GO.Pro.resilience

#this is intersection list from Mito (GO plus Mitocarta.2048) and Pro.resilience (299 protein sets)
genes_mito_synaptic <- c(
  "Mcu", "Dhrs7b", "Gad1", "Pick1", "Cox4i1", "Pdha2", "Lars2", "Idh2", "Mgst3",
  "Lrpprc", "Cpt1a", "Acad9", "Gsk3a", "Nfs1", "Timm8b", "Hsdl2", "Pdha1", "Eri3",
  "L2hgdh", "Acads", "Sult4a1", "Idh3b", "Bckdhb", "Ndufb7", "Mpc2", "Mfn2", "Mrpl32",
  "Timm13", "Bcat2", "Slc8a3", "Ckap4", "Slc25a3", "Rap1gds1", "Iscu", "Ahcyl1",
  "Lyrm7", "Cyb5r1", "Slc25a11", "Pdhb", "Tmem65", "Sdhd", "Gk", "Idh3a", "Slc25a13",
  "Cs", "Gcsh", "Bdh1", "Agpat5", "Hibadh", "Rps15a", "D2hgdh", "Slc25a46", "Fam162a",
  "Tmem126b", "Ndufv3", "Dnm1l", "Nipsnap1", "Dbt", "Rab35", "Prkce", "Tsc22d1",
  "Rps3", "Sdhc", "Ndufaf1", "Atad1", "Mtx2", "Gsk3b", "Ndufs8", "Gramd4", "Dnajc19",
  "Timm44", "Ndufa3", "Rrm1", "Romo1"
)
genes_mito_synaptic

##  [1] "Mcu"      "Dhrs7b"   "Gad1"     "Pick1"    "Cox4i1"   "Pdha2"   
##  [7] "Lars2"    "Idh2"     "Mgst3"    "Lrpprc"   "Cpt1a"    "Acad9"   
## [13] "Gsk3a"    "Nfs1"     "Timm8b"   "Hsdl2"    "Pdha1"    "Eri3"    
## [19] "L2hgdh"   "Acads"    "Sult4a1"  "Idh3b"    "Bckdhb"   "Ndufb7"  
## [25] "Mpc2"     "Mfn2"     "Mrpl32"   "Timm13"   "Bcat2"    "Slc8a3"  
## [31] "Ckap4"    "Slc25a3"  "Rap1gds1" "Iscu"     "Ahcyl1"   "Lyrm7"   
## [37] "Cyb5r1"   "Slc25a11" "Pdhb"     "Tmem65"   "Sdhd"     "Gk"      
## [43] "Idh3a"    "Slc25a13" "Cs"       "Gcsh"     "Bdh1"     "Agpat5"  
## [49] "Hibadh"   "Rps15a"   "D2hgdh"   "Slc25a46" "Fam162a"  "Tmem126b"
## [55] "Ndufv3"   "Dnm1l"    "Nipsnap1" "Dbt"      "Rab35"    "Prkce"   
## [61] "Tsc22d1"  "Rps3"     "Sdhc"     "Ndufaf1"  "Atad1"    "Mtx2"    
## [67] "Gsk3b"    "Ndufs8"   "Gramd4"   "Dnajc19"  "Timm44"   "Ndufa3"  
## [73] "Rrm1"     "Romo1"

#saveRDS(genes_mito_synaptic, file = 'GO.Mitocarta.Mito.resilience.rds')

genes2 <- c(
    "Olfm3", "Ica1", "Slc4a10", "Adam11", "Fbxo41", "Plaa", "Actn4", "Camk4", "Asap1",
    "Plcb1", "Ctnna2", "Porcn", "Map2", "P2ry1", "Vac14", "Sgip1", "Arhgef2", "Numb",
    "Adcy1", "Actn1", "Amot", "Rab35", "Dclk1", "Rab3b", "Plekha5", "Ctnnd1", "Gsk3b",
    "Clasp2", "Hcn1", "Ppp1ca", "Dlg3", "Srgap2c", "Gnai2", "Nf1", "Sh3gl1", "Grm3",
    "Kalrn", "Ap1b1", "Gphn", "Gad1", "Synpo", "Cdk5", "Rpl13a", "Pick1", "Nptx2",
    "Rtn4", "Sipa1l1", "Rplp0", "Prkar1b", "Rpl30", "Dlgap4", "Slc4a8", "Cacng2",
    "Rpl5", "Rps15a", "Cplx1", "Eif4g3", "Grin2c", "Aak1", "Rpl10", "Cyfip2", "Cadps",
    "Gnb5", "Dnm1l", "Cpne4", "Prkce", "Rpl13", "Gng3", "Rpl9", "Calb1", "Rps17",
    "Cacng3", "Rps3", "Lrrc4b", "Cbln4", "Ppp2r1a", "Rps5", "Rph3a", "Cplx3", "Rps25",
    "Rpl36", "Syngap1", "Atad1", "Dmtn", "Cacng8", "Rimbp2", "Atp2b2", "Shisa7",
    "Gad2", "Rpl28", "Htr2a", "Elmod1", "Snap25", "Slc8a3", "Gria3", "Cadps2", "Ywhaq",
    "Syt12", "Ctnnb1", "Tln2"
)
# Remove ribosomal proteins from genes2
genes_no_ribo <- genes2[!grepl("^Rpl|^Rps|^Rp", genes2)]

# View result
print(genes_no_ribo)

##  [1] "Olfm3"   "Ica1"    "Slc4a10" "Adam11"  "Fbxo41"  "Plaa"    "Actn4"  
##  [8] "Camk4"   "Asap1"   "Plcb1"   "Ctnna2"  "Porcn"   "Map2"    "P2ry1"  
## [15] "Vac14"   "Sgip1"   "Arhgef2" "Numb"    "Adcy1"   "Actn1"   "Amot"   
## [22] "Rab35"   "Dclk1"   "Rab3b"   "Plekha5" "Ctnnd1"  "Gsk3b"   "Clasp2" 
## [29] "Hcn1"    "Ppp1ca"  "Dlg3"    "Srgap2c" "Gnai2"   "Nf1"     "Sh3gl1" 
## [36] "Grm3"    "Kalrn"   "Ap1b1"   "Gphn"    "Gad1"    "Synpo"   "Cdk5"   
## [43] "Pick1"   "Nptx2"   "Rtn4"    "Sipa1l1" "Prkar1b" "Dlgap4"  "Slc4a8" 
## [50] "Cacng2"  "Cplx1"   "Eif4g3"  "Grin2c"  "Aak1"    "Cyfip2"  "Cadps"  
## [57] "Gnb5"    "Dnm1l"   "Cpne4"   "Prkce"   "Gng3"    "Calb1"   "Cacng3" 
## [64] "Lrrc4b"  "Cbln4"   "Ppp2r1a" "Cplx3"   "Syngap1" "Atad1"   "Dmtn"   
## [71] "Cacng8"  "Rimbp2"  "Atp2b2"  "Shisa7"  "Gad2"    "Htr2a"   "Elmod1" 
## [78] "Snap25"  "Slc8a3"  "Gria3"   "Cadps2"  "Ywhaq"   "Syt12"   "Ctnnb1" 
## [85] "Tln2"

#saveRDS(genes_no_ribo, file = 'GO.Synaptic.based.15.04.rds')

# First list
Ribosomal <- c(
  "Eif1", "Rpl13a", "Eif3m", "Lars2", "Rpl5", "Rps15a", "Eif4g3",
  "Rpl10", "Farsb", "Rpl13", "Rpl9", "Rps17", "Rps3", "Rps5",
  "Rpl36", "Rpl28", "Mrpl32", "Rps29", "Rplp0", "Rpl30",
  "Lrpprc", "Samd4b", "Rps25", "Ppp1ca", "Msi2"
)

# Second list (provided inline)
additional_genes <- c(
  "Rpl13", "Rpl9", "Rps17", "Eif1", "Rps3", "Rpl13a", "Rps5",
  "Rpl36", "Eif3m", "Rpl28", "Lars2", "Rpl5", "Rps15a", "Eif4g3",
  "Mrpl32", "Rpl10", "Rps29", "Farsb"
)

# Combine and remove duplicates
combined_unique_genes <- unique(c(Ribosomal, additional_genes))

# View result
print(combined_unique_genes)

##  [1] "Eif1"   "Rpl13a" "Eif3m"  "Lars2"  "Rpl5"   "Rps15a" "Eif4g3" "Rpl10" 
##  [9] "Farsb"  "Rpl13"  "Rpl9"   "Rps17"  "Rps3"   "Rps5"   "Rpl36"  "Rpl28" 
## [17] "Mrpl32" "Rps29"  "Rplp0"  "Rpl30"  "Lrpprc" "Samd4b" "Rps25"  "Ppp1ca"
## [25] "Msi2"

#saveRDS(combined_unique_genes, file = 'GO.Ribosomal.15.04.rds')

GO.Pro.resilience

Upasna Srivastava

2025-04-14