RNAseq of L.major/amazonensis: Look for common mouse/human up/down genes.
atb abelew@gmail.com
2016-10-03
1 Using previous DE analyses, look for what is in common
I want to look for common parasite genes in the set of up/down comparisons between metacylic and amastigote 4 hour samples.
tt <- sm(loadme(filename="xrefs.rda.xz"))
lmajor_hsapiens <- read.csv(file="csv/lmajor_metac_vs_amast4.csv")
lmajor_mmusculus <- read.csv(file="csv/lmajor_metac_vs_amast4_mmusculus.csv")
lmajor_hsapiens_sig <- get_sig_genes(table=lmajor_hsapiens, p=0.05, fc=0.6)## Assuming the fold changes are on the log scale and so taking >< 0## After (adj)p filter, the up genes table has 1732 genes.## After (adj)p filter, the down genes table has 1492 genes.## Assuming the fold changes are on the log scale and so taking -1.0 * fc## After fold change filter, the up genes table has 556 genes.## After fold change filter, the down genes table has 736 genes.lmajor_mmusculus_sig <- get_sig_genes(table=lmajor_mmusculus, p=0.05, fc=0.6)## Assuming the fold changes are on the log scale and so taking >< 0## After (adj)p filter, the up genes table has 1460 genes.## After (adj)p filter, the down genes table has 1502 genes.## Assuming the fold changes are on the log scale and so taking -1.0 * fc## After fold change filter, the up genes table has 517 genes.## After fold change filter, the down genes table has 787 genes.lm_hs_up <- lmajor_hsapiens_sig[["up_genes"]][, c("X", "logFC")]
lm_mm_up <- lmajor_mmusculus_sig[["up_genes"]][, c("X", "logFC")]
lm_hs_down <- lmajor_hsapiens_sig[["down_genes"]][, c("X", "logFC")]
lm_mm_down <- lmajor_mmusculus_sig[["down_genes"]][, c("X", "logFC")]
hsmm_up <- merge(lm_hs_up, lm_mm_up, by="X", all=TRUE)
hsmm_down <- merge(lm_hs_down, lm_mm_down, by="X", all=TRUE)
tt <- sm(require.auto("hs229/Vennerable"))
library(Vennerable)
up_ones <- c("hs" = sum(!is.na(hsmm_up[[2]]) & is.na(hsmm_up[[3]])),
"mm" = sum(is.na(hsmm_up[[2]]) & !is.na(hsmm_up[[3]])))
up_twos <- c("hs&mm" = sum(!is.na(hsmm_up[[2]]) & !is.na(hsmm_up[[3]])))
up_twos_table <- hsmm_up[ !is.na(hsmm_up[[2]]) & !is.na(hsmm_up[[3]]), ]
hs_mm_up_venn <- plot_fun_venn(ones=up_ones, twos=up_twos)
up_twos_table$X <- gsub(pattern="\\-[0-9]", replace="", x=up_twos_table$X)
down_ones <- c("hs" = sum(!is.na(hsmm_down[[2]]) & is.na(hsmm_down[[3]])),
"mm" = sum(is.na(hsmm_down[[2]]) & !is.na(hsmm_down[[3]])))
down_twos <- c("hs&mm" = sum(!is.na(hsmm_down[[2]]) & !is.na(hsmm_down[[3]])))
down_twos_table <- hsmm_down[ !is.na(hsmm_down[[2]]) & !is.na(hsmm_down[[3]]), ]
hs_mm_down_venn <- plot_fun_venn(ones=down_ones, twos=down_twos)
down_twos_table$X <- gsub(pattern="\\-[0-9]", replace="", x=down_twos_table$X)
## Get the big table from the previous cross referencing
big_table <- tri_sci_sig_fas_sec
big_shared_hs_mm_up <- merge(up_twos_table, big_table, by.x="X", by.y="ID", all.x=TRUE)
big_shared_hs_mm_down <- merge(down_twos_table, big_table, by.x="X", by.y="ID", all.x=TRUE)
write.csv(file="csv/big_shared_hs_mm_up.csv", x=big_shared_hs_mm_up)
up_lmonly_idx <- is.na(big_shared_hs_mm_up$tritryp_brucei_homologs) & is.na(big_shared_hs_mm_up$tritryp_cruzi_homologs)
up_lmonly <- big_shared_hs_mm_up[up_lmonly_idx, ]
write.csv(file="csv/big_shared_hsmm_up_lmonly.csv", x=up_lmonly)
up_lmtc_idx <- is.na(big_shared_hs_mm_up$tritryp_brucei_homologs) & !is.na(big_shared_hs_mm_up$tritryp_cruzi_homologs)
up_lmtc <- big_shared_hs_mm_up[up_lmtc_idx, ]
write.csv(file="csv/big_shared_hsmm_up_lmtc.csv", x=up_lmtc)
up_lmtb_idx <- !is.na(big_shared_hs_mm_up$tritryp_brucei_homologs) & is.na(big_shared_hs_mm_up$tritryp_cruzi_homologs)
up_lmtb <- big_shared_hs_mm_up[up_lmtb_idx, ]
write.csv(file="csv/big_shared_hsmm_up_lmtb.csv", x=up_lmtb)
up_lmtbtc_idx <- !is.na(big_shared_hs_mm_up$tritryp_brucei_homologs) & !is.na(big_shared_hs_mm_up$tritryp_cruzi_homologs)
up_lmtbtc <- big_shared_hs_mm_up[up_lmtbtc_idx, ]
write.csv(file="csv/big_shared_hsmm_up_lmtbtc.csv", x=up_lmtbtc)
write.csv(file="csv/big_shared_hs_mm_down.csv", x=big_shared_hs_mm_down)
down_lmonly_idx <- is.na(big_shared_hs_mm_down$tritryp_brucei_homologs) & is.na(big_shared_hs_mm_down$tritryp_cruzi_homologs)
down_lmonly <- big_shared_hs_mm_down[down_lmonly_idx, ]
write.csv(file="csv/big_shared_hsmm_down_lmonly.csv", x=down_lmonly)
down_lmtc_idx <- is.na(big_shared_hs_mm_down$tritryp_brucei_homologs) & !is.na(big_shared_hs_mm_down$tritryp_cruzi_homologs)
down_lmtc <- big_shared_hs_mm_down[down_lmtc_idx, ]
write.csv(file="csv/big_shared_hsmm_down_lmtc.csv", x=down_lmtc)
down_lmtb_idx <- !is.na(big_shared_hs_mm_down$tritryp_brucei_homologs) & is.na(big_shared_hs_mm_down$tritryp_cruzi_homologs)
down_lmtb <- big_shared_hs_mm_down[down_lmtb_idx, ]
write.csv(file="csv/big_shared_hsmm_down_lmtb.csv", x=down_lmtb)
down_lmtbtc_idx <- !is.na(big_shared_hs_mm_down$tritryp_brucei_homologs) & !is.na(big_shared_hs_mm_down$tritryp_cruzi_homologs)
down_lmtbtc <- big_shared_hs_mm_down[down_lmtbtc_idx, ]
write.csv(file="csv/big_shared_hsmm_down_lmtbtc.csv", x=down_lmtbtc)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