install packages:
if(!requireNamespace("BiocManager", quietly = TRUE))
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## anyMissing, rowMedianslibrary(AnnotationDbi)
library(org.Hs.eg.db)## library(clusterProfiler)## ## clusterProfiler v4.12.6 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
##
## Please cite:
##
## T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan,
## X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal
## enrichment tool for interpreting omics data. The Innovation. 2021,
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library(enrichplot)
library(pathview)## ##############################################################################
## Pathview is an open source software package distributed under GNU General
## Public License version 3 (GPLv3). Details of GPLv3 is available at
## http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
## formally cite the original Pathview paper (not just mention it) in publications
## or products. For details, do citation("pathview") within R.
##
## The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
## license agreement (details at http://www.kegg.jp/kegg/legal.html).
## ##############################################################################library(DOSE)## DOSE v3.30.5 For help: https://yulab-smu.top/biomedical-knowledge-mining-book/
##
## If you use DOSE in published research, please cite:
## Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609library(biomaRt)
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## plotMAlibrary(AnnotationDbi)create custom gene list based on race genes in Venn Diagram:
AA_gene_list <- list(symbol = c("RNU6-1199P","LOC107984850","FHAD1-AS1","FAM131C","RNU1-4",
"FAM43B", "LINC02596","NCMAP","FAM110D","TINAGL1","LCK","RNU6-880P",
"RPL9P12","LINC01360","MIR760","CYMP-AS1","ADAM30","RPL22P6",
"MIR8083","RN7SL612P","FCRL3","RN7SL464P","RN7SKP276","LOC124900536",
"FLJ33534","LINC02613","LINC03050","LRRTM4-AS1","ANAPC1P3","DBF4P2",
"SLC30A6P1","FAM138B","CDRT15P3","ASDURF","RNU6-642P","NPPC",
"LINC00691","ACTL11P","GABRR3","HNRNPA1P17","CD96","RPL10P7",
"LINC01471","HMGN1P10","HLMR1","SSBL6P","RNU4-38P","RNU6-4P",
"RTP2","GBA3","LOC105374524", "RNU6-310P","COMMD5P1","PCAT4",
"LOC152845","RNU1-36P","RNU7-149P","CIR1P2","FABP2","RNA5SP165",
"TUBB7P","DUX4L7","RPL23AP84","RNY3P1","LOC124900205", "EDIL3",
"PCBP2P3","MTCO2P22","LOC345576","MIR5706","EPIST","VTRNA1-3",
"STK32A","LINC01847","MIR5003","FAM153A","LOC645853","FOXO1B",
"KU-MEL-3","RN7SL554P","ELOVL2-AS1","H1-6","RNU2-62P","H4C11",
"DDR1","MICB","NFKBIL1","DXO","PPT2-EGFL8","LOC105375026",
"ADGRF4","RN7SK","LINC01611","NOX3","UNCX","LOC124900237",
"TRIL","LINC01449","MIR6839","LAMB4","H4P1","TAS2R40",
"IQCA1L","MICU3","DKK4","RNU6ATAC32P", "SOX17","RPS23P1",
"RN7SKP153","ZFAT-AS1","RNA5SP278","RPS6P11","LOC100130801","NDUFA5P3",
"SNORD121B","BANCR","TRPM6","RNA5SP288","TNFSF8","MIR4480",
"RNU2-18P","RNU6-1212P","EBLN1","ENKUR","FXYD4","SNORD3J",
"LOC105378318", "RPL22P18","RN7SL644P","SNRPGP12","MIR548E","JAKMIP3",
"SCGB1C1","OR51R1P","RPS15AP31","LOC124902803","LOC100420122","OR5B3",
"MS4A10","SLC22A10","MRGPRD","LINC02737","MTCO1P15","RPS2P39",
"HSPD1P12","GOT2P3","MIR920","OR8S1","AQP5-AS1","TMPRSS12",
"RPL35AP29","APOF","RASSF3-DT","WIF1","LRRC10","MTCH2P2",
"RN7SKP11","RNU6-1068P","RNA5SP375","MIR4499","CSNK1A1L","MIR3168",
"RPL36P19","RNY3P2","SOX21","RNU1-27P","DOCK11P1","MIR6076",
"OTX2","RN7SL530P","RNA5SP387","SNORD116-17","OCA2","LINC02915",
"RNA5SP393","TGM7","RNU5B-1","LOXL1","ADAMTS7P1","RNU7-79P",
"LINC02253","OR4F15","MSLN","LOC100505915","HS3ST2","MTCH2P3",
"CNTNAP4","SLC38A8","MIR6776","RPL21P122","RNU6-862P","CCL15",
"RNA5SP441","LOC124904136", "LOC124904137", "HOXB9","HOXB13","GH1",
"LRRC37A7P","CCBE1","RNU6-346P","CREB3L3","CRB3","RPS27AP19",
"AP1M2","LOC105372281", "NXNL1","SLC5A5","LOC124904695", "GPR42",
"MIR642A","FOXA3","RNU6-317P","NLRP11","RPS3P1","PAX1",
"HNRNPA3P2","CTCFL","FLJ16779","RIPK4","LOC124905172", "IGLV1-50",
"GRK3-AS1","LOC105372988","MIR3928","LOC124900492", "MIR222","MIR545",
"MIR548AN","IRS4"))
EA_gene_list <- list(symbol = c("ANKRD65","CFAP74","PLA2G5","RPS3AP11","TMEM61",
"PLPP3","LOC100421400","RNA5SP20","H3P3","RPL26P9",
"PALMD","RN7SL432P","CASQ2","RPL22P5","RNU1-68P",
"RPS10P6","PGLYRP4","LINC02772","LOC124900450","RGS5-AS1",
"FMO7P","LINC01732","AVPR1B","LINC02771","SPATA17-AS1",
"RNA5S6","RPL6P3","LOC105373418","RNU4-73P","LOC124900541",
"LINC01946","LOC124907760","VN1R18P","LOC388996","TEKT4",
"LOC107985789","RNU4-48P","MIR128-1","LOC107985953","CCDC148-AS1",
"LOC124900531","HOXD9","MTND4LP16","KIAA2012-AS1","CMKLR2",
"C2orf80","CXCR1","GAPDHP49","RNU6-788P","CIAO2AP1",
"GCSHP6","RN7SL217P","ITIH1","CCDC137P2","ABCF2P1",
"LOC124909397","EPHA6","CCDC54","PRR23E","RNA5SP139",
"JMJD4P1","CLSTN2-AS1","CPB1","RNA5SP146","TMEM212",
"RNU6-547P","NLGN1","LINC02069","MIR3137","MIR572",
"PFDN1P2","ZEB2P1","MTCYBP43","RPL17P19","RNU1-63P",
"GC","RPL5P12","ADH4","MIR8066","RN7SL55P",
"RNU6-1217P","RN7SL311P","LOC729558","FAM218A","WWC2-AS1",
"RPSAP70","DUX4L4","LINC01511","MIR6075","PLCXD3",
"LOC101928651","LOC101930276","KRT18P16","LOC402229","MIR874",
"LOC124901194","SPINK7","GLULP1","LINC02227","KCNIP1",
"KCNIP1-OT1","SLC34A1","LOC729707","RNU1-64P","H3C9P",
"MIR3143","POM121L2","OR2W6P","OR1F12P","PRR3",
"MRPS18B","LSM2","TCP11","LOC101929309","PRIM2BP",
"LOC100422587","KHDC3L","RNA5SP210","LOC100127917","LOC100133102",
"LINC02532","RNU6-960P","RPS27AP11","KRT18P22","OR2A4",
"LINC01013","LINC02524","LOC105378044","TBXT","CPVL-AS1",
"MARK2P7","RAMP3","IGFBP1","RNU2-29P","POMZP3",
"TFPI2-DT","HMGB3P21","RPL36P12","RNU6-177P","MIR6509",
"MTCO1P55","CNTNAP2","FAM66E","LINC03019","RN7SL303P",
"SCARA5","LINC00967","RNY3P14","RNU6-1197P","FABP12",
"MIOXP1","RPS6P9","AURKBP1","MIR4662B","LOC101930090",
"FAM88C","RN7SL422P","TMEM252-DT","OR13C5","FKTN-AS1",
"RNA5SP295","ASTN2-AS1","DIP2C","GATA3","PSME2P6",
"RNU7-77P","LOC100130881","CTSLP3","RNA5SP312","MTND1P20",
"RNU6-833P","SFRP5","DNMBP-AS1","MIR1307","LOC124900312",
"RN7SKP158","DCDC1","TBX10","MIR6754","HNRNPCP6",
"LOC100420803","MMP13","APOA4","LOC105369576","HIGD1AP8",
"ART4","GYS2","RNA5SP354","ADCY6-DT","LOC122455340",
"ATF7-NPFF","EPYC","RNU4-41P","LOC107984548","RNU7-170P",
"MIR4304","RNU6-59P","ATP8A2","LINC00365","MIR548AS",
"NALF1","RPL21P107","LINC00567","TRDJ3","LOC100533628",
"LINC02307","ATP5F1CP1","LINC02284","KCNH5","RN7SL108P",
"LOC100422491","CTXN2","LIPC-AS1","MGC15885","LINC02204",
"LINC01580","LOC124900383","LINC02186","CDH16","RNU4-36P",
"HSD17B2","ALOX12B","ARHGEF15","DNAH9","CCL13",
"DUSP14","KRT16","MIR6784","IGBP1C","LOC100996361",
"LOC124900398","ELOA3DP","ST8SIA3","LOC105372145","SLC25A6P4",
"MIR5684","RPS18P13","BNIP3P34","RN7SL789P","CYP2B6",
"RN7SL836P","FGF21","MIR7975","LAMP5-AS1","AIMP1P1",
"OTOR","RPS27AP2","LINC00851","CST2","LOC100419562",
"LOC149684","RNU6-1146P","MIR6724-4","RNGTTP1","DNMT3L-AS1",
"SGSM1","MIR3199-1","SLC5A1","LOC100500719","CSF2RBP1",
"LL22NC01-81G9.3","APOBEC3B-AS1","TMA7B","ZBED1","FRMPD4",
"LOC100132857","RAI2","RN7SL48P","SPACA5","MIR6894",
"GOT2P6","RN7SL581P","P2RY10","MTCO1P19","COL4A6",
"MIR3978","RHOXF1","MAGEA1"))convert to data frame:
AA_gene_list <- as.data.frame(AA_gene_list)
EA_gene_list <- as.data.frame(EA_gene_list)convert symbol to ENSEMBL ID:
ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
# Query biomaRt to convert gene symbols to Ensembl IDs for AA
AA_gene_list <- getBM(attributes = c("external_gene_name", "ensembl_gene_id"),
filters = "external_gene_name",
values = AA_gene_list,
mart = ensembl)
# Query biomaRt to convert gene symbols to Ensembl IDs for EA
EA_gene_list <- getBM(attributes = c("external_gene_name", "ensembl_gene_id"),
filters = "external_gene_name",
values = EA_gene_list,
mart = ensembl)
# View the result
print(AA_gene_list)## external_gene_name ensembl_gene_id
## 1 RNU1-4 ENSG00000291399
## 2 TUBB7P ENSG00000283593
## 3 RPL23AP84 ENSG00000283660
## 4 MIR4499 ENSG00000263978
## 5 RNY3P2 ENSG00000199788
## 6 CSNK1A1L ENSG00000180138
## 7 MIR3168 ENSG00000264226
## 8 RIPK4 ENSG00000183421
## 9 RPL36P19 ENSG00000232540
## 10 FLJ16779 ENSG00000275620
## 11 HNRNPA3P2 ENSG00000227688
## 12 ENKUR ENSG00000151023
## 13 RPS3P1 ENSG00000291542
## 14 GBA3 ENSG00000291927
## 15 RNU1-27P ENSG00000206596
## 16 SOX21 ENSG00000125285
## 17 HS3ST2 ENSG00000122254
## 18 TRIL ENSG00000255690
## 19 MIR548AN ENSG00000263515
## 20 CNTNAP4 ENSG00000152910
## 21 OCA2 ENSG00000277361
## 22 MTCO2P22 ENSG00000270225
## 23 RNU6-1212P ENSG00000252832
## 24 MIR4480 ENSG00000263584
## 25 PCBP2P3 ENSG00000248826
## 26 EDIL3 ENSG00000164176
## 27 CCBE1 ENSG00000183287
## 28 STK32A ENSG00000169302
## 29 SNRPGP12 ENSG00000226734
## 30 ADAMTS7P1 ENSG00000281976
## 31 LAMB4 ENSG00000091128
## 32 RN7SL644P ENSG00000264313
## 33 LRRTM4-AS1 ENSG00000234653
## 34 LINC03050 ENSG00000235725
## 35 RPL22P18 ENSG00000230171
## 36 CCL15 ENSG00000275528
## 37 ANAPC1P3 ENSG00000230395
## 38 IGLV1-50 ENSG00000211645
## 39 RNU6-346P ENSG00000252097
## 40 RPL10P7 ENSG00000242052
## 41 RNA5SP387 ENSG00000201096
## 42 LRRC37A7P ENSG00000265158
## 43 CTCFL ENSG00000124092
## 44 RNA5SP288 ENSG00000251884
## 45 HMGN1P10 ENSG00000244101
## 46 IRS4 ENSG00000133124
## 47 LRRC10 ENSG00000198812
## 48 RNY3P1 ENSG00000201955
## 49 MIR5706 ENSG00000264536
## 50 MIR5003 ENSG00000265160
## 51 DBF4P2 ENSG00000271635
## 52 RNA5SP165 ENSG00000252951
## 53 SSBL6P ENSG00000244429
## 54 SNORD121B ENSG00000238300
## 55 IQCA1L ENSG00000278685
## 56 RN7SL554P ENSG00000240936
## 57 RN7SK ENSG00000283293
## 58 PAX1 ENSG00000125813
## 59 CRB3 ENSG00000130545
## 60 RNU6-1068P ENSG00000222890
## 61 RN7SKP11 ENSG00000252827
## 62 FOXA3 ENSG00000170608
## 63 FXYD4 ENSG00000150201
## 64 SNORD3J ENSG00000221400
## 65 SLC38A8 ENSG00000166558
## 66 RPS3P1 ENSG00000230935
## 67 MIR6776 ENSG00000273606
## 68 CDRT15P3 ENSG00000274362
## 69 MTCH2P2 ENSG00000258262
## 70 JAKMIP3 ENSG00000188385
## 71 RNU6-317P ENSG00000206758
## 72 TUBB7P ENSG00000283655
## 73 MSLN ENSG00000102854
## 74 NOX3 ENSG00000074771
## 75 TUBB7P ENSG00000173876
## 76 MIR548E ENSG00000221214
## 77 OTX2 ENSG00000165588
## 78 MIR3928 ENSG00000264141
## 79 FOXO1B ENSG00000214295
## 80 H1-6 ENSG00000187475
## 81 MICB ENSG00000204516
## 82 EBLN1 ENSG00000223601
## 83 MTCH2P3 ENSG00000260438
## 84 MRGPRD ENSG00000172938
## 85 MICB ENSG00000231179
## 86 NPPC ENSG00000163273
## 87 GH1 ENSG00000259384
## 88 TAS2R40 ENSG00000221937
## 89 RNU6-642P ENSG00000200029
## 90 MICB ENSG00000234218
## 91 NDUFA5P3 ENSG00000234853
## 92 RPS27AP19 ENSG00000269228
## 93 DDR1 ENSG00000229767
## 94 RNU1-36P ENSG00000202000
## 95 NFKBIL1 ENSG00000236346
## 96 MICB ENSG00000224378
## 97 PPT2-EGFL8 ENSG00000258388
## 98 DXO ENSG00000225682
## 99 MIR6839 ENSG00000275667
## 100 RN7SL530P ENSG00000239910
## 101 GRK3-AS1 ENSG00000234884
## 102 DXO ENSG00000204348
## 103 MIR6076 ENSG00000278038
## 104 NFKBIL1 ENSG00000236196
## 105 AP1M2 ENSG00000129354
## 106 MICB ENSG00000227772
## 107 MIR760 ENSG00000211575
## 108 FAM43B ENSG00000183114
## 109 DDR1 ENSG00000137332
## 110 MIR642A ENSG00000207773
## 111 NFKBIL1 ENSG00000234530
## 112 FABP2 ENSG00000145384
## 113 OCA2 ENSG00000104044
## 114 SCGB1C1 ENSG00000188076
## 115 RASSF3-DT ENSG00000256670
## 116 DDR1 ENSG00000223680
## 117 GBA3 ENSG00000249948
## 118 NXNL1 ENSG00000171773
## 119 DDR1 ENSG00000230456
## 120 DXO ENSG00000236765
## 121 DXO ENSG00000234798
## 122 MICB ENSG00000238289
## 123 NFKBIL1 ENSG00000235125
## 124 DDR1 ENSG00000204580
## 125 WIF1 ENSG00000156076
## 126 RPL35AP29 ENSG00000244540
## 127 MIR545 ENSG00000207820
## 128 LOXL1 ENSG00000129038
## 129 NFKBIL1 ENSG00000206440
## 130 H4C11 ENSG00000197238
## 131 OR5B3 ENSG00000172769
## 132 DXO ENSG00000206346
## 133 DDR1 ENSG00000215522
## 134 RNU6-862P ENSG00000199674
## 135 DDR1 ENSG00000234078
## 136 TNFSF8 ENSG00000106952
## 137 RNU5B-1 ENSG00000200156
## 138 APOF ENSG00000175336
## 139 DOCK11P1 ENSG00000259000
## 140 ADGRF4 ENSG00000153294
## 141 RNU2-62P ENSG00000222800
## 142 H4P1 ENSG00000240680
## 143 DXO ENSG00000224313
## 144 RPS23P1 ENSG00000243504
## 145 RNA5SP375 ENSG00000199845
## 146 MIR222 ENSG00000207725
## 147 MICB ENSG00000231372
## 148 RNU6-310P ENSG00000207385
## 149 COMMD5P1 ENSG00000173966
## 150 MICB ENSG00000206449
## 151 RNU6-880P ENSG00000207256
## 152 ADAM30 ENSG00000134249
## 153 NFKBIL1 ENSG00000227565
## 154 RNU2-18P ENSG00000223156
## 155 CREB3L3 ENSG00000060566
## 156 TGM7 ENSG00000159495
## 157 MTCO1P15 ENSG00000255350
## 158 RNA5SP393 ENSG00000200293
## 159 NFKBIL1 ENSG00000204498
## 160 TINAGL1 ENSG00000142910
## 161 TRPM6 ENSG00000119121
## 162 GOT2P3 ENSG00000233719
## 163 ASDURF ENSG00000286053
## 164 NCMAP ENSG00000184454
## 165 RN7SL464P ENSG00000243872
## 166 TMPRSS12 ENSG00000186452
## 167 HSPD1P12 ENSG00000255964
## 168 BANCR ENSG00000278910
## 169 HNRNPA1P17 ENSG00000243188
## 170 SLC5A5 ENSG00000105641
## 171 VTRNA1-3 ENSG00000202515
## 172 DKK4 ENSG00000104371
## 173 OR8S1 ENSG00000284723
## 174 RNU7-149P ENSG00000252548
## 175 FAM153A ENSG00000170074
## 176 RPS2P39 ENSG00000240698
## 177 TUBB7P ENSG00000251297
## 178 DUX4L7 ENSG00000281652
## 179 CCL15 ENSG00000275718
## 180 MIR920 ENSG00000216192
## 181 LINC01449 ENSG00000224017
## 182 RNU4-38P ENSG00000201342
## 183 ACTL11P ENSG00000234667
## 184 NLRP11 ENSG00000179873
## 185 HOXB9 ENSG00000170689
## 186 GABRR3 ENSG00000183185
## 187 UNCX ENSG00000164853
## 188 OR4F15 ENSG00000182854
## 189 PCAT4 ENSG00000251321
## 190 RN7SL612P ENSG00000266160
## 191 RNU7-79P ENSG00000251891
## 192 SLC22A10 ENSG00000184999
## 193 ADAMTS7P1 ENSG00000274376
## 194 RN7SKP153 ENSG00000201896
## 195 RN7SKP276 ENSG00000252051
## 196 FAM131C ENSG00000185519
## 197 RNU6-4P ENSG00000206932
## 198 KU-MEL-3 ENSG00000205444
## 199 CIR1P2 ENSG00000250215
## 200 RNA5SP278 ENSG00000252864
## 201 MICU3 ENSG00000155970
## 202 EPIST ENSG00000249082
## 203 RPL23AP84 ENSG00000261914
## 204 RPL21P122 ENSG00000241185
## 205 SLC30A6P1 ENSG00000232277
## 206 LINC01847 ENSG00000253311
## 207 RNU1-4 ENSG00000207389
## 208 AQP5-AS1 ENSG00000257588
## 209 ELOVL2-AS1 ENSG00000230314
## 210 SNORD116-17 ENSG00000206656
## 211 LINC01611 ENSG00000231776
## 212 MS4A10 ENSG00000172689
## 213 LINC02253 ENSG00000259485
## 214 HOXB13 ENSG00000159184
## 215 GPR42 ENSG00000126251
## 216 LINC02915 ENSG00000175746
## 217 CDRT15P3 ENSG00000186825
## 218 OR51R1P ENSG00000237272
## 219 LINC00691 ENSG00000224074
## 220 SOX17 ENSG00000164736
## 221 RTP2 ENSG00000198471
## 222 ZFAT-AS1 ENSG00000248492
## 223 RNA5SP441 ENSG00000252618
## 224 RNU6ATAC32P ENSG00000251835
## 225 CD96 ENSG00000153283
## 226 LINC01471 ENSG00000239921
## 227 FCRL3 ENSG00000160856
## 228 LINC02737 ENSG00000256684
## 229 LCK ENSG00000182866
## 230 CDRT15P3 ENSG00000290618
## 231 HLMR1 ENSG00000243818
## 232 RPL22P6 ENSG00000268993
## 233 MIR8083 ENSG00000274940
## 234 FAM138B ENSG00000226516
## 235 RNU6-1199P ENSG00000223181
## 236 LINC02613 ENSG00000231367
## 237 FAM110D ENSG00000197245
## 238 LINC01360 ENSG00000233973
## 239 FHAD1-AS1 ENSG00000233485
## 240 CYMP-AS1 ENSG00000235407
## 241 LINC02596 ENSG00000233431print(EA_gene_list)## external_gene_name ensembl_gene_id
## 1 ZBED1 ENSG00000292345
## 2 RNGTTP1 ENSG00000237731
## 3 ST8SIA3 ENSG00000177511
## 4 NALF1 ENSG00000204442
## 5 MIR6724-4 ENSG00000275692
## 6 CST2 ENSG00000170369
## 7 ATP8A2 ENSG00000132932
## 8 TRDJ3 ENSG00000211828
## 9 LINC02307 ENSG00000258969
## 10 ATP5F1CP1 ENSG00000224004
## 11 RNU6-59P ENSG00000207518
## 12 OTOR ENSG00000125879
## 13 KCNH5 ENSG00000140015
## 14 RAI2 ENSG00000131831
## 15 DNMT3L-AS1 ENSG00000232010
## 16 MIR6724-4 ENSG00000288308
## 17 P2RY10 ENSG00000078589
## 18 RAMP3 ENSG00000122679
## 19 RPL21P107 ENSG00000225239
## 20 LINC00567 ENSG00000259831
## 21 MIR548AS ENSG00000263741
## 22 SLC25A6P4 ENSG00000266909
## 23 HIGD1AP8 ENSG00000237303
## 24 GYS2 ENSG00000111713
## 25 LINC03019 ENSG00000285506
## 26 FAM66E ENSG00000292390
## 27 HMGB3P21 ENSG00000224551
## 28 RN7SL422P ENSG00000274852
## 29 RNA5SP295 ENSG00000199525
## 30 CIAO2AP1 ENSG00000234048
## 31 RNA5SP312 ENSG00000252877
## 32 MIR6894 ENSG00000277474
## 33 LINC00365 ENSG00000224511
## 34 RPL5P12 ENSG00000242697
## 35 MIR1307 ENSG00000283867
## 36 KRT18P22 ENSG00000218153
## 37 RPL17P19 ENSG00000241261
## 38 ELOA3DP ENSG00000288616
## 39 MTND1P20 ENSG00000226794
## 40 RPS27AP11 ENSG00000218208
## 41 LINC02524 ENSG00000233534
## 42 DUSP14 ENSG00000275932
## 43 WWC2-AS1 ENSG00000251128
## 44 CCDC137P2 ENSG00000239350
## 45 MTCO1P55 ENSG00000241926
## 46 ALOX12B ENSG00000179477
## 47 ARHGEF15 ENSG00000198844
## 48 CYP2B6 ENSG00000197408
## 49 RN7SKP158 ENSG00000222385
## 50 BNIP3P34 ENSG00000269509
## 51 RNU2-29P ENSG00000222355
## 52 DNAH9 ENSG00000007174
## 53 SLC34A1 ENSG00000131183
## 54 MIR572 ENSG00000207716
## 55 RNU1-63P ENSG00000206629
## 56 RN7SL55P ENSG00000243227
## 57 MIR8066 ENSG00000273882
## 58 C2orf80 ENSG00000188674
## 59 MIR3978 ENSG00000265584
## 60 OR13C5 ENSG00000277556
## 61 PLA2G5 ENSG00000127472
## 62 RNA5SP210 ENSG00000212336
## 63 RN7SL311P ENSG00000265892
## 64 OR2W6P ENSG00000168126
## 65 PFDN1P2 ENSG00000248188
## 66 TMA7B ENSG00000225528
## 67 RNU4-41P ENSG00000201296
## 68 RN7SL108P ENSG00000243546
## 69 MTCO1P19 ENSG00000237300
## 70 APOBEC3B-AS1 ENSG00000262679
## 71 CNTNAP2 ENSG00000174469
## 72 RNU4-36P ENSG00000201164
## 73 AIMP1P1 ENSG00000234187
## 74 ZBED1 ENSG00000214717
## 75 PLPP3 ENSG00000162407
## 76 GAPDHP49 ENSG00000234285
## 77 MIR3199-1 ENSG00000264073
## 78 CMKLR2 ENSG00000283448
## 79 FGF21 ENSG00000105550
## 80 KHDC3L ENSG00000203908
## 81 SGSM1 ENSG00000167037
## 82 COL4A6 ENSG00000197565
## 83 RNU6-547P ENSG00000252082
## 84 RNA5SP146 ENSG00000222675
## 85 TBXT ENSG00000164458
## 86 LINC01511 ENSG00000281736
## 87 EPYC ENSG00000083782
## 88 ABCF2P1 ENSG00000242159
## 89 RNU7-77P ENSG00000253054
## 90 RNU6-833P ENSG00000200356
## 91 RPS18P13 ENSG00000243455
## 92 PSME2P6 ENSG00000227462
## 93 RN7SL48P ENSG00000266710
## 94 SLC5A1 ENSG00000100170
## 95 POMZP3 ENSG00000276464
## 96 RNU6-177P ENSG00000223189
## 97 FRMPD4 ENSG00000169933
## 98 CNTNAP2 ENSG00000278728
## 99 SPACA5 ENSG00000171489
## 100 LSM2 ENSG00000204392
## 101 PRR3 ENSG00000204576
## 102 MRPS18B ENSG00000204568
## 103 RN7SL581P ENSG00000242657
## 104 LL22NC01-81G9.3 ENSG00000215403
## 105 LSM2 ENSG00000224979
## 106 MAGEA1 ENSG00000198681
## 107 LINC00851 ENSG00000237282
## 108 LSM2 ENSG00000236826
## 109 MRPS18B ENSG00000227420
## 110 LAMP5-AS1 ENSG00000225988
## 111 MRPS18B ENSG00000233813
## 112 IGFBP1 ENSG00000146678
## 113 APOBEC3B-AS1 ENSG00000249310
## 114 GATA3 ENSG00000107485
## 115 PRR3 ENSG00000228186
## 116 MIR6509 ENSG00000277138
## 117 MIR4304 ENSG00000265526
## 118 PRR3 ENSG00000223887
## 119 MIR5684 ENSG00000263800
## 120 RPS27AP2 ENSG00000232333
## 121 RNU6-1146P ENSG00000252091
## 122 PRR3 ENSG00000229202
## 123 LSM2 ENSG00000231502
## 124 H3C9P ENSG00000220875
## 125 POMZP3 ENSG00000146707
## 126 RN7SL836P ENSG00000241226
## 127 CTSLP3 ENSG00000280913
## 128 RHOXF1 ENSG00000101883
## 129 CSF2RBP1 ENSG00000232254
## 130 MRPS18B ENSG00000223775
## 131 PRR3 ENSG00000233564
## 132 MRPS18B ENSG00000229861
## 133 OR2A4 ENSG00000180658
## 134 HNRNPCP6 ENSG00000213305
## 135 LINC02186 ENSG00000261856
## 136 GCSHP6 ENSG00000270538
## 137 LSM2 ENSG00000172850
## 138 RPSAP70 ENSG00000250327
## 139 MTCYBP43 ENSG00000250624
## 140 CDH16 ENSG00000166589
## 141 MRPS18B ENSG00000203624
## 142 RPL36P12 ENSG00000213361
## 143 KRT18P16 ENSG00000235275
## 144 LIPC-AS1 ENSG00000259293
## 145 LINC02204 ENSG00000280639
## 146 LSM2 ENSG00000225998
## 147 PRR3 ENSG00000223766
## 148 DIP2C ENSG00000151240
## 149 SFRP5 ENSG00000120057
## 150 CPB1 ENSG00000153002
## 151 KRT16 ENSG00000186832
## 152 GC ENSG00000145321
## 153 JMJD4P1 ENSG00000249505
## 154 MIR3143 ENSG00000265565
## 155 POM121L2 ENSG00000158553
## 156 APOA4 ENSG00000110244
## 157 MRPS18B ENSG00000226111
## 158 PRR3 ENSG00000206491
## 159 MIR6754 ENSG00000278349
## 160 LINC02284 ENSG00000259719
## 161 RNU6-1217P ENSG00000223208
## 162 ATF7-NPFF ENSG00000267281
## 163 CCL13 ENSG00000181374
## 164 MTND4LP16 ENSG00000234731
## 165 GOT2P6 ENSG00000214745
## 166 LINC01511 ENSG00000250584
## 167 MIR6075 ENSG00000273742
## 168 DNMBP-AS1 ENSG00000227695
## 169 TBX10 ENSG00000167800
## 170 RNY3P14 ENSG00000207036
## 171 DCDC1 ENSG00000170959
## 172 TCP11 ENSG00000124678
## 173 HSD17B2 ENSG00000086696
## 174 OR1F12P ENSG00000220721
## 175 SPINK7 ENSG00000145879
## 176 HOXD9 ENSG00000128709
## 177 IGBP1C ENSG00000266826
## 178 MIR128-1 ENSG00000207654
## 179 MIR874 ENSG00000216009
## 180 PRIM2BP ENSG00000283453
## 181 MMP13 ENSG00000137745
## 182 VN1R18P ENSG00000275423
## 183 RNU4-48P ENSG00000202429
## 184 KCNIP1 ENSG00000182132
## 185 PLCXD3 ENSG00000182836
## 186 FAM88C ENSG00000204802
## 187 TMEM252-DT ENSG00000226337
## 188 AURKBP1 ENSG00000230948
## 189 RNA5SP139 ENSG00000201210
## 190 FKTN-AS1 ENSG00000228317
## 191 ASTN2-AS1 ENSG00000229105
## 192 MIR4662B ENSG00000263735
## 193 ADH4 ENSG00000198099
## 194 CPVL-AS1 ENSG00000229452
## 195 CTXN2 ENSG00000233932
## 196 DUX4L4 ENSG00000258834
## 197 MIOXP1 ENSG00000253292
## 198 RNU6-960P ENSG00000200926
## 199 ZEB2P1 ENSG00000249506
## 200 MGC15885 ENSG00000259458
## 201 TFPI2-DT ENSG00000234695
## 202 RN7SL217P ENSG00000264706
## 203 CMKLR2 ENSG00000183671
## 204 RNA5S6 ENSG00000200624
## 205 CXCR1 ENSG00000163464
## 206 RNU1-68P ENSG00000275229
## 207 FAM218A ENSG00000250486
## 208 RN7SL303P ENSG00000240116
## 209 RNU7-170P ENSG00000239082
## 210 MIR6784 ENSG00000277249
## 211 ANKRD65 ENSG00000235098
## 212 EPHA6 ENSG00000080224
## 213 RNU6-1197P ENSG00000212485
## 214 H3P3 ENSG00000234202
## 215 RN7SL432P ENSG00000242769
## 216 ART4 ENSG00000111339
## 217 RNA5SP354 ENSG00000212549
## 218 RPL6P3 ENSG00000229022
## 219 RNU1-64P ENSG00000202313
## 220 LINC02227 ENSG00000276778
## 221 KCNIP1-OT1 ENSG00000253647
## 222 AVPR1B ENSG00000198049
## 223 MIR3137 ENSG00000265333
## 224 ITIH1 ENSG00000055957
## 225 SCARA5 ENSG00000168079
## 226 LINC01013 ENSG00000228495
## 227 ADCY6-DT ENSG00000257660
## 228 DUSP14 ENSG00000276023
## 229 RNU4-73P ENSG00000200034
## 230 CFAP74 ENSG00000142609
## 231 NLGN1 ENSG00000169760
## 232 MIR7975 ENSG00000275863
## 233 FABP12 ENSG00000197416
## 234 TEKT4 ENSG00000163060
## 235 CCDC54 ENSG00000138483
## 236 LINC02532 ENSG00000235142
## 237 RNU6-788P ENSG00000212269
## 238 CCDC148-AS1 ENSG00000227480
## 239 PALMD ENSG00000099260
## 240 RPS3AP11 ENSG00000230116
## 241 RN7SL789P ENSG00000242436
## 242 LINC00967 ENSG00000253138
## 243 LINC01946 ENSG00000223647
## 244 PRR23E ENSG00000214324
## 245 TMEM212 ENSG00000186329
## 246 LINC03019 ENSG00000254813
## 247 KIAA2012-AS1 ENSG00000222035
## 248 FAM66E ENSG00000225725
## 249 PGLYRP4 ENSG00000163218
## 250 CLSTN2-AS1 ENSG00000250433
## 251 LINC02069 ENSG00000229433
## 252 FMO7P ENSG00000230231
## 253 RNA5SP20 ENSG00000251785
## 254 RPL26P9 ENSG00000226128
## 255 TMEM61 ENSG00000143001
## 256 LINC02772 ENSG00000271736
## 257 LINC01732 ENSG00000237292
## 258 RGS5-AS1 ENSG00000232892
## 259 SPATA17-AS1 ENSG00000234070
## 260 LINC02771 ENSG00000224535
## 261 CASQ2 ENSG00000118729
## 262 RPL22P5 ENSG00000268074extract ENSEMBL ID for use in DAVID:
AA_ensembl_ID <- as.data.frame(AA_gene_list$ensembl_gene_id)
EA_ensembl_ID <- as.data.frame(EA_gene_list$ensembl_gene_id)export to excel:
write.csv(AA_ensembl_ID, "/Users/ewamble/Dropbox/RNAseq/THP1/AA_ensembl_ID.csv", row.names = FALSE)
write.csv(EA_ensembl_ID, "/Users/ewamble/Dropbox/RNAseq/THP1/EA_ensembl_ID.csv", row.names = FALSE)