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Add new overrepresentation analysis #23

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53 changes: 52 additions & 1 deletion StressGraphletSignificance.R
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Original file line number Diff line number Diff line change
Expand Up @@ -212,4 +212,55 @@ txid224308_onetail <- inner_join(txid224308_onetail, graphlet_key)
txid6239_onetail <- inner_join(txid6239_onetail, graphlet_key)
txid559292_onetail <- inner_join(txid559292_onetail, graphlet_key)
txid7227_onetail <- inner_join(txid7227_onetail, graphlet_key)
txid7955_onetail <- inner_join(txid7955_onetail, graphlet_key)
txid7955_onetail <- inner_join(txid7955_onetail, graphlet_key)

# Joining in common names to B. subtilis and D. rerio
## B. subtilis
ppi_224308 <- read_csv("txid224308-protein_protein_interaction.csv")
reg_224308 <- read_csv("txid224308-regulatory_interaction.csv")
stress_ppi_224308 <- read_csv("txid224308/stress_ppi.csv")
stress_reg_224308 <- read_csv("txid224308/stress_reg.csv")

stress_net_224308_ppi <- rbind(
inner_join(stress_ppi_224308, ppi_224308, by = c("id1", "id2")) %>% select(id1, id2, name1, name2),
inner_join(stress_ppi_224308, ppi_224308, by = c("id1", "id2")) %>% rename(id2 = id1, id1 = id2, name2 = name1, name1 = name2) %>% select(id1, id2, name1, name2)
)

stress_net_224308_ppi <- stress_net_224308_ppi %>%
mutate(geneName1 = str_c(str_to_lower(str_sub(name1, 1, 1)), str_sub(name1, 2))) %>%
mutate(geneName2 = str_c(str_to_lower(str_sub(name2, 1, 1)), str_sub(name2, 2))) %>%
select(id1, id2, geneName1, geneName2)

stress_net_224308_reg <- inner_join(stress_reg_224308, reg_224308, by = c("id1", "id2")) %>% select(id1, id2, geneName1, geneName2)

## D. rerio
stress_ppi_7955 <- read_csv("txid7955/stress_ppi.csv")
stress_reg_7955 <- read_csv("txid7955/stress_reg.csv")
ppi_7955 <- read_csv("txid7955-protein_protein_interaction.csv")
reg_7955 <- read_csv("txid7955-regulatory_interaction.csv")

stress_net_7955_ppi <- rbind(
inner_join(stress_ppi_7955, ppi_7955, by = c("id1", "id2")) %>% select(id1, geneName1, id2, geneName2),
inner_join(stress_ppi_7955, ppi_7955, by = c("id1", "id2")) %>% rename(id2 = id1, id1 = id2, geneName2 = geneName1, geneName1 = geneName2) %>% select(id1, id2, geneName1, geneName2)
)
# get missing common
stress_net_7955_ppi %>%
filter(str_starts(geneName1, "Q") | str_starts(geneName2, "Q"))
# replace missing names
stress_net_7955_ppi <- stress_net_7955_ppi %>%
mutate(geneName1 = replace(geneName1, geneName1 == 'Q7T3D1', 'ero1a')) %>%
mutate(geneName2 = replace(geneName2, geneName2 == 'Q7T3D1', 'ero1a')) %>%
mutate(geneName1 = replace(geneName1, geneName1 == 'Q7ZV14', 'gpx8')) %>%
mutate(geneName2 = replace(geneName2, geneName2 == 'Q7ZV14', 'gpx8')) %>%
select(id1, id2, geneName1, geneName2)


stress_net_7955_reg <- inner_join(stress_reg_7955, reg_7955, by = c("id1", "id2")) %>% select(id1, id2, geneName1, geneName2)
# add in the single missing geneName
stress_net_7955_reg <- stress_net_7955_reg %>%
mutate(geneName2 = replace(geneName2, geneName2 == '-', 'zgc:103499'))

write_csv(stress_net_7955_reg, "txid7955/stress_reg_names.csv")
write_csv(stress_net_7955_ppi, "txid7955/stress_ppi_names.csv")
write_csv(stress_net_224308_reg, "txid224308/stress_reg_names.csv")
write_csv(stress_net_224308_ppi, "txid224308/stress_ppi_names.csv")
6,442 changes: 6,442 additions & 0 deletions data/oxidative_stress/txid224308-protein_protein_interaction.csv
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5,635 changes: 5,635 additions & 0 deletions data/oxidative_stress/txid224308-regulatory_interaction.csv
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286 changes: 140 additions & 146 deletions data/oxidative_stress/txid224308/nx.html
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35 changes: 35 additions & 0 deletions data/oxidative_stress/txid224308/stress_ppi_names.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
id1,id2,geneName1,geneName2
BSU_13180,BSU_29740,metE,ccpA
BSU_13180,BSU_21860,metE,brxA
BSU_13180,BSU_23990,metE,brxB
BSU_29740,BSU_40100,ccpA,ahpF
BSU_29740,BSU_40090,ccpA,ahpC
BSU_29470,BSU_29740,ackA,ccpA
BSU_12420,BSU_29740,yjoB,ccpA
BSU_12420,BSU_21860,yjoB,brxA
BSU_40090,BSU_40100,ahpC,ahpF
BSU_11500,BSU_25200,spxA,sigA
BSU_08720,BSU_29470,ygaF,ackA
BSU_08820,BSU_12420,katA,yjoB
BSU_08820,BSU_39050,katA,katE
BSU_08820,BSU_38630,katA,katX
BSU_38630,BSU_39050,katX,katE
BSU_13150,BSU_21860,ohrR,brxA
BSU_13150,BSU_23990,ohrR,brxB
BSU_29740,BSU_13180,ccpA,metE
BSU_21860,BSU_13180,brxA,metE
BSU_23990,BSU_13180,brxB,metE
BSU_40100,BSU_29740,ahpF,ccpA
BSU_40090,BSU_29740,ahpC,ccpA
BSU_29740,BSU_29470,ccpA,ackA
BSU_29740,BSU_12420,ccpA,yjoB
BSU_21860,BSU_12420,brxA,yjoB
BSU_40100,BSU_40090,ahpF,ahpC
BSU_25200,BSU_11500,sigA,spxA
BSU_29470,BSU_08720,ackA,ygaF
BSU_12420,BSU_08820,yjoB,katA
BSU_39050,BSU_08820,katE,katA
BSU_38630,BSU_08820,katX,katA
BSU_39050,BSU_38630,katE,katX
BSU_21860,BSU_13150,brxA,ohrR
BSU_23990,BSU_13150,brxB,ohrR
40 changes: 40 additions & 0 deletions data/oxidative_stress/txid224308/stress_reg_names.csv
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@@ -0,0 +1,40 @@
id1,id2,geneName1,geneName2
BSU_04730,BSU_38630,sigB,katX
BSU_04730,BSU_29760,sigB,brxC
BSU_04730,BSU_11500,sigB,spx
BSU_04730,BSU_39050,sigB,katE
BSU_04730,BSU_04730,sigB,sigB
BSU_29740,BSU_29470,ccpA,ackA
BSU_29740,BSU_04730,ccpA,sigB
BSU_25760,BSU_17970,sigK,cotM
BSU_25760,BSU_28410,sigK,gerE
BSU_25760,BSU_25760,sigK,sigK
BSU_00370,BSU_14220,abrB,ahpA
BSU_00370,BSU_15320,abrB,sigE
BSU_00370,BSU_00370,abrB,abrB
BSU_15320,BSU_17970,sigE,cotM
BSU_15320,BSU_25760,sigE,sigK
BSU_11500,BSU_21680,spx,msrB
BSU_11500,BSU_21690,spx,msrA
BSU_25200,BSU_11500,sigA,spx
BSU_25200,BSU_08730,sigA,perR
BSU_25200,BSU_40100,sigA,ahpF
BSU_25200,BSU_40090,sigA,ahpC
BSU_25200,BSU_29740,sigA,ccpA
BSU_25200,BSU_13150,sigA,ohrR
BSU_25200,BSU_13140,sigA,ohrA
BSU_25200,BSU_00370,sigA,abrB
BSU_25200,BSU_29470,sigA,ackA
BSU_25200,BSU_15320,sigA,sigE
BSU_25200,BSU_04730,sigA,sigB
BSU_25200,BSU_21680,sigA,msrB
BSU_25200,BSU_21690,sigA,msrA
BSU_25200,BSU_25200,sigA,sigA
BSU_28410,BSU_25760,gerE,sigK
BSU_28410,BSU_17970,gerE,cotM
BSU_13150,BSU_13140,ohrR,ohrA
BSU_08730,BSU_11500,perR,spx
BSU_08730,BSU_08820,perR,katA
BSU_08730,BSU_40090,perR,ahpC
BSU_08730,BSU_40100,perR,ahpF
BSU_08730,BSU_08730,perR,perR
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