diff --git a/StressGraphletSignificance.R b/StressGraphletSignificance.R index a81eb21..9bdf10e 100644 --- a/StressGraphletSignificance.R +++ b/StressGraphletSignificance.R @@ -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) \ No newline at end of file +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") diff --git a/data/oxidative_stress/txid224308-protein_protein_interaction.csv b/data/oxidative_stress/txid224308-protein_protein_interaction.csv new file mode 100644 index 0000000..81b8dda --- /dev/null +++ b/data/oxidative_stress/txid224308-protein_protein_interaction.csv @@ -0,0 +1,6442 @@ +"id1","id2","name1","name2","geneName1","geneName2","altName1","altName2","source","sourceLink","intType","species" +"BSU_00010","BSU_00330","DnaA","DnaH","dnaA","BSU_00330","DnaA","YabA","subtiwiki","224308.BSU00010/224308.BSU00330","physical","txid224308" 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