From 3ee3ea62ee9fb56044bc91799fb038b17159ed78 Mon Sep 17 00:00:00 2001 From: raynamharris Date: Sun, 9 Feb 2020 10:45:46 -0800 Subject: [PATCH] script to make suppl tables, new fig 7 --- .../GeneLists/indicators/indicatorsgenes.csv | 1652 +++++++++++++++++ .../GeneLists/uniq_lists/uniqgenes.csv | 19 + ASE_analysis/genelists.R | 121 ++ 3 files changed, 1792 insertions(+) create mode 100644 ASE_analysis/GeneLists/indicators/indicatorsgenes.csv create mode 100644 ASE_analysis/GeneLists/uniq_lists/uniqgenes.csv create mode 100644 ASE_analysis/genelists.R diff --git a/ASE_analysis/GeneLists/indicators/indicatorsgenes.csv b/ASE_analysis/GeneLists/indicators/indicatorsgenes.csv new file mode 100644 index 0000000..d83c44e --- /dev/null +++ b/ASE_analysis/GeneLists/indicators/indicatorsgenes.csv @@ -0,0 +1,1652 @@ +group,geneid +bldg_time,102085159 +bldg_time,102092819 +female_sex,101911765 +female_sex,102083460 +female_sex,102083485 +female_sex,102083489 +female_sex,102083691 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+pit_tissue,102093951 +pit_tissue,102093964 +pit_tissue,102094177 +pit_tissue,102094196 +pit_tissue,102094225 +pit_tissue,102094231 +pit_tissue,102094488 +pit_tissue,102094607 +pit_tissue,102094668 +pit_tissue,102094854 +pit_tissue,102094878 +pit_tissue,102094902 +pit_tissue,102095053 +pit_tissue,102095073 +pit_tissue,102095098 +pit_tissue,102095221 +pit_tissue,102095224 +pit_tissue,102095314 +pit_tissue,102095367 +pit_tissue,102095388 +pit_tissue,102095512 +pit_tissue,102095564 +pit_tissue,102095717 +pit_tissue,102095790 +pit_tissue,102095808 +pit_tissue,102095818 +pit_tissue,102095857 +pit_tissue,102096050 +pit_tissue,102096087 +pit_tissue,102096219 +pit_tissue,102096227 +pit_tissue,102096289 +pit_tissue,102096293 +pit_tissue,102096435 +pit_tissue,102096500 +pit_tissue,102096550 +pit_tissue,102096692 +pit_tissue,102096788 +pit_tissue,102096933 +pit_tissue,102096957 +pit_tissue,102096988 +pit_tissue,102097207 +pit_tissue,102097233 +pit_tissue,102097269 +pit_tissue,102097327 +pit_tissue,102097365 +pit_tissue,102097408 +pit_tissue,102097499 +pit_tissue,102097615 +pit_tissue,102097683 +pit_tissue,102097709 +pit_tissue,102097778 +pit_tissue,102097780 +pit_tissue,102097833 +pit_tissue,102097852 +pit_tissue,102097958 +pit_tissue,102097997 +pit_tissue,102098089 +pit_tissue,102098160 +pit_tissue,102098215 +pit_tissue,102098243 +pit_tissue,102098247 +pit_tissue,102098287 +pit_tissue,102098310 +pit_tissue,102098364 +pit_tissue,102098378 +pit_tissue,102098645 +pit_tissue,102098700 +pit_tissue,102098781 +pit_tissue,102098819 +pit_tissue,102099014 +pit_tissue,102099021 +pit_tissue,103620141 +pit_tissue,103895691 +pit_tissue,103902009 +pit_tissue,104077518 +pit_tissue,104295350 +pit_tissue,104840137 +pit_tissue,105401351 +pit_tissue,105408443 +pit_tissue,105409193 +pit_tissue,105412779 +pit_tissue,106886033 +pit_tissue,106891296 +pit_tissue,106891544 +pit_tissue,108505458 +pit_tissue,110355073 +pit_tissue,110355826 +pit_tissue,110357056 +pit_tissue,110362376 diff --git a/ASE_analysis/GeneLists/uniq_lists/uniqgenes.csv b/ASE_analysis/GeneLists/uniq_lists/uniqgenes.csv new file mode 100644 index 0000000..5793a14 --- /dev/null +++ b/ASE_analysis/GeneLists/uniq_lists/uniqgenes.csv @@ -0,0 +1,19 @@ +sex,stage,hypothalamus,pituitary,gonad +female,control,NA,NA,LOC102088141 ZNF593 TPH1 SFR1 LOC102095212 ACSS3 MCM2 ITGA11 IRF8 SLC16A1 LOC102090529 UBXN2A Tmem207 IL21R LOC102098758 LOC102096501 PCIF1 LRRC57 TPI1 EYS ZNF131 BFSP2 KBTBD12 ACSL5 FAM65C KCNG4 ccnjl +female,bldg,CREB5 LAPTM5,UNC45A MECR PRDX1 LOC102088968 SEPT9,IL13RA2 LOC106891379 +female,lay,DNAJB5 FHL2 ZSWIM6 CACNG3 SPG21 CUTA POU3F2 GAL3ST1 LOC102089183 PPARGC1B LCOR LOC102093436 SLC1A2 IFFO2 KCNH6 LOC102084653 ONECUT1 HMGXB3 LOC102095914 FAM131A RRAS2 NDNF RBM19 KCNQ3 DUSP6 RHBDD1 GLI2 LOC108449003 FRMPD4 TLN1 RFX4,PUS3 NFE2L2 YIPF5 MCM6 SUMO2 HNRNPDL ACAD11 ECHDC3 EGR1 LXN CTC1 XPNPEP1 HMGCLL1 PTER UNC13C MRPL19 RAB29 HEATR6 TCP1 PRPS2 JAKMIP2 PDLIM7 PSMC6 NPHP4 EIF4ENIF1 LTA4H UNK LOC102097594 GSTK1 SMG6 SMS ST3GAL2 LOC102086622 LOC102097155 MRPS23 RFX2 LOC102093755 LOC106145850 KDM3A FZD2 NDFIP1 CDH9 mtg2 PALB2 IRF7 PDZRN4 FGF5 DIS3L2 PHF5A FAM161A TENM3 PITX3 XPO6 IL12RB2 DHRS7B ZNF346 PSMD7 ATOX1 ATP5C1 LOC102098778 LOC104025898 PLAG1 MAP3K4 HM13 BAHCC1 SLC30A1 MRPL37 TRMT11 BMP5 CAMKK2 ATP10D SH3YL1 ANKDD1A GRAMD1C ITGBL1 TMEM132D EAF1 SEC23B PDE7A MFSD13A TSPAN3,SPP1 POLR1A slc12a8 RASGEF1B TMPRSS13 MAP1LC3C TDO2 ZFAND4 OVOL2 SLC5A9 NID2 FPGT CLUAP1 SLMAP GIF FRMD4B NIPAL1 LOC106900125 SALL4 LGALS3 TICRR DZIP1L LOC102096613 MED26 SUCNR1 RNF34 MB21D1 ARHGEF17 NUDT5 LOC102086208 LOC102084031 FZD7 LOC102093413 LOC102098019 GPR157 LOC102087329 mansc1 LOC102087423 PCBP3 CD82 OTX1 LOC102098914 F13A1 RGS3 OSR1 LOC102093322 DHRS7 TSPAN1 SDK1 OPRL1 TCN2 CAPN9 LAMA4 SLC26A2 PTPN23 GALNT12 WT1 SAMD4A ADGRL4 OLFM4 ZC3H12A MPZL2 adamts1 TTI2 LOC102083464 MSC ERBB2 LOC102094835 FILIP1 DNAH9 THBS2 VWA1 FOXK1 MYL9 SNX8 GLIPR1 CDC73 ANO1 SCNN1B MAMDC2 LOC102092463 STK17B ITGB6 RMDN2 MYOF MYLIP TNIP2 LOC102093782 CENPF TNC TC2N cracr2b SLC9A1 AARS2 HOXB4 NSUN4 ANXA8L1 LOC102098107 LOC102086499 Rnf223 METTL4 +female,inc-d3,ENOPH1 LRCH3 PHF14 ACOX1 NT5C1A EPN3 PRKCB TMEM206 RNMT KIAA1024 RB1CC1 LOC102084181 SUSD4 ACOX3 VWA5B1 PLCL1 GRID1 SYN2 SEMA4B CPNE7 LOC102089629 TCF7L2 CSRNP3 DLX5 COPS2 LOC102089053 LOC106145742,BRD7 QARS ALDH1A2 SOX18 CAPS2 PBX3 LOC102096126 FARP2 ST5 OAF MTRF1L,SLC35C1 LOC102083717 CCSER1 SULF1 +female,inc-d9,NA,NA,LOC102094268 TSPO COG3 FLOT2 SBSPON LOC102087515 NDUFA4 +female,inc-d17,p2ry1 ZBTB41 KCNJ6 COPS5 NUDT14 PRPF6,MED22,LOC102094759 AURKA GEM BBS2 +female,hatch,JPH3 GLB1L2 SNCG SORD rubcn ASPHD2 NPY RNF157 GRAMD4,USP35 SCG3,PAPD7 STK10 KCNK17 CAPN14 RASL11A TMEM100 +female,n5,EPS15L1 KATNAL1 SLC25A25 GUF1 SEC14L5 PTPRG PDGFA ABHD10 NMBR REEP2 LOC102097375 TADA3 DBI CPNE8 EXOC4,LOC102086694 LOC102085362 AGR2 PTGR2 MTHFD1 COL20A1 ADAL ARF4,HNF1B LOC102094992 PLK3 IL15 LEF1 CENPI DTL BMP2 TOR4A ACAA2 LOC102092620 +female,n9,PDE9A PRDM12 LASP1,PHF21B,SESN2 SMTNL2 DIABLO +male,control,NA,NA,ARMC4 TFPI +male,bldg,YWHAQ DDX58 C1QL3 wasf1 TMEM62,filip1l KBTBD4 PTPMT1 TMEM38B PHACTR4 ELP3 OSGIN1 LOC108506594 PANK2 LOC102085860 DHX32,tmem120a CFAP65 ABCB11 PGM2 CPSF3 +male,lay,ASAP3 plxna1 lrp6 HMGCR TXNL4A,HAUS2 TMPRSS2 MED17 MAN2A1 FAM189A1 CHRNA1 PACS1 CEP131 DYRK3 ZNF608 CTSS BRD1 EHMT1 TXNDC12 PINK1 RNF24 ZCCHC6 ATP5O BAP1 RBM34 DYRK1A LOC102083498 JAK2 WASL PBDC1 KDM3B ANXA6 ST7L TIMM21 KNTC1 USP28 ZNF385C KIAA1328 HRH1 SLC39A11 LOC102087856 PTPN13 FREM1 SMARCA2 RABEPK MAP3K2 GLIS3 VPS37C FGF16 COL4A3 NADSYN1 LOC102086007 ANKMY2 ARNTL PJA2 plpp6 CTBP1 LOC102086205 TSEN54 VAV3 GTPBP10 LOC102096682 PATZ1 PAIP2 TMEM87A STK39 MTCP1 SREBF2 E2F3 FGFR1 MBD4 LOC102084049 FRMD4A GTF3C5 MUC13 TRA2B DCXR PNPLA4 BTBD10 ANXA7 LOC102086952 LOC102084665 SLC12A5 RNF144B PAPD4,RRP15 mia2 LOC102086172 CENPL DIMT1 TMEM17 KIF24 LOC102084670 CCDC60 PPP2R3C CCDC73 ZPBP TRIM66 SMIM8 FOXRED2 LOC102087304 ACTL7A Mdn1 EMC8 VPS13D MYO1H LOC102095575 FBXO38 AGBL3 LOC102094086 MFGE8 TXNDC5 LOC102085755 DENND2C ACKR2 PIDD1 SPATA16 SLC19A1 AXDND1 LOC106145879 LOC105407116 MTTP CFAP161 ESYT3 TMPPE WDR63 NEURL2 ADCK1 CCDC39 ANGEL2 PSMA1 ANKRD31 sfmbt1 SPATA5 PHF2 ANAPC7 IFIH1 FABP6 SPATA5L1 PAK2 TOPAZ1 TRPM1 DCUN1D3 +male,inc-d3,KLHDC4 PEX12 ZNF318 ANGPTL1 ADGRB3 FAM105A PDCL FAT1 SNUPN POLE2 FGD6 RNPEPL1 RNF146 calb1 GABRB1 MGAT4A CSPG5 mto1 DAPK1 VAX1,NIT2 DOCK11 TMEM200A GNPAT,CENPH PDCL2 FBXO6 BOC +male,inc-d9,SMAP2 PRKAR2B WDR59 SLC5A3 NDFIP2 st6gal1 HSDL2,SMIM14 RAB39A,SLC25A48 SLCO4C1 CEP55 KIF18B ATAD3A +male,inc-d17,LOC102097452 FAM185A ADGRL3 TBC1D2 MIGA1,CWC27,INTS12 TSHZ1 EEF2KMT +male,hatch,HMGB3 CDC42EP4 PTPN9 TWF2 STAM SNX30 TMEM104 RHBDL3 LGI1 SDPR PCYOX1 DRP2 LMBRD2 NUP58 adgra3 NPR3 PTCHD1 HAPLN4 PLGRKT EFCAB2 NXPH1 ATPAF2 ZCCHC9 TRMT44 ABLIM1 LPL RSBN1L PMP22 ALCAM FAM78A NDUFAF5 GAREM1,FRZB REEP5 STAT4 VEPH1,PLK4 PPP1R9B prok2 STK31 BANP +male,n5,LOC102084357 SRGAP2 AGTPBP1 NCAN DNAJC11 PRNP CADPS2 GNPDA1 TRAF3 B3GALT6 HSD17B12 PRKCH GAB3 LOC102090224 POLR3D,FGF13 ELL2 DUSP10 UMODL1 ZDHHC21 ADRM1 SRPRB ZNF335 DNAJC21 STRADA,WBSCR27 SMARCAL1 CDCA4 LOC102098475 NUSAP1 KIAA2026 CEP112 LOC102097215 +male,n9,SH3GL2,AP5M1,RHOF ZW10 LOC102089167 NUBPL DNAH7 DBNDD2 SLX4 CCDC77 MEIG1 PHF20 TFAP2A SNAPC3 KIAA0196 diff --git a/ASE_analysis/genelists.R b/ASE_analysis/genelists.R new file mode 100644 index 0000000..933a556 --- /dev/null +++ b/ASE_analysis/genelists.R @@ -0,0 +1,121 @@ +# from many files to two. indicator and unique genes +library(tidyverse) +library(cowplot) + +# formatting and color +stagelevels <- c("control", "bldg", "lay", "inc-d3", "inc-d9", "inc-d17", + "hatch", "n5", "n9") + +stagelevelsnohiphen <- c("control", "bldg", "lay", + "incd3", "incd9", "incd17", + "hatch", "n5", "n9") + +tissuelevels <- c("hyp", "pit", "gon") +sexlevels <- c("female", "male") + + +colorsstage <- c("control" = "#cc4c02", "bldg"= "#fe9929", "lay"= "#fed98e", + "incd3"= "#78c679", "incd9"= "#31a354", "incd17"= "#006837", + "hatch"= "#08519c","n5"= "#3182bd", "n9"= "#6baed6") + +colorstissue <- c("hyp" = "#d95f02", + "pit" = "#1b9e77", + "gon" = "#7570b3") + +colorssex <- c("female" = "#969696", "male" = "#525252") + +colorsall <- c(colorstissue, colorssex, colorsstage) + + +## indicator genes + +data_path <- "./GeneLists/indicators/" # path to the data +files <- dir(data_path, pattern = "*.txt") # get file names +filesdf <- as.data.frame(files) + +indicatorsgenes <- files %>% + set_names() %>% + map_df(~ read.table(file.path(data_path, .), sep = "\t", + row.names = NULL, fill=TRUE), .id = "source") %>% + mutate_at(.vars = "source", .funs = gsub, + pattern = ".txt", replacement = "") %>% + dplyr::rename("group" = "source", "geneid" = "V1") %>% + dplyr::filter(!geneid %in% group) %>% + mutate_at(.vars = "group", .funs = gsub, + pattern = "_df", replacement = "") +head(indicatorsgenes) + +# this nex summary confirms data fromfigure 7 +indsum <- indicatorsgenes %>% group_by(group) %>% + summarize(ASEcount = n()) %>% arrange(desc(ASEcount)) %>% + dplyr::mutate(level = sapply(strsplit(as.character(group),'\\_'), "[", 2), + group = sapply(strsplit(as.character(group),'\\_'), "[", 1)) + + +indsum$group <- factor(indsum$group, + levels = c( + sexlevels, tissuelevels, + stagelevelsnohiphen) +) + + + +themeASEcount <- function () { + theme_classic(base_size = 10) + + theme( + panel.grid.major = element_blank(), + panel.grid.minor = element_blank(), + legend.position = "none") +} + +a <- indsum %>% + filter(level != "time") %>% + ggplot(aes(x = group, y = ASEcount, + fill = group, label = ASEcount)) + + geom_bar(stat = "identity") + + geom_text(vjust = -0.5, size = 3) + + themeASEcount() + + scale_fill_manual(values = colorsall) + + labs(x = "Sex, Tissue", y = "Allele-Specific Expression Gene Count") + +b <- indsum %>% + filter(level == "time") %>% + ggplot(aes(x = group, y = ASEcount, + fill = group, label = ASEcount)) + + geom_bar(stat = "identity") + + geom_text(vjust = -0.5, size = 3) + + themeASEcount() + + scale_fill_manual(values = colorsall) + + labs(x = "Parental Stage", y = NULL) + +plot_grid(a,b, rel_widths = c(0.45, 0.55)) + +## unique genes + +data_path <- "./GeneLists/uniq_lists/" # path to the data +files <- dir(data_path, pattern = "*.txt") # get file names +filesdf <- as.data.frame(files) + +uniqgenes <- files %>% + set_names() %>% + map_df(~ read_delim(file.path(data_path, .), delim = "\t"), .id = "source") %>% + mutate_at(.vars = "source", .funs = gsub, + pattern = "_uniq.txt", replacement = "") %>% + dplyr::select(source, To) %>% + dplyr::rename("comparison" = "source", "gene" = "To") %>% + group_by(comparison) %>% + summarize(genes = str_c(gene, collapse = " ")) %>% + dplyr::mutate(sex = sapply(strsplit(comparison,'\\_'), "[", 1), + tissue = sapply(strsplit(comparison,'\\_'), "[", 2), + stage = sapply(strsplit(comparison,'\\_'), "[", 3)) %>% + select(sex, tissue, stage, genes) %>% + pivot_wider(names_from = tissue, values_from = genes) %>% + select(sex, stage, hypothalamus, pituitary, gonad) + +uniqgenes$stage <- factor(uniqgenes$stage, levels = stagelevels) + +uniqgenes <- uniqgenes %>% dplyr::arrange(sex, stage) +head(uniqgenes) + +write_csv(indicatorsgenes, "./GeneLists/indicators/indicatorsgenes.csv") +write_csv(uniqgenes, "./GeneLists/uniq_lists/uniqgenes.csv") \ No newline at end of file