1. GO富集分析
输入数据
使用 enrichGO {clusterProfiler} 函数得到
ONTOLOGY ID Term GeneRatio BgRatio pvalue p.adjust qvalue geneID Count BP GO:0032496 response to lipopolysaccharide 37/163 330/18670 1.5814603638303e-30 6.42863637897019e-27 3.03973328879383e-27 PTGS2/OPRM1/CASP9/JUN/CASP3/CASP8/PRKCA/MAOB/RELA/AKT1/FOS/MAPK1/IL10RA/NFKBIA/CYP1A2/GJA1/CYP1A1/ICAM1/IL1B/CCL2/SELE/VCAM1/CXCL8/NOS3/THBD/SERPINE1/MPO/GSTP1/CXCL11/CXCL2/PPARD/HSF1/CXCL10/CHUK/NOS2/MAPK8/SLPI 37 BP GO:0009410 response to xenobiotic stimulus 33/163 292/18670 2.45410686916945e-27 2.49398610579345e-24 1.17926293239563e-24 PTGS1/HSP90AB1/DPEP1/NR3C1/DRD1/OPRM1/CASP9/SLC6A3/PPARG/F7/RELA/EGFR/RB1/POR/SOD1/HSPA5/CYP3A4/CYP1A2/CYP1A1/ICAM1/NR1I2/CYP1B1/GSTP1/NQO1/AHR/CHEK2/HSF1/E2F1/GSTM1/GSTM2/HTR3A/DRD5/PPP3CA 33 BP GO:0070482 response to oxygen levels 35/163 394/18670 2.17944286618462e-25 1.42764451182279e-22 6.75051175914656e-23 PTGS2/SLC6A4/BCL2/CASP3/PLAU/PPARG/DPP4/F7/AKT1/VEGFA/CDKN1A/MMP2/TP53/RAF1/HIF1A/HMOX1/CAV1/MYC/CYP1A1/ICAM1/VCAM1/CCNB1/PLAT/COL1A1/NFE2L2/PSMD3/SLC2A4/PPARA/PPARD/HSF1/E2F1/NPEPPS/HK2/NOS2/OPRD1 35 BP GO:0000302 response to reactive oxygen species 29/163 232/18670 2.45842843364319e-25 1.42764451182279e-22 6.75051175914656e-23 DPEP1/BCL2/JUN/CASP3/MMP3/RELA/EGFR/AKT1/FOS/MMP2/MMP9/MAPK1/SOD1/STAT1/CDK1/HMOX1/NOS3/CYP1B1/COL1A1/MPO/NCF1/GSTP1/NFE2L2/NQO1/HSF1/CHUK/CDK2/MAPK8/AKR1C3 29 BP GO:0035690 cellular response to drug 34/163 369/18670 3.4482057729442e-25 1.55743960744646e-22 7.36423829403053e-23 PTGS2/HSP90AB1/DPEP1/NR3C1/KCNH2/DRD1/CHRM3/CHRM1/CHRM2/OPRM1/CASP9/NCOA1/MMP3/RELA/EGFR/MAPK1/TP53/SOD1/CDK1/HSPA5/HMOX1/MYC/ICAM1/IL1B/CYP1B1/NFE2L2/NQO1/AHR/CHEK2/HSF1/GSTM2/NOS2/CDK2/PPP3CA 34 BP GO:0006979 response to oxidative stress 36/163 451/18670 1.66747198700319e-24 6.77827362716795e-22 3.20505668238718e-22 PTGS1/PTGS2/DPEP1/BCL2/JUN/CASP3/MMP3/RELA/EGFR/AKT1/FOS/MMP2/MMP9/MAPK1/TP53/SOD1/HIF1A/STAT1/CDK1/HMOX1/DUOX2/NOS3/HSPB1/CYP1B1/COL1A1/MPO/NCF1/GSTP1/NFE2L2/NQO1/PARP1/HSF1/CHUK/CDK2/MAPK8/AKR1C3 36 BP GO:0048545 response to steroid hormone 33/163 385/18670 1.89346097619388e-23 6.99719897111647e-21 3.30857391629667e-21 ESR1/PTGS2/PGR/NR3C2/NR3C1/BCL2/CASP9/CASP3/RXRA/NCOA1/MAOB/AR/PPARG/RELA/EGFR/CCND1/FOS/CDKN1A/RB1/CAV1/ICAM1/NR1I2/COL1A1/GSTP1/PARP1/NR1I3/CLDN4/PPARA/PPARD/SPP1/CA2/ESR2/AKR1C3 33 BP GO:0034599 cellular response to oxidative stress 30/163 302/18670 3.24691868673181e-23 1.01528649704345e-20 4.80070730524072e-21 DPEP1/BCL2/JUN/MMP3/RELA/EGFR/AKT1/FOS/MMP2/MMP9/MAPK1/TP53/SOD1/HIF1A/CDK1/HMOX1/NOS3/HSPB1/CYP1B1/MPO/NCF1/GSTP1/NFE2L2/NQO1/PARP1/HSF1/CHUK/CDK2/MAPK8/AKR1C3 30 BP GO:0036293 response to decreased oxygen levels 32/163 370/18670 7.24580831527128e-23 2.1038722001127e-20 9.94800449901154e-21 PTGS2/SLC6A4/BCL2/CASP3/PLAU/DPP4/F7/AKT1/VEGFA/MMP2/TP53/RAF1/HIF1A/HMOX1/CAV1/MYC/CYP1A1/ICAM1/VCAM1/CCNB1/PLAT/NFE2L2/PSMD3/SLC2A4/PPARA/PPARD/HSF1/E2F1/NPEPPS/HK2/NOS2/OPRD1 32 BP GO:1901654 response to ketone 25/163 193/18670 2.57152525208506e-22 6.96883343315051e-20 3.29516148091742e-20 NR3C1/CASP9/NCOA1/AKR1B1/MAOB/AR/PPARG/F7/RELA/EGFR/AKT1/CCND1/BCL2L1/FOS/CDKN1A/ELK1/ACACA/CAV1/ICAM1/PARP1/AHR/CLDN4/HSF1/SPP1/AKR1C3 25 CC GO:0045121 membrane raft 21/163 315/19717 1.81311664017309e-13 3.15340889482025e-11 2.20276752028326e-11 PTGS2/ADRA1A/ADRA1B/SLC6A4/OPRM1/CASP3/CASP8/SLC6A3/DPP4/EGFR/MAPK1/HMOX1/CAV1/GJA1/ICAM1/SELE/NOS3/SLC2A4/CTSD/OPRD1/IKBKB 21 CC GO:0098857 membrane microdomain 21/163 316/19717 1.92869045554755e-13 3.15340889482025e-11 2.20276752028326e-11 PTGS2/ADRA1A/ADRA1B/SLC6A4/OPRM1/CASP3/CASP8/SLC6A3/DPP4/EGFR/MAPK1/HMOX1/CAV1/GJA1/ICAM1/SELE/NOS3/SLC2A4/CTSD/OPRD1/IKBKB 21 CC GO:0098589 membrane region 21/163 328/19717 3.97985873745076e-13 4.33804602382133e-11 3.03027840711163e-11 PTGS2/ADRA1A/ADRA1B/SLC6A4/OPRM1/CASP3/CASP8/SLC6A3/DPP4/EGFR/MAPK1/HMOX1/CAV1/GJA1/ICAM1/SELE/NOS3/SLC2A4/CTSD/OPRD1/IKBKB 21 CC GO:0099056 integral component of presynaptic membrane 10/163 73/19717 4.4851060198081e-10 2.09518524068178e-08 1.46356091172685e-08 DRD1/CHRM3/CHRM1/ADRA1A/CHRM2/SLC6A4/OPRM1/SLC6A3/HTR3A/OPRD1 10 CC GO:0090575 RNA polymerase II transcription factor complex 13/163 163/19717 1.00518364994313e-09 4.10868816914256e-08 2.87006384260079e-08 JUN/RXRA/PPARG/FOS/RB1/TP53/HIF1A/NR1I2/NR1I3/PPARA/PPARD/E2F1/E2F2 13 CC GO:0098889 intrinsic component of presynaptic membrane 10/163 82/19717 1.44898833016726e-09 5.26465759960769e-08 3.67754932919643e-08 DRD1/CHRM3/CHRM1/ADRA1A/CHRM2/SLC6A4/OPRM1/SLC6A3/HTR3A/OPRD1 10 CC GO:0099699 integral component of synaptic membrane 12/163 152/19717 5.08227019700573e-09 1.66190235442087e-07 1.16089750815815e-07 DRD1/CHRM3/CHRM1/ADRA1A/CHRM2/SLC6A4/OPRM1/GABRA1/SLC6A3/HTR3A/ADRA2C/OPRD1 12 CC GO:0099240 intrinsic component of synaptic membrane 12/163 164/19717 1.20106415365455e-08 3.50514545965721e-07 2.44846793737523e-07 DRD1/CHRM3/CHRM1/ADRA1A/CHRM2/SLC6A4/OPRM1/GABRA1/SLC6A3/HTR3A/ADRA2C/OPRD1 12 CC GO:0044798 nuclear transcription factor complex 13/163 201/19717 1.28629191180081e-08 3.50514545965721e-07 2.44846793737523e-07 JUN/RXRA/PPARG/FOS/RB1/TP53/HIF1A/NR1I2/NR1I3/PPARA/PPARD/E2F1/E2F2 13 CC GO:1902911 protein kinase complex 9/163 109/19717 3.04068484378838e-07 6.62869295945867e-06 4.6303762182602e-06 CCND1/CDKN1A/RB1/CDK1/CCNB1/INSRR/CHUK/CDK2/IKBKB 9 MF GO:0004879 nuclear receptor activity 12/163 47/17697 9.78928688129919e-15 2.35921813839311e-12 1.39110918839515e-12 ESR1/PGR/NR3C1/RXRA/AR/PPARG/NR1I2/AHR/NR1I3/PPARA/PPARD/ESR2 12 MF GO:0003707 steroid hormone receptor activity 12/163 56/17697 9.74209610940774e-14 1.56523010824484e-11 9.2293542089126e-12 ESR1/PGR/NR3C2/NR3C1/RXRA/AR/PPARG/NR1I2/NR1I3/PPARA/PPARD/ESR2 12 MF GO:1901338 catecholamine binding 7/163 20/17697 3.46353852211326e-10 4.17356391914648e-08 2.46093526571205e-08 DRD1/ADRB2/ADRA2A/SLC6A3/ADRB1/ADRA2C/DRD5 7 MF GO:0008227 G protein-coupled amine receptor activity 9/163 59/17697 3.23843538177788e-09 2.85377499970365e-07 1.68272384782701e-07 CHRM3/CHRM1/ADRA1A/CHRM2/ADRA1B/ADRB2/ADRA2A/ADRB1/ADRA2C 9 MF GO:0044389 ubiquitin-like protein ligase binding 17/163 308/17697 3.85992531368166e-09 2.85377499970365e-07 1.68272384782701e-07 HSP90AB1/KCNH2/BCL2/JUN/CASP8/RELA/EGFR/CDKN1A/RB1/TP53/NFKBIA/HIF1A/STAT1/HSPA5/CCNB1/CHEK2/ERBB3 17 MF GO:0004935 adrenergic receptor activity 6/163 17/17697 6.33570976790423e-09 3.39312456458871e-07 2.00075045302239e-07 ADRA1A/ADRA1B/ADRB2/ADRA2A/ADRB1/ADRA2C 6 MF GO:0035173 histone kinase activity 6/163 17/17697 6.33570976790423e-09 3.39312456458871e-07 2.00075045302239e-07 PRKCA/CDK1/PRKCB/CCNB1/CDK2/CHEK1 6 MF GO:0001085 RNA polymerase II transcription factor binding 12/163 155/17697 2.06730745911782e-08 9.96442195294789e-07 5.87550541012433e-07 ESR1/JUN/AR/PPARG/FOS/RB1/TP53/ELK1/NFE2L2/AHR/PPARA/PPARD 12 MF GO:0020037 heme binding 11/163 135/17697 4.82788914751304e-08 2.11549324463753e-06 1.24739719600815e-06 PTGS1/PTGS2/HMOX1/CYP3A4/CYP1A2/CYP1A1/DUOX2/NOS3/CYP1B1/MPO/NOS2 11 MF GO:0031625 ubiquitin protein ligase binding 15/163 290/17697 7.84571185204766e-08 3.15136092723914e-06 1.85819491232708e-06 HSP90AB1/KCNH2/BCL2/JUN/CASP8/RELA/EGFR/CDKN1A/RB1/TP53/NFKBIA/HIF1A/HSPA5/CHEK2/ERBB3 15
代码
# 输入文件需要有3列信息：
#ONTOLOGY：GO分类，BP/CC/MF
#Term：GO名称
#Count：富集在每个Term上基因数目
library(ggpubr)
inputFile = "input.txt" # 输入文件
outFile = "barplot1.pdf" # 输出文件
setwd("")
rt = read.table(inputFile, header = T, sep = "\t", check.names = F) #读取输入文件
# 绘制
pdf(file = outFile, width = 7, height = 5)
ggbarplot(rt, x = "Term", y = "Count", fill = "ONTOLOGY", color = "white",
orientation = "horiz", #横向显示
palette = "aaas", #配色方案
legend = "right", #图例位置
sort.val = "asc", #上升排序，区别于desc
sort.by.groups = TRUE) + #按组排序
scale_y_continuous(expand = c(0, 0)) + # 连续数据位置标度(x & y)
scale_x_discrete(expand = c(0,0)) # 离散数据的位置尺度
dev.off()
