC00467 -1.3848838
95 LINC00844 LINC00844 -0.8087702
96 ZFHX3-AS1 ZFHX3-AS1 -1.6656193
97 ENSG00000287158 LINC03214 -1.4928563
98 LINC01994 LINC01994 -0.8380970
99 ENSG00000258162 PPFIA2-AS2 -1.5247043
100 MIR3659HG MIR3659HG 1.5856483
101 JAKMIP2-AS1 JAKMIP2-AS1 -1.3164264
102 RHOQ-AS1 RHOQ-AS1 -1.7468010
103 LINC02796 LINC02796 -0.6065784
104 LINC02934 LINC02934 -0.4288249
105 PRKCA-AS1 PRKCA-AS1 -0.8366604
106 DPP10-AS3 DPP10-AS3 -1.3361915
107 RBMS3-AS3 RBMS3-AS3 -1.5543115
108 AP1AR AP1AR 1.4325981
109 LINC03051 LINC03051 0.4705735
110 LINC02895 LINC02895 -0.6752028
p_val_adj_reactive_vs_homeostatic pct.1_reactive pct.2_homeostatic
1 7.531054e-150 0.999 0.999
2 3.217635e-142 0.982 0.973
3 1.110663e-96 0.490 0.805
4 2.329931e-71 0.778 0.929
5 5.668776e-74 0.508 0.236
6 3.898459e-29 0.506 0.307
7 3.852364e-63 0.465 0.742
8 3.239197e-43 0.162 0.015
9 5.064069e-48 0.169 0.406
10 5.037861e-37 0.061 0.229
11 2.687424e-45 0.048 0.230
12 2.245548e-29 0.836 0.818
13 1.320335e-42 0.643 0.837
14 2.420831e-26 0.010 0.106
15 2.568512e-39 0.064 0.239
16 8.304380e-52 0.319 0.567
17 4.620217e-22 0.003 0.078
18 2.254361e-26 0.019 0.125
19 1.138365e-39 0.055 0.226
20 1.491509e-31 0.063 0.219
21 2.997658e-34 0.067 0.232
22 6.510260e-20 0.013 0.095
23 2.371079e-22 0.095 0.234
24 5.578605e-21 0.525 0.708
25 1.251068e-05 0.051 0.012
26 6.826476e-27 0.076 0.225
27 3.420788e-20 0.006 0.080
28 1.476041e-32 0.162 0.369
29 2.343689e-19 0.359 0.552
30 3.494285e-21 0.055 0.175
31 3.023175e-23 0.021 0.120
32 4.971655e-29 0.711 0.625
33 3.112172e-17 0.007 0.075
34 3.222778e-19 0.052 0.163
35 9.870437e-17 0.020 0.099
36 2.104432e-19 0.016 0.100
37 1.479314e-21 0.061 0.183
38 3.463486e-15 0.254 0.408
39 1.372355e-12 0.152 0.279
40 1.277363e-19 0.060 0.178
41 1.698291e-16 0.031 0.119
42 9.932642e-18 0.104 0.234
43 2.567255e-11 0.177 0.083
44 8.193928e-18 0.023 0.109
45 4.533165e-17 0.247 0.126
46 8.319323e-10 0.072 0.016
47 1.104988e-07 0.207 0.123
48 1.490042e-10 0.150 0.263
49 1.165603e-13 0.034 0.115
50 8.703296e-12 0.026 0.094
51 5.590474e-10 0.014 0.068
52 4.050410e-15 0.048 0.144
53 1.642947e-11 0.014 0.073
54 2.308796e-04 0.187 0.254
55 6.921594e-11 0.011 0.065
56 4.400615e-11 0.017 0.078
57 3.655561e-19 0.241 0.413
58 3.007789e-14 0.073 0.181
59 4.258019e-16 0.064 0.173
60 2.123997e-11 0.012 0.068
61 2.003744e-08 0.033 0.096
62 4.434546e-15 0.169 0.312
63 1.663182e-11 0.017 0.080
64 1.042241e-05 0.054 0.013
65 1.767182e-13 0.012 0.075
66 2.808869e-11 0.015 0.074
67 8.706967e-10 0.053 0.132
68 1.408456e-11 0.059 0.150
69 2.947967e-06 0.020 0.067
70 3.181638e-07 0.019 0.068
71 5.277608e-12 0.037 0.116
72 6.212818e-12 0.045 0.127
73 2.448193e-09 0.081 0.023
74 1.435700e-11 0.065 0.156
75 3.363365e-13 0.041 0.127
76 5.706931e-07 0.041 0.103
77 4.163614e-07 0.021 0.072
78 3.282729e-10 0.121 0.228
79 1.107380e-06 0.091 0.034
80 4.561151e-09 0.019 0.074
81 6.773300e-12 0.330 0.475
82 4.979919e-12 0.129 0.242
83 2.349247e-11 0.067 0.158
84 1.666430e-11 0.080 0.178
85 1.691957e-06 0.112 0.049
86 2.362974e-09 0.236 0.362
87 1.194161e-09 0.029 0.093
88 1.303006e-09 0.081 0.171
89 8.009277e-07 0.032 0.089
90 1.352302e-08 0.179 0.096
91 8.015808e-06 0.458 0.421
92 5.918311e-11 0.154 0.275
93 1.982926e-05 0.019 0.063
94 1.892471e-07 0.031 0.089
95 1.232605e-09 0.101 0.200
96 1.276877e-07 0.028 0.085
97 3.588883e-07 0.037 0.098
98 1.670540e-05 0.072 0.142
99 7.016993e-05 0.024 0.070
100 5.929153e-04 0.087 0.039
101 1.995836e-04 0.031 0.078
102 3.953795e-04 0.024 0.066
103 2.010877e-06 0.120 0.209
104 3.256543e-07 0.264 0.388
105 7.953078e-03 0.070 0.125
106 4.968059e-05 0.025 0.071
107 6.315568e-04 0.024 0.065
108 2.143264e-02 0.074 0.034
109 6.502419e-05 0.736 0.746
110 6.031012e-03 0.073 0.130
GENENAME
1 metastasis associated lung adenocarcinoma transcript 1
2 nuclear paraspeckle assembly transcript 1
3 MIR9-1 host gene
4 OBI1 antisense RNA 1
5 SLC44A3 antisense RNA 1
6 X inactive specific transcript
7 MIR9-2 host gene
8 PARD6G antisense RNA 1
9 POT1 antisense RNA 1
10 PCDH9 antisense RNA 2
11 UFL1 antisense RNA 1
12 long intergenic non-protein coding RNA, p53 induced transcript
13 small nucleolar RNA host gene 14
14 long intergenic non-protein coding RNA 2232
15 GNG12, DIRAS3 and WLS antisense RNA 1
16 MIR4300 host gene
17 HOXB cluster antisense RNA 1
18 PAX8 antisense RNA 1
19 ZBTB47 and NKTR antisense RNA 1
20 long intergenic non-protein coding RNA 412
21 long intergenic non-protein coding RNA 3122
22 A2ML1 antisense RNA 1
23 RFX4 antisense RNA 1
24 LMCD1 antisense RNA 1
25 long intergenic non-protein coding RNA 2608
26 long intergenic non-protein coding RNA 1376
27 long intergenic non-protein coding RNA 1727
28 SLC38A4 antisense RNA 1
29 long intergenic non-protein coding RNA 1748
30 HECTD2 antisense RNA 1
31 HEY2 antisense RNA 1
32 PTCHD1 and PHEX antisense RNA
33 LRP4 antisense RNA 1
34 long intergenic non-protein coding RNA 1572
35 ANK2 antisense RNA 1
36 PKIA antisense RNA 1
37 DBX2 antisense RNA 1
38 ENTPD1 antisense RNA 1
39 GBX2 and ASB18 antisense RNA 1
40 long intergenic non-protein coding RNA 173
41 RAP2C antisense RNA 1
42 RASSF8 antisense RNA 1
43 TET2 antisense RNA 1
44 LIFR antisense RNA 1
45 BAALC antisense RNA 1
46 SOCS2 antisense RNA 1
47 adaptor related protein complex 1 subunit sigma 2
48 GASK1B antisense RNA 1
49 long intergenic non-protein coding RNA 960
50 ATP13A4 antisense RNA 1
51 long intergenic non-protein coding RNA 1414
52 SLC28A2 antisense RNA 1
53 MIR4500 host gene
54 long intergenic non-protein coding RNA 499
55 MIDEAS antisense RNA 1
56 SNED1 antisense RNA 1
57 MEF2C antisense RNA 1
58 HEXIM2 antisense RNA 1
59 ZKSCAN7 ZNF cluster antisense RNA 1
60 long intergenic non-protein coding RNA 3062
61 CALCRL and TFPI antisense RNA 1
62 FSIP2 antisense RNA 1
63 USP3 antisense RNA 1
64 long intergenic non-protein coding RNA 378
65 NECTIN3 antisense RNA 1
66 WEE2 antisense RNA 1
67 PDE7B antisense RNA 1
68 ZNF337 antisense RNA 1
69 MIR219A2 host gene
70 long intergenic non-protein coding RNA 1117
71 IPO9 antisense RNA 1
72 long intergenic non-protein coding RNA 2580
73 OTX2 antisense RNA 1
74 LIX1 and RIOK2 antisense RNA 1
75 SYNPO2L antisense RNA 1
76 ANKRD17 antisense RNA1
77 long intergenic non-protein coding RNA 240
78 BDNF antisense RNA
79 long intergenic non-protein coding RNA 862
80 BCL10 antisense RNA 1
81 NR2F1 regulatory antisense RNA 1
82 long intergenic non-protein coding RNA 2614
83 PDK4 antisense RNA 1
84 TMEM72 antisense RNA 1
85 UBE2D3 antisense RNA 1
86 EIF1B antisense RNA 1
87 DAAM2 antisense RNA 1
88 MIR9-3 host gene
89 LSAMP antisense RNA 1
90 SMIM29 antisense RNA 1
91 long intergenic non-protein coding RNA 472
92 ITGA9 antisense RNA 1
93 ZFPM2 antisense RNA 1
94 long intergenic non-protein coding RNA 467
95 long intergenic non-protein coding RNA 844
96 ZFHX3 antisense RNA 1
97 long intergenic non-protein coding RNA 3214
98 long intergenic non-protein coding RNA 1994
99 PPFIA2 antisense RNA 2
100 MIR3659 host gene
101 JAKMIP2 antisense RNA 1
102 RHOQ antisense RNA 1
103 long intergenic non-protein coding RNA 2796
104 long intergenic non-protein coding RNA 2934
105 PRKCA antisense RNA 1
106 DPP10 antisense RNA 3
107 RBMS3 antisense RNA 3
108 adaptor related protein complex 1 associated regulatory protein
109 long intergenic non-protein coding RNA 3051
110 long intergenic non-protein coding RNA 2895
avg_log2FC_PD_vs_C p_val_adj_PD_vs_C pct.1_PD pct.2_C same_direction
1 -1.0785343 1.865112e-203 0.999 0.999 TRUE
2 0.8786913 3.328073e-112 0.978 0.969 TRUE
3 -0.6348170 7.969543e-50 0.559 0.729 TRUE
4 -0.6859095 4.279446e-73 0.753 0.874 TRUE
5 1.6386193 5.365303e-49 0.406 0.229 TRUE
6 1.2858607 1.699511e-82 0.563 0.321 TRUE
7 -0.5590838 3.337703e-32 0.541 0.682 TRUE
8 2.7031355 3.111727e-34 0.118 0.022 TRUE
9 -1.1404088 1.163515e-32 0.208 0.354 TRUE
10 -1.7008230 2.031888e-33 0.071 0.185 TRUE
11 -1.4241608 1.211450e-24 0.100 0.206 TRUE
12 0.5638433 3.761286e-42 0.856 0.811 TRUE
13 -0.5304722 1.524741e-28 0.684 0.788 TRUE
14 -3.3450042 5.692130e-36 0.009 0.084 TRUE
15 -1.2630328 9.127518e-23 0.087 0.185 TRUE
16 -0.3826847 3.402057e-06 0.402 0.481 TRUE
17 -4.0556306 9.086220e-28 0.005 0.062 TRUE
18 -2.0379081 3.852329e-26 0.023 0.096 TRUE
19 -1.1977744 1.730185e-13 0.121 0.203 TRUE
20 -1.0041436 1.908970e-14 0.108 0.192 TRUE
21 -0.7953887 2.527353e-11 0.132 0.213 TRUE
22 -2.2663428 2.598023e-20 0.015 0.071 TRUE
23 -1.4020254 2.488793e-19 0.095 0.188 TRUE
24 -0.4804939 1.602651e-22 0.553 0.682 TRUE
25 3.3371588 8.973627e-33 0.092 0.011 TRUE
26 -0.9334588 2.621275e-13 0.120 0.205 TRUE
27 -2.1462329 3.682758e-16 0.022 0.076 TRUE
28 -0.5356175 6.442011e-08 0.227 0.311 TRUE
29 -0.5107564 2.094936e-18 0.365 0.491 TRUE
30 -1.0857890 2.722708e-14 0.077 0.153 TRUE
31 -1.4310725 3.328734e-10 0.044 0.098 TRUE
32 0.3840640 3.855021e-07 0.652 0.606 TRUE
33 -2.4653985 2.536101e-13 0.014 0.057 TRUE
34 -1.2175268 7.039090e-14 0.066 0.137 TRUE
35 -2.0617487 7.873702e-13 0.027 0.077 TRUE
36 -1.7806304 5.116827e-10 0.032 0.080 TRUE
37 -1.0621147 9.223505e-10 0.082 0.147 TRUE
38 -0.6912777 3.844297e-16 0.270 0.382 TRUE
39 -0.8578170 1.973130e-18 0.140 0.247 TRUE
40 -0.8934571 7.264393e-11 0.069 0.135 TRUE
41 -1.2403898 7.949843e-12 0.053 0.114 TRUE
42 -0.8599095 4.999190e-10 0.125 0.200 TRUE
43 1.1735145 2.246857e-15 0.173 0.086 TRUE
44 -1.3251389 9.795100e-08 0.051 0.100 TRUE
45 1.2507027 1.965654e-08 0.190 0.119 TRUE
46 2.5328871 3.205104e-13 0.061 0.014 TRUE
47 1.2481882 7.443896e-18 0.215 0.116 TRUE
48 -0.9390244 7.411156e-16 0.138 0.233 TRUE
49 -1.4989419 6.298500e-10 0.038 0.087 TRUE
50 -1.8837620 6.789299e-11 0.026 0.072 TRUE
51 -2.2000756 1.084779e-11 0.019 0.062 TRUE
52 -1.0324631 2.030816e-08 0.072 0.131 TRUE
53 -1.8622106 1.004560e-09 0.020 0.060 TRUE
54 -1.4627475 1.924047e-18 0.145 0.241 TRUE
55 -1.7928889 3.561712e-10 0.014 0.051 TRUE
56 -1.6182813 8.616760e-10 0.022 0.064 TRUE
57 -0.3033979 1.693342e-03 0.323 0.398 TRUE
58 -0.6881924 1.129753e-07 0.100 0.164 TRUE
59 -0.7325966 1.846123e-05 0.094 0.149 TRUE
60 -1.7315357 2.687633e-07 0.019 0.054 TRUE
61 -1.6336982 2.237494e-11 0.033 0.083 TRUE
62 -0.5366656 4.912220e-06 0.207 0.278 TRUE
63 -1.4075043 1.038754e-07 0.026 0.066 TRUE
64 1.9176396 1.354137e-12 0.061 0.015 TRUE
65 -1.5334647 2.083619e-04 0.028 0.061 TRUE
66 -1.5212145 3.770219e-07 0.023 0.060 TRUE
67 -1.2077131 1.396314e-09 0.048 0.101 TRUE
68 -0.8570729 8.650509e-08 0.076 0.134 TRUE
69 -1.9527912 1.067118e-10 0.024 0.068 TRUE
70 -1.6799383 5.811928e-10 0.015 0.053 TRUE
71 -1.0080648 6.225659e-05 0.050 0.092 TRUE
72 -0.9498066 7.167198e-05 0.066 0.111 TRUE
73 1.4726849 2.411075e-05 0.066 0.029 TRUE
74 -0.8830735 3.146696e-05 0.087 0.139 TRUE
75 -0.8009231 1.895176e-03 0.064 0.106 TRUE
76 -1.5731402 1.310611e-08 0.032 0.076 TRUE
77 -1.6760204 3.061914e-08 0.026 0.066 TRUE
78 -0.6863693 9.725967e-07 0.139 0.206 TRUE
79 1.0898264 6.905976e-09 0.096 0.043 TRUE
80 -1.5546684 4.077856e-05 0.027 0.061 TRUE
81 -0.3255635 8.698939e-05 0.385 0.458 TRUE
82 -0.6547661 9.459607e-04 0.168 0.223 TRUE
83 -0.7743301 2.033560e-03 0.090 0.135 TRUE
84 -0.5999107 2.813741e-03 0.114 0.164 TRUE
85 1.1927386 9.762336e-07 0.100 0.051 TRUE
86 -0.4332346 8.009286e-05 0.293 0.360 TRUE
87 -1.2034929 1.563902e-02 0.039 0.069 TRUE
88 -0.7669306 1.351762e-03 0.100 0.148 TRUE
89 -1.3777549 3.701280e-05 0.040 0.078 TRUE
90 1.1038821 1.475434e-03 0.128 0.082 TRUE
91 0.5760819 3.018961e-07 0.482 0.420 TRUE
92 -0.3769998 1.344479e-02 0.211 0.268 TRUE
93 -1.5876122 5.350543e-05 0.020 0.051 TRUE
94 -1.0521023 1.956912e-03 0.043 0.079 TRUE
95 -0.5279199 4.012277e-02 0.120 0.166 TRUE
96 -1.1075559 1.683174e-02 0.042 0.074 TRUE
97 -1.1679230 8.163301e-03 0.047 0.081 TRUE
98 -0.8802699 2.367852e-05 0.072 0.121 TRUE
99 -1.3962449 2.191334e-04 0.027 0.060 TRUE
100 1.1126372 1.843104e-05 0.090 0.046 TRUE
101 -1.3442059 3.803868e-04 0.029 0.061 TRUE
102 -1.6176164 1.415566e-03 0.026 0.055 TRUE
103 -0.5799762 4.504183e-03 0.128 0.179 TRUE
104 -0.3467941 1.448512e-02 0.300 0.366 TRUE
105 -1.0205611 8.579029e-06 0.054 0.100 TRUE
106 -1.1193793 9.337767e-03 0.026 0.054 TRUE
107 -1.3326728 2.169708e-03 0.024 0.052 TRUE
108 1.0889663 8.213554e-04 0.070 0.034 TRUE
109 0.2826169 5.626406e-03 0.730 0.721 TRUE
110 -0.8321417 9.758364e-04 0.074 0.118 TRUE
priority_score cluster_support max_cluster_log2FC min_cluster_p_val_adj
1 354.015516 2;4;5;8 1.3149729 2.926163e-97
2 255.223524 1;6;7;8 1.4606620 1.946829e-151
3 146.842468 2;4;5;7 0.7948607 6.914674e-40
4 144.467581 2;4;6;7 0.9249589 7.845489e-84
5 125.350396 0 2.6318030 4.176317e-204
6 112.503255 0;3;4;7;10 1.1923412 3.021222e-125
7 95.417476 2;4 0.6745209 9.437479e-26
8 82.441924 6;8 4.1735190 3.363576e-214
9 81.949433 2;4 1.1451353 2.298637e-31
10 72.660344 2;4;5 1.3935093 1.109563e-12
11 72.189536 2 1.3424072 1.360686e-14
12 71.318503 3;6;8 0.7965285 4.272232e-41
13 70.969735 2 0.8193956 1.111942e-41
14 67.754023 5;11 3.6210213 6.509256e-107
15 64.006673 2;4;5 1.4041813 4.308952e-23
16 58.307826 2;3;5 1.8450863 9.231737e-122
17 56.938886 2;5 2.9027138 2.636680e-36
18 55.550349 2;5 2.4566705 3.170504e-46
19 55.221473 3;5 1.4767218 1.459588e-24
20 47.203896 4;5 0.8428831 7.421299e-05
21 46.799253 4;7 0.9274611 1.787341e-16
22 43.885270 2;4 1.6467829 4.940196e-19
23 43.199705 2;4;5 1.5930094 1.596581e-15
24 43.052703 5;7 0.4457738 4.973616e-09
25 42.720101 1;6;7 1.6710392 1.689881e-20
26 41.258237 4 0.4509406 3.927515e-03
27 41.199102 2;10;11 4.6998013 2.416280e-30
28 40.584637 2;3;5 0.7505358 1.132269e-13
29 37.348681 2;5 0.6427965 6.295001e-11
30 36.496381 2;4 1.1059567 3.210999e-10
31 36.062049 2;5 1.3852956 1.791840e-09
32 35.926515 0;6;7 0.8676164 8.143973e-27
33 34.782422 2;4 2.3657208 3.717968e-16
34 34.322020 4;5 1.1045737 7.269607e-08
35 32.775540 5 2.5314869 1.754555e-23
36 32.658673 5 2.4170409 2.764130e-24
37 32.655858 2;5 1.2350251 4.092195e-12
38 31.245598 <NA> NA NA
39 31.216196 2;5;7 1.1462196 7.985402e-19
40 31.176916 2;5 1.2749371 7.326753e-11
41 29.850350 <NA> NA NA
42 28.229413 2 1.0222454 1.488441e-06
43 27.958578 6;7 2.2797812 1.333389e-59
44 27.785250 5 1.2771772 1.360718e-03
45 27.270696 0 2.7566790 1.200305e-78
46 27.010758 0 2.8286122 8.106778e-27
47 26.728447 0;3 1.5687449 1.019470e-24
48 26.658016 4 0.8293094 1.575930e-15
49 25.441690 5 2.1796840 5.237064e-23
50 25.172387 4 1.8819046 5.391534e-23
51 24.839213 2;10 2.8311254 2.494682e-34
52 24.371913 2;7 1.0704871 9.315530e-03
53 24.101035 2;5 2.1459210 1.322867e-14
54 24.082050 4;8;10 3.4282197 0.000000e+00
55 23.505812 2;4 1.6265430 2.576288e-05
56 23.082742 5 2.0470659 3.612157e-14
57 22.245884 3;7 0.9091691 6.246858e-26
58 22.094919 7 0.4143896 8.413223e-03
59 21.938076 4 0.8738634 7.876410e-14
60 21.560609 2;4 1.8210760 5.930170e-22
61 21.442051 2;5 1.4127708 2.597650e-07
62 20.958046 2 0.6580104 6.408539e-05
63 20.946831 2;4 1.7040296 1.778819e-04
64 20.894712 0;3 1.8897189 8.321567e-17
65 20.874848 2 1.5981382 4.199725e-02
66 20.799186 5 1.4883684 1.762868e-05
67 20.242445 2;4 1.6355935 7.396749e-14
68 19.691185 4 0.8476863 5.142744e-14
69 19.344665 5;9 1.7112196 4.223296e-08
70 19.167141 5 2.6165048 6.948591e-35
71 17.820135 4 1.2404632 1.797973e-15
72 17.682804 <NA> NA NA
73 17.603416 7;8 3.4438702 3.668336e-63
74 17.485600 2 0.9192580 2.025225e-02
75 17.261319 4 0.5470568 1.309821e-03
76 17.227682 4;5 2.0368111 5.405044e-10
77 17.114455 5 1.6956866 4.117233e-10
78 16.976388 2 0.8261983 3.513250e-05
79 16.764976 3;6;8 1.3677539 2.616717e-08
80 16.423492 2 1.2887431 3.758900e-03
81 16.056556 3;4 0.5010869 1.400262e-09
82 15.904114 <NA> NA NA
83 15.125653 4 0.2756608 3.954770e-02
84 14.937964 4 0.7539576 2.823794e-12
85 14.610818 6;8 1.5674839 3.087805e-12
86 13.674803 7 0.7806955 1.070834e-14
87 13.653635 4;5 1.6322204 4.532332e-05
88 13.536046 2 1.5494248 1.092159e-25
89 13.375417 <NA> NA NA
90 13.364886 0 2.7640326 6.933817e-78
91 13.114646 6;7;8 1.5762592 2.152036e-71
92 13.071870 3;7 0.7464233 5.393400e-12
93 12.470204 5 1.5966198 9.232406e-03
94 11.868386 <NA> NA NA
95 11.642475 5 1.4773086 4.441577e-25
96 11.440897 4 1.1097092 1.199136e-04
97 11.193954 2;7 1.2583703 2.484989e-04
98 11.121155 2 1.4438382 3.915877e-15
99 10.734090 2;9 1.8534743 4.156685e-04
100 10.659743 7 1.5354408 2.199742e-28
101 9.780282 <NA> NA NA
102 9.616473 5 1.8828749 5.360613e-06
103 9.229553 2 0.9005814 1.062043e-05
104 9.101940 7;8 0.8216365 8.853810e-06
105 9.023248 4 1.2247618 4.484259e-13
106 8.789141 5 2.6642721 5.164084e-30
107 8.750171 2 1.7099427 3.936510e-04
108 7.275958 <NA> NA NA
109 7.189884 6 0.3686788 1.478167e-06
110 6.737577 4 0.5336785 2.611942e-02
<- priority_astro_lncRNAs %>% filter (> 0 ,> 0 <- priority_astro_lncRNAs %>% filter (< 0 ,< 0
gene gene_symbol_for_plot avg_log2FC_reactive_vs_homeostatic
1 NEAT1 NEAT1 1.3745627
2 SLC44A3-AS1 SLC44A3-AS1 2.1948605
3 XIST XIST 1.0386112
4 PARD6G-AS1 PARD6G-AS1 3.7422278
5 LINC-PINT LINC-PINT 0.6813181
6 LINC02608 LINC02608 2.4331917
7 PTCHD1-AS PTCHD1-AS 0.8249788
8 TET2-AS1 TET2-AS1 1.5461079
9 BAALC-AS1 BAALC-AS1 1.9699019
10 SOCS2-AS1 SOCS2-AS1 2.9038008
11 AP1S2 AP1S2 1.3954165
12 LINC00378 LINC00378 2.1267031
13 OTX2-AS1 OTX2-AS1 2.9017871
14 LINC00862 LINC00862 1.5586712
15 UBE2D3-AS1 UBE2D3-AS1 1.6360227
16 ENSG00000225339 SMIM29-AS1 1.5609970
17 LINC00472 LINC00472 0.9223688
18 MIR3659HG MIR3659HG 1.5856483
19 AP1AR AP1AR 1.4325981
20 LINC03051 LINC03051 0.4705735
p_val_adj_reactive_vs_homeostatic pct.1_reactive pct.2_homeostatic
1 3.217635e-142 0.982 0.973
2 5.668776e-74 0.508 0.236
3 3.898459e-29 0.506 0.307
4 3.239197e-43 0.162 0.015
5 2.245548e-29 0.836 0.818
6 1.251068e-05 0.051 0.012
7 4.971655e-29 0.711 0.625
8 2.567255e-11 0.177 0.083
9 4.533165e-17 0.247 0.126
10 8.319323e-10 0.072 0.016
11 1.104988e-07 0.207 0.123
12 1.042241e-05 0.054 0.013
13 2.448193e-09 0.081 0.023
14 1.107380e-06 0.091 0.034
15 1.691957e-06 0.112 0.049
16 1.352302e-08 0.179 0.096
17 8.015808e-06 0.458 0.421
18 5.929153e-04 0.087 0.039
19 2.143264e-02 0.074 0.034
20 6.502419e-05 0.736 0.746
GENENAME
1 nuclear paraspeckle assembly transcript 1
2 SLC44A3 antisense RNA 1
3 X inactive specific transcript
4 PARD6G antisense RNA 1
5 long intergenic non-protein coding RNA, p53 induced transcript
6 long intergenic non-protein coding RNA 2608
7 PTCHD1 and PHEX antisense RNA
8 TET2 antisense RNA 1
9 BAALC antisense RNA 1
10 SOCS2 antisense RNA 1
11 adaptor related protein complex 1 subunit sigma 2
12 long intergenic non-protein coding RNA 378
13 OTX2 antisense RNA 1
14 long intergenic non-protein coding RNA 862
15 UBE2D3 antisense RNA 1
16 SMIM29 antisense RNA 1
17 long intergenic non-protein coding RNA 472
18 MIR3659 host gene
19 adaptor related protein complex 1 associated regulatory protein
20 long intergenic non-protein coding RNA 3051
avg_log2FC_PD_vs_C p_val_adj_PD_vs_C pct.1_PD pct.2_C same_direction
1 0.8786913 3.328073e-112 0.978 0.969 TRUE
2 1.6386193 5.365303e-49 0.406 0.229 TRUE
3 1.2858607 1.699511e-82 0.563 0.321 TRUE
4 2.7031355 3.111727e-34 0.118 0.022 TRUE
5 0.5638433 3.761286e-42 0.856 0.811 TRUE
6 3.3371588 8.973627e-33 0.092 0.011 TRUE
7 0.3840640 3.855021e-07 0.652 0.606 TRUE
8 1.1735145 2.246857e-15 0.173 0.086 TRUE
9 1.2507027 1.965654e-08 0.190 0.119 TRUE
10 2.5328871 3.205104e-13 0.061 0.014 TRUE
11 1.2481882 7.443896e-18 0.215 0.116 TRUE
12 1.9176396 1.354137e-12 0.061 0.015 TRUE
13 1.4726849 2.411075e-05 0.066 0.029 TRUE
14 1.0898264 6.905976e-09 0.096 0.043 TRUE
15 1.1927386 9.762336e-07 0.100 0.051 TRUE
16 1.1038821 1.475434e-03 0.128 0.082 TRUE
17 0.5760819 3.018961e-07 0.482 0.420 TRUE
18 1.1126372 1.843104e-05 0.090 0.046 TRUE
19 1.0889663 8.213554e-04 0.070 0.034 TRUE
20 0.2826169 5.626406e-03 0.730 0.721 TRUE
priority_score cluster_support max_cluster_log2FC min_cluster_p_val_adj
1 255.223524 1;6;7;8 1.4606620 1.946829e-151
2 125.350396 0 2.6318030 4.176317e-204
3 112.503255 0;3;4;7;10 1.1923412 3.021222e-125
4 82.441924 6;8 4.1735190 3.363576e-214
5 71.318503 3;6;8 0.7965285 4.272232e-41
6 42.720101 1;6;7 1.6710392 1.689881e-20
7 35.926515 0;6;7 0.8676164 8.143973e-27
8 27.958578 6;7 2.2797812 1.333389e-59
9 27.270696 0 2.7566790 1.200305e-78
10 27.010758 0 2.8286122 8.106778e-27
11 26.728447 0;3 1.5687449 1.019470e-24
12 20.894712 0;3 1.8897189 8.321567e-17
13 17.603416 7;8 3.4438702 3.668336e-63
14 16.764976 3;6;8 1.3677539 2.616717e-08
15 14.610818 6;8 1.5674839 3.087805e-12
16 13.364886 0 2.7640326 6.933817e-78
17 13.114646 6;7;8 1.5762592 2.152036e-71
18 10.659743 7 1.5354408 2.199742e-28
19 7.275958 <NA> NA NA
20 7.189884 6 0.3686788 1.478167e-06
gene gene_symbol_for_plot avg_log2FC_reactive_vs_homeostatic
1 MALAT1 MALAT1 -1.0845420
2 MIR9-1HG MIR9-1HG -1.1546672
3 OBI1-AS1 OBI1-AS1 -0.7804023
4 MIR9-2HG MIR9-2HG -0.9675675
5 POT1-AS1 POT1-AS1 -1.5792964
6 PCDH9-AS2 PCDH9-AS2 -1.9696666
7 UFL1-AS1 UFL1-AS1 -2.2780168
8 SNHG14 SNHG14 -0.7431429
9 LINC02232 LINC02232 -3.5482579
10 GNG12-AS1 GNG12-AS1 -2.1136746
11 MIR4300HG MIR4300HG -1.3761905
12 HOXB-AS1 HOXB-AS1 -4.5063008
13 PAX8-AS1 PAX8-AS1 -2.4511875
14 ZBTB47-AS1 ZBTB47-AS1 -2.3180731
15 LINC00412 LINC00412 -1.6541773
16 LINC03122 LINC03122 -1.8833119
17 A2ML1-AS1 A2ML1-AS1 -2.8471687
18 ENSG00000257545 RFX4-AS1 -1.5686148
19 LMCD1-AS1 LMCD1-AS1 -0.5235736
20 LINC01376 LINC01376 -1.5774871
21 LINC01727 LINC01727 -4.1531683
22 SLC38A4-AS1 SLC38A4-AS1 -1.0271390
23 LINC01748 LINC01748 -0.5289954
24 HECTD2-AS1 HECTD2-AS1 -1.3889513
25 HEY2-AS1 HEY2-AS1 -2.6337186
26 LRP4-AS1 LRP4-AS1 -3.2142539
27 LINC01572 LINC01572 -1.4602397
28 ANK2-AS1 ANK2-AS1 -2.6043069
29 PKIA-AS1 PKIA-AS1 -2.9101779
30 DBX2-AS1 DBX2-AS1 -1.7286998
31 ENTPD1-AS1 ENTPD1-AS1 -0.6786507
32 GBX2-AS1 GBX2-AS1 -0.7910011
33 LINC00173 LINC00173 -1.2509725
34 RAP2C-AS1 RAP2C-AS1 -1.7403309
35 RASSF8-AS1 RASSF8-AS1 -1.0654679
36 LIFR-AS1 LIFR-AS1 -2.3646125
37 GASK1B-AS1 GASK1B-AS1 -0.7620764
38 LINC00960 LINC00960 -1.8085364
39 ATP13A4-AS1 ATP13A4-AS1 -2.0601332
40 LINC01414 LINC01414 -2.4219273
41 SLC28A2-AS1 SLC28A2-AS1 -1.2546195
42 MIR4500HG MIR4500HG -2.4564245
43 LINC00499 LINC00499 -1.2669032
44 MIDEAS-AS1 MIDEAS-AS1 -2.1047880
45 SNED1-AS1 SNED1-AS1 -2.0433184
46 MEF2C-AS1 MEF2C-AS1 -0.7341850
47 HEXIM2-AS1 HEXIM2-AS1 -0.9379578
48 ZKSCAN7-AS1 ZKSCAN7-AS1 -1.1009480
49 LINC03062 LINC03062 -2.5855973
50 CALCRL-AS1 CALCRL-AS1 -1.4599570
51 FSIP2-AS1 FSIP2-AS1 -0.7595069
52 USP3-AS1 USP3-AS1 -1.7767793
53 NECTIN3-AS1 NECTIN3-AS1 -2.9074828
54 WEE2-AS1 WEE2-AS1 -2.3028693
55 PDE7B-AS1 PDE7B-AS1 -1.1195818
56 ZNF337-AS1 ZNF337-AS1 -0.9198971
57 MIR219A2HG MIR219A2HG -1.8896088
58 LINC01117 LINC01117 -1.7541741
59 IPO9-AS1 IPO9-AS1 -1.3286924
60 LINC02580 LINC02580 -1.3816355
61 LIX1-AS1 LIX1-AS1 -1.2574453
62 SYNPO2L-AS1 SYNPO2L-AS1 -1.2648196
63 ENSG00000303699 ANKRD17-AS1 -1.5284179
64 LINC00240 LINC00240 -1.5438983
65 BDNF-AS BDNF-AS -0.7941867
66 BCL10-AS1 BCL10-AS1 -2.1383304
67 NR2F1-AS1 NR2F1-AS1 -0.5012591
68 LINC02614 LINC02614 -0.9224436
69 PDK4-AS1 PDK4-AS1 -1.0305083
70 TMEM72-AS1 TMEM72-AS1 -1.0091249
71 EIF1B-AS1 EIF1B-AS1 -0.5186210
72 DAAM2-AS1 DAAM2-AS1 -1.7214142
73 MIR9-3HG MIR9-3HG -1.0149620
74 LSAMP-AS1 LSAMP-AS1 -1.4696069
75 ITGA9-AS1 ITGA9-AS1 -0.5956222
76 ZFPM2-AS1 ZFPM2-AS1 -1.9082963
77 LINC00467 LINC00467 -1.3848838
78 LINC00844 LINC00844 -0.8087702
79 ZFHX3-AS1 ZFHX3-AS1 -1.6656193
80 ENSG00000287158 LINC03214 -1.4928563
81 LINC01994 LINC01994 -0.8380970
82 ENSG00000258162 PPFIA2-AS2 -1.5247043
83 JAKMIP2-AS1 JAKMIP2-AS1 -1.3164264
84 RHOQ-AS1 RHOQ-AS1 -1.7468010
85 LINC02796 LINC02796 -0.6065784
86 LINC02934 LINC02934 -0.4288249
87 PRKCA-AS1 PRKCA-AS1 -0.8366604
88 DPP10-AS3 DPP10-AS3 -1.3361915
89 RBMS3-AS3 RBMS3-AS3 -1.5543115
90 LINC02895 LINC02895 -0.6752028
p_val_adj_reactive_vs_homeostatic pct.1_reactive pct.2_homeostatic
1 7.531054e-150 0.999 0.999
2 1.110663e-96 0.490 0.805
3 2.329931e-71 0.778 0.929
4 3.852364e-63 0.465 0.742
5 5.064069e-48 0.169 0.406
6 5.037861e-37 0.061 0.229
7 2.687424e-45 0.048 0.230
8 1.320335e-42 0.643 0.837
9 2.420831e-26 0.010 0.106
10 2.568512e-39 0.064 0.239
11 8.304380e-52 0.319 0.567
12 4.620217e-22 0.003 0.078
13 2.254361e-26 0.019 0.125
14 1.138365e-39 0.055 0.226
15 1.491509e-31 0.063 0.219
16 2.997658e-34 0.067 0.232
17 6.510260e-20 0.013 0.095
18 2.371079e-22 0.095 0.234
19 5.578605e-21 0.525 0.708
20 6.826476e-27 0.076 0.225
21 3.420788e-20 0.006 0.080
22 1.476041e-32 0.162 0.369
23 2.343689e-19 0.359 0.552
24 3.494285e-21 0.055 0.175
25 3.023175e-23 0.021 0.120
26 3.112172e-17 0.007 0.075
27 3.222778e-19 0.052 0.163
28 9.870437e-17 0.020 0.099
29 2.104432e-19 0.016 0.100
30 1.479314e-21 0.061 0.183
31 3.463486e-15 0.254 0.408
32 1.372355e-12 0.152 0.279
33 1.277363e-19 0.060 0.178
34 1.698291e-16 0.031 0.119
35 9.932642e-18 0.104 0.234
36 8.193928e-18 0.023 0.109
37 1.490042e-10 0.150 0.263
38 1.165603e-13 0.034 0.115
39 8.703296e-12 0.026 0.094
40 5.590474e-10 0.014 0.068
41 4.050410e-15 0.048 0.144
42 1.642947e-11 0.014 0.073
43 2.308796e-04 0.187 0.254
44 6.921594e-11 0.011 0.065
45 4.400615e-11 0.017 0.078
46 3.655561e-19 0.241 0.413
47 3.007789e-14 0.073 0.181
48 4.258019e-16 0.064 0.173
49 2.123997e-11 0.012 0.068
50 2.003744e-08 0.033 0.096
51 4.434546e-15 0.169 0.312
52 1.663182e-11 0.017 0.080
53 1.767182e-13 0.012 0.075
54 2.808869e-11 0.015 0.074
55 8.706967e-10 0.053 0.132
56 1.408456e-11 0.059 0.150
57 2.947967e-06 0.020 0.067
58 3.181638e-07 0.019 0.068
59 5.277608e-12 0.037 0.116
60 6.212818e-12 0.045 0.127
61 1.435700e-11 0.065 0.156
62 3.363365e-13 0.041 0.127
63 5.706931e-07 0.041 0.103
64 4.163614e-07 0.021 0.072
65 3.282729e-10 0.121 0.228
66 4.561151e-09 0.019 0.074
67 6.773300e-12 0.330 0.475
68 4.979919e-12 0.129 0.242
69 2.349247e-11 0.067 0.158
70 1.666430e-11 0.080 0.178
71 2.362974e-09 0.236 0.362
72 1.194161e-09 0.029 0.093
73 1.303006e-09 0.081 0.171
74 8.009277e-07 0.032 0.089
75 5.918311e-11 0.154 0.275
76 1.982926e-05 0.019 0.063
77 1.892471e-07 0.031 0.089
78 1.232605e-09 0.101 0.200
79 1.276877e-07 0.028 0.085
80 3.588883e-07 0.037 0.098
81 1.670540e-05 0.072 0.142
82 7.016993e-05 0.024 0.070
83 1.995836e-04 0.031 0.078
84 3.953795e-04 0.024 0.066
85 2.010877e-06 0.120 0.209
86 3.256543e-07 0.264 0.388
87 7.953078e-03 0.070 0.125
88 4.968059e-05 0.025 0.071
89 6.315568e-04 0.024 0.065
90 6.031012e-03 0.073 0.130
GENENAME avg_log2FC_PD_vs_C
1 metastasis associated lung adenocarcinoma transcript 1 -1.0785343
2 MIR9-1 host gene -0.6348170
3 OBI1 antisense RNA 1 -0.6859095
4 MIR9-2 host gene -0.5590838
5 POT1 antisense RNA 1 -1.1404088
6 PCDH9 antisense RNA 2 -1.7008230
7 UFL1 antisense RNA 1 -1.4241608
8 small nucleolar RNA host gene 14 -0.5304722
9 long intergenic non-protein coding RNA 2232 -3.3450042
10 GNG12, DIRAS3 and WLS antisense RNA 1 -1.2630328
11 MIR4300 host gene -0.3826847
12 HOXB cluster antisense RNA 1 -4.0556306
13 PAX8 antisense RNA 1 -2.0379081
14 ZBTB47 and NKTR antisense RNA 1 -1.1977744
15 long intergenic non-protein coding RNA 412 -1.0041436
16 long intergenic non-protein coding RNA 3122 -0.7953887
17 A2ML1 antisense RNA 1 -2.2663428
18 RFX4 antisense RNA 1 -1.4020254
19 LMCD1 antisense RNA 1 -0.4804939
20 long intergenic non-protein coding RNA 1376 -0.9334588
21 long intergenic non-protein coding RNA 1727 -2.1462329
22 SLC38A4 antisense RNA 1 -0.5356175
23 long intergenic non-protein coding RNA 1748 -0.5107564
24 HECTD2 antisense RNA 1 -1.0857890
25 HEY2 antisense RNA 1 -1.4310725
26 LRP4 antisense RNA 1 -2.4653985
27 long intergenic non-protein coding RNA 1572 -1.2175268
28 ANK2 antisense RNA 1 -2.0617487
29 PKIA antisense RNA 1 -1.7806304
30 DBX2 antisense RNA 1 -1.0621147
31 ENTPD1 antisense RNA 1 -0.6912777
32 GBX2 and ASB18 antisense RNA 1 -0.8578170
33 long intergenic non-protein coding RNA 173 -0.8934571
34 RAP2C antisense RNA 1 -1.2403898
35 RASSF8 antisense RNA 1 -0.8599095
36 LIFR antisense RNA 1 -1.3251389
37 GASK1B antisense RNA 1 -0.9390244
38 long intergenic non-protein coding RNA 960 -1.4989419
39 ATP13A4 antisense RNA 1 -1.8837620
40 long intergenic non-protein coding RNA 1414 -2.2000756
41 SLC28A2 antisense RNA 1 -1.0324631
42 MIR4500 host gene -1.8622106
43 long intergenic non-protein coding RNA 499 -1.4627475
44 MIDEAS antisense RNA 1 -1.7928889
45 SNED1 antisense RNA 1 -1.6182813
46 MEF2C antisense RNA 1 -0.3033979
47 HEXIM2 antisense RNA 1 -0.6881924
48 ZKSCAN7 ZNF cluster antisense RNA 1 -0.7325966
49 long intergenic non-protein coding RNA 3062 -1.7315357
50 CALCRL and TFPI antisense RNA 1 -1.6336982
51 FSIP2 antisense RNA 1 -0.5366656
52 USP3 antisense RNA 1 -1.4075043
53 NECTIN3 antisense RNA 1 -1.5334647
54 WEE2 antisense RNA 1 -1.5212145
55 PDE7B antisense RNA 1 -1.2077131
56 ZNF337 antisense RNA 1 -0.8570729
57 MIR219A2 host gene -1.9527912
58 long intergenic non-protein coding RNA 1117 -1.6799383
59 IPO9 antisense RNA 1 -1.0080648
60 long intergenic non-protein coding RNA 2580 -0.9498066
61 LIX1 and RIOK2 antisense RNA 1 -0.8830735
62 SYNPO2L antisense RNA 1 -0.8009231
63 ANKRD17 antisense RNA1 -1.5731402
64 long intergenic non-protein coding RNA 240 -1.6760204
65 BDNF antisense RNA -0.6863693
66 BCL10 antisense RNA 1 -1.5546684
67 NR2F1 regulatory antisense RNA 1 -0.3255635
68 long intergenic non-protein coding RNA 2614 -0.6547661
69 PDK4 antisense RNA 1 -0.7743301
70 TMEM72 antisense RNA 1 -0.5999107
71 EIF1B antisense RNA 1 -0.4332346
72 DAAM2 antisense RNA 1 -1.2034929
73 MIR9-3 host gene -0.7669306
74 LSAMP antisense RNA 1 -1.3777549
75 ITGA9 antisense RNA 1 -0.3769998
76 ZFPM2 antisense RNA 1 -1.5876122
77 long intergenic non-protein coding RNA 467 -1.0521023
78 long intergenic non-protein coding RNA 844 -0.5279199
79 ZFHX3 antisense RNA 1 -1.1075559
80 long intergenic non-protein coding RNA 3214 -1.1679230
81 long intergenic non-protein coding RNA 1994 -0.8802699
82 PPFIA2 antisense RNA 2 -1.3962449
83 JAKMIP2 antisense RNA 1 -1.3442059
84 RHOQ antisense RNA 1 -1.6176164
85 long intergenic non-protein coding RNA 2796 -0.5799762
86 long intergenic non-protein coding RNA 2934 -0.3467941
87 PRKCA antisense RNA 1 -1.0205611
88 DPP10 antisense RNA 3 -1.1193793
89 RBMS3 antisense RNA 3 -1.3326728
90 long intergenic non-protein coding RNA 2895 -0.8321417
p_val_adj_PD_vs_C pct.1_PD pct.2_C same_direction priority_score
1 1.865112e-203 0.999 0.999 TRUE 354.015516
2 7.969543e-50 0.559 0.729 TRUE 146.842468
3 4.279446e-73 0.753 0.874 TRUE 144.467581
4 3.337703e-32 0.541 0.682 TRUE 95.417476
5 1.163515e-32 0.208 0.354 TRUE 81.949433
6 2.031888e-33 0.071 0.185 TRUE 72.660344
7 1.211450e-24 0.100 0.206 TRUE 72.189536
8 1.524741e-28 0.684 0.788 TRUE 70.969735
9 5.692130e-36 0.009 0.084 TRUE 67.754023
10 9.127518e-23 0.087 0.185 TRUE 64.006673
11 3.402057e-06 0.402 0.481 TRUE 58.307826
12 9.086220e-28 0.005 0.062 TRUE 56.938886
13 3.852329e-26 0.023 0.096 TRUE 55.550349
14 1.730185e-13 0.121 0.203 TRUE 55.221473
15 1.908970e-14 0.108 0.192 TRUE 47.203896
16 2.527353e-11 0.132 0.213 TRUE 46.799253
17 2.598023e-20 0.015 0.071 TRUE 43.885270
18 2.488793e-19 0.095 0.188 TRUE 43.199705
19 1.602651e-22 0.553 0.682 TRUE 43.052703
20 2.621275e-13 0.120 0.205 TRUE 41.258237
21 3.682758e-16 0.022 0.076 TRUE 41.199102
22 6.442011e-08 0.227 0.311 TRUE 40.584637
23 2.094936e-18 0.365 0.491 TRUE 37.348681
24 2.722708e-14 0.077 0.153 TRUE 36.496381
25 3.328734e-10 0.044 0.098 TRUE 36.062049
26 2.536101e-13 0.014 0.057 TRUE 34.782422
27 7.039090e-14 0.066 0.137 TRUE 34.322020
28 7.873702e-13 0.027 0.077 TRUE 32.775540
29 5.116827e-10 0.032 0.080 TRUE 32.658673
30 9.223505e-10 0.082 0.147 TRUE 32.655858
31 3.844297e-16 0.270 0.382 TRUE 31.245598
32 1.973130e-18 0.140 0.247 TRUE 31.216196
33 7.264393e-11 0.069 0.135 TRUE 31.176916
34 7.949843e-12 0.053 0.114 TRUE 29.850350
35 4.999190e-10 0.125 0.200 TRUE 28.229413
36 9.795100e-08 0.051 0.100 TRUE 27.785250
37 7.411156e-16 0.138 0.233 TRUE 26.658016
38 6.298500e-10 0.038 0.087 TRUE 25.441690
39 6.789299e-11 0.026 0.072 TRUE 25.172387
40 1.084779e-11 0.019 0.062 TRUE 24.839213
41 2.030816e-08 0.072 0.131 TRUE 24.371913
42 1.004560e-09 0.020 0.060 TRUE 24.101035
43 1.924047e-18 0.145 0.241 TRUE 24.082050
44 3.561712e-10 0.014 0.051 TRUE 23.505812
45 8.616760e-10 0.022 0.064 TRUE 23.082742
46 1.693342e-03 0.323 0.398 TRUE 22.245884
47 1.129753e-07 0.100 0.164 TRUE 22.094919
48 1.846123e-05 0.094 0.149 TRUE 21.938076
49 2.687633e-07 0.019 0.054 TRUE 21.560609
50 2.237494e-11 0.033 0.083 TRUE 21.442051
51 4.912220e-06 0.207 0.278 TRUE 20.958046
52 1.038754e-07 0.026 0.066 TRUE 20.946831
53 2.083619e-04 0.028 0.061 TRUE 20.874848
54 3.770219e-07 0.023 0.060 TRUE 20.799186
55 1.396314e-09 0.048 0.101 TRUE 20.242445
56 8.650509e-08 0.076 0.134 TRUE 19.691185
57 1.067118e-10 0.024 0.068 TRUE 19.344665
58 5.811928e-10 0.015 0.053 TRUE 19.167141
59 6.225659e-05 0.050 0.092 TRUE 17.820135
60 7.167198e-05 0.066 0.111 TRUE 17.682804
61 3.146696e-05 0.087 0.139 TRUE 17.485600
62 1.895176e-03 0.064 0.106 TRUE 17.261319
63 1.310611e-08 0.032 0.076 TRUE 17.227682
64 3.061914e-08 0.026 0.066 TRUE 17.114455
65 9.725967e-07 0.139 0.206 TRUE 16.976388
66 4.077856e-05 0.027 0.061 TRUE 16.423492
67 8.698939e-05 0.385 0.458 TRUE 16.056556
68 9.459607e-04 0.168 0.223 TRUE 15.904114
69 2.033560e-03 0.090 0.135 TRUE 15.125653
70 2.813741e-03 0.114 0.164 TRUE 14.937964
71 8.009286e-05 0.293 0.360 TRUE 13.674803
72 1.563902e-02 0.039 0.069 TRUE 13.653635
73 1.351762e-03 0.100 0.148 TRUE 13.536046
74 3.701280e-05 0.040 0.078 TRUE 13.375417
75 1.344479e-02 0.211 0.268 TRUE 13.071870
76 5.350543e-05 0.020 0.051 TRUE 12.470204
77 1.956912e-03 0.043 0.079 TRUE 11.868386
78 4.012277e-02 0.120 0.166 TRUE 11.642475
79 1.683174e-02 0.042 0.074 TRUE 11.440897
80 8.163301e-03 0.047 0.081 TRUE 11.193954
81 2.367852e-05 0.072 0.121 TRUE 11.121155
82 2.191334e-04 0.027 0.060 TRUE 10.734090
83 3.803868e-04 0.029 0.061 TRUE 9.780282
84 1.415566e-03 0.026 0.055 TRUE 9.616473
85 4.504183e-03 0.128 0.179 TRUE 9.229553
86 1.448512e-02 0.300 0.366 TRUE 9.101940
87 8.579029e-06 0.054 0.100 TRUE 9.023248
88 9.337767e-03 0.026 0.054 TRUE 8.789141
89 2.169708e-03 0.024 0.052 TRUE 8.750171
90 9.758364e-04 0.074 0.118 TRUE 6.737577
cluster_support max_cluster_log2FC min_cluster_p_val_adj
1 2;4;5;8 1.3149729 2.926163e-97
2 2;4;5;7 0.7948607 6.914674e-40
3 2;4;6;7 0.9249589 7.845489e-84
4 2;4 0.6745209 9.437479e-26
5 2;4 1.1451353 2.298637e-31
6 2;4;5 1.3935093 1.109563e-12
7 2 1.3424072 1.360686e-14
8 2 0.8193956 1.111942e-41
9 5;11 3.6210213 6.509256e-107
10 2;4;5 1.4041813 4.308952e-23
11 2;3;5 1.8450863 9.231737e-122
12 2;5 2.9027138 2.636680e-36
13 2;5 2.4566705 3.170504e-46
14 3;5 1.4767218 1.459588e-24
15 4;5 0.8428831 7.421299e-05
16 4;7 0.9274611 1.787341e-16
17 2;4 1.6467829 4.940196e-19
18 2;4;5 1.5930094 1.596581e-15
19 5;7 0.4457738 4.973616e-09
20 4 0.4509406 3.927515e-03
21 2;10;11 4.6998013 2.416280e-30
22 2;3;5 0.7505358 1.132269e-13
23 2;5 0.6427965 6.295001e-11
24 2;4 1.1059567 3.210999e-10
25 2;5 1.3852956 1.791840e-09
26 2;4 2.3657208 3.717968e-16
27 4;5 1.1045737 7.269607e-08
28 5 2.5314869 1.754555e-23
29 5 2.4170409 2.764130e-24
30 2;5 1.2350251 4.092195e-12
31 <NA> NA NA
32 2;5;7 1.1462196 7.985402e-19
33 2;5 1.2749371 7.326753e-11
34 <NA> NA NA
35 2 1.0222454 1.488441e-06
36 5 1.2771772 1.360718e-03
37 4 0.8293094 1.575930e-15
38 5 2.1796840 5.237064e-23
39 4 1.8819046 5.391534e-23
40 2;10 2.8311254 2.494682e-34
41 2;7 1.0704871 9.315530e-03
42 2;5 2.1459210 1.322867e-14
43 4;8;10 3.4282197 0.000000e+00
44 2;4 1.6265430 2.576288e-05
45 5 2.0470659 3.612157e-14
46 3;7 0.9091691 6.246858e-26
47 7 0.4143896 8.413223e-03
48 4 0.8738634 7.876410e-14
49 2;4 1.8210760 5.930170e-22
50 2;5 1.4127708 2.597650e-07
51 2 0.6580104 6.408539e-05
52 2;4 1.7040296 1.778819e-04
53 2 1.5981382 4.199725e-02
54 5 1.4883684 1.762868e-05
55 2;4 1.6355935 7.396749e-14
56 4 0.8476863 5.142744e-14
57 5;9 1.7112196 4.223296e-08
58 5 2.6165048 6.948591e-35
59 4 1.2404632 1.797973e-15
60 <NA> NA NA
61 2 0.9192580 2.025225e-02
62 4 0.5470568 1.309821e-03
63 4;5 2.0368111 5.405044e-10
64 5 1.6956866 4.117233e-10
65 2 0.8261983 3.513250e-05
66 2 1.2887431 3.758900e-03
67 3;4 0.5010869 1.400262e-09
68 <NA> NA NA
69 4 0.2756608 3.954770e-02
70 4 0.7539576 2.823794e-12
71 7 0.7806955 1.070834e-14
72 4;5 1.6322204 4.532332e-05
73 2 1.5494248 1.092159e-25
74 <NA> NA NA
75 3;7 0.7464233 5.393400e-12
76 5 1.5966198 9.232406e-03
77 <NA> NA NA
78 5 1.4773086 4.441577e-25
79 4 1.1097092 1.199136e-04
80 2;7 1.2583703 2.484989e-04
81 2 1.4438382 3.915877e-15
82 2;9 1.8534743 4.156685e-04
83 <NA> NA NA
84 5 1.8828749 5.360613e-06
85 2 0.9005814 1.062043e-05
86 7;8 0.8216365 8.853810e-06
87 4 1.2247618 4.484259e-13
88 5 2.6642721 5.164084e-30
89 2 1.7099427 3.936510e-04
90 4 0.5336785 2.611942e-02
Step 12.9: Visualize Top lncRNA Candidates
We visualize the top shared candidates when they exist.
If no shared candidates are found, we visualize the top candidates from the reactive/stress-like state comparison.
<- priority_astro_lncRNAs %>% slice_head (n = 12 ) %>% pull (gene)if (length (top_lncRNAs_for_plot) == 0 ) {<- reactive_lncRNA_candidates %>% slice_head (n = 12 ) %>% pull (gene)<- intersect (top_lncRNAs_for_plot, rownames (SO_astro))
[1] "MALAT1" "NEAT1" "MIR9-1HG" "OBI1-AS1" "SLC44A3-AS1"
[6] "XIST" "MIR9-2HG" "PARD6G-AS1" "POT1-AS1" "PCDH9-AS2"
[11] "UFL1-AS1" "LINC-PINT"
if (length (top_lncRNAs_for_plot) > 0 ) {FeaturePlot (features = top_lncRNAs_for_plot,reduction = "umap_astro" ,ncol = 4 ,pt.size = 0.5 else {message ("No lncRNA candidates available for FeaturePlot." )
if (length (top_lncRNAs_for_plot) > 0 ) {DotPlot (features = top_lncRNAs_for_plot,group.by = "astro_state_refined" + RotatedAxis () + labs (title = "Top lncRNA Candidates by Refined Astrocyte State" )else {message ("No lncRNA candidates available for DotPlot." )
if (length (top_lncRNAs_for_plot) > 0 ) {DotPlot (features = top_lncRNAs_for_plot,group.by = "condition" + RotatedAxis () + labs (title = "Top lncRNA Candidates by Condition" )else {message ("No lncRNA candidates available for DotPlot." )
Warning: Scaling data with a low number of groups may produce misleading
results
Step 12.10: Save Astrocyte DE and lncRNA Discovery Results
saveRDS (file.path (results_dir, "SO_astro_step12_5_fernando_lncRNA_analysis.rds" )saveRDS (file.path (results_dir, "SO_astro_step12_5_main_DE_subset.rds" )write.csv (file.path (results_dir, "Step12_5_astro_state_cluster_summary.csv" ),row.names = FALSE write.csv (file.path (results_dir, "Step12_5_astro_state_group_summary.csv" ),row.names = FALSE write.csv (file.path (results_dir, "Step12_5_DE_reactive_stress_like_PD_vs_homeostatic_like_C.csv" ),row.names = FALSE write.csv (file.path (results_dir, "Step12_5_DE_PD_vs_C_astrocytes.csv" ),row.names = FALSE write.csv (file.path (results_dir, "Step12_5_astro_cluster_markers_annotated.csv" ),row.names = FALSE write.csv (file.path (results_dir, "Step12_5_reactive_stress_state_lncRNA_candidates.csv" ),row.names = FALSE write.csv (file.path (results_dir, "Step12_5_PD_lncRNA_candidates.csv" ),row.names = FALSE write.csv (file.path (results_dir, "Step12_5_cluster_lncRNA_candidates.csv" ),row.names = FALSE write.csv (file.path (results_dir, "Step12_5_priority_astro_lncRNA_candidates.csv" ),row.names = FALSE write.csv (file.path (results_dir, "Step12_5_driver_like_lncRNA_candidates.csv" ),row.names = FALSE write.csv (file.path (results_dir, "Step12_5_defender_like_lncRNA_candidates.csv" ),row.names = FALSE write.csv (data.frame (setting = c ("input_object" ,"state_definition" ,"reactive_stress_like_PD_clusters" ,"homeostatic_like_C_clusters" ,"excluded_from_main_DE_clusters" ,"combined_reactivity_score_usage" ,"min_pct_use" ,"logfc_threshold_use" ,"p_adj_cutoff" ,"lncRNA_logfc_cutoff" ,"n_main_DE_cells" ,"n_reactive_lncRNA_candidates" ,"n_PD_lncRNA_candidates" ,"n_cluster_lncRNA_candidates" ,"n_priority_lncRNAs" ,"n_driver_like_lncRNAs" ,"n_defender_like_lncRNAs" value = c ("cluster-based refined astrocyte states" ,paste (reactive_stress_clusters, collapse = "," ),paste (homeostatic_clusters, collapse = "," ),paste (c ("1" , "3" , "7" , "9" , "10" , "11" ), collapse = "," ),"z-scored summary/visualization only; not used for main DE grouping" ,ncol (SO_astro_main_DE),nrow (reactive_lncRNA_candidates),nrow (PD_lncRNA_candidates),nrow (cluster_lncRNA_candidates),nrow (priority_astro_lncRNAs),nrow (driver_lncRNAs),nrow (defender_lncRNAs)file.path (results_dir, "Step12_5_analysis_settings.csv" ),row.names = FALSE
Interpretation Note
This analysis prioritizes lncRNAs that are associated with astrocyte state and/or PD status.
The strongest candidates are not simply the most significant DE genes. They are candidates that satisfy several criteria:
1. lncRNA-like gene annotation or symbol pattern
2. differential expression in cluster-defined reactive/stress-like astrocytes
3. differential expression in PD astrocytes
4. optional support from astrocyte subcluster markers
5. interpretable direction of changeThe final candidate list should be treated as a hypothesis-generating result. Any top lncRNA should be checked manually using genome annotation databases and literature before being described as novel or biologically meaningful.
