diff --git a/404.html b/404.html index 0e6bc2a..a1b74c3 100644 --- a/404.html +++ b/404.html @@ -24,7 +24,7 @@ EnrichGT - 0.2.3 + 0.2.5 + + + + + +
+ + + + +
+
+

Fusing multiple enrichment results generated from different databases

+ + + +
c_fusing.Rmd
+
+ + + +
+library(EnrichGT)
+#> Loading required package: dplyr
+#> 
+#> Attaching package: 'dplyr'
+#> The following objects are masked from 'package:stats':
+#> 
+#>     filter, lag
+#> The following objects are masked from 'package:base':
+#> 
+#>     intersect, setdiff, setequal, union
+#> Loading required package: tibble
+#> Loading required package: gt
+#> Loading required package: cli
+#> 
+#> ── EnrichGT ────────────────────────────────────────────────────────────────────
+#> ℹ View your enrichment result by entring `EnrichGT(result)`
+#> → by Zhiming Ye, https://github.com/ZhimingYe/EnrichGT
+
+

Summary +

+

The default setting of clusterProfiler only supports +enrichment from a single database (which is reasonable for accurate +p-values). However, a single database often lacks sufficient coverage. +Frequently, we need to cross-reference GO, KEGG, Reactome, and other +databases. EnrichGT offers a method to integrate results from multiple +database sources, providing us with a coherent way to interpret these +results through gt presentation.

+
+
+

Example1: Merging ORA results from GO + KEGG +

+

First, we should generate a list containing different +enrichment results.

+
+suppressPackageStartupMessages({library(tidyverse)
+library(clusterProfiler)
+library(org.Hs.eg.db)})
+data(geneList, package="DOSE")
+gene <- names(geneList)[abs(geneList) > 2]
+ego <- enrichGO(gene          = gene,
+                universe      = names(geneList),
+                OrgDb         = org.Hs.eg.db,
+                ont           = "CC",
+                pAdjustMethod = "BH",
+                pvalueCutoff  = 0.01,
+                qvalueCutoff  = 0.05,
+                readable      = TRUE)
+kk <- enrichKEGG(gene         = gene,
+                 organism     = 'hsa',
+                 pvalueCutoff = 0.05)
+#> Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
+#> Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
+
+ora_result_list<-list(ego,kk)
+

We can see the list contains GO and KEGG results.

+
+str(ora_result_list,max.level = 1)
+#> List of 2
+#>  $ :Formal class 'enrichResult' [package "DOSE"] with 15 slots
+#>  $ :Formal class 'enrichResult' [package "DOSE"] with 15 slots
+

Next, simple bring it to EnrichGT(), like regular +enrichment objects.

+
+ora_result_list_egt<-ora_result_list |> EnrichGT()
+#> Loading required package: proxy
+#> 
+#> Attaching package: 'proxy'
+#> The following object is masked from 'package:IRanges':
+#> 
+#>     as.matrix
+#> The following object is masked from 'package:S4Vectors':
+#> 
+#>     as.matrix
+#> The following objects are masked from 'package:stats':
+#> 
+#>     as.dist, dist
+#> The following object is masked from 'package:base':
+#> 
+#>     as.matrix
+#> Loading required package: text2vec
+#> 
+#> Attaching package: 'text2vec'
+#> The following object is masked from 'package:BiocGenerics':
+#> 
+#>     normalize
+#> Joining with `by = join_by(ID)`
+

+
+ora_result_list_egt@gt_object
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Parse form: ora_result_list
Split into 15 Clusters. Generated by github@zhimingye/EnrichGT
DescriptionCountPCTPadjgeneID
Cluster_1
+
chromosome, centromeric region
+
GO:0000775
+		2110.04.0e-09CDCA8, CDC20, CENPE, NDC80, TOP2A, HJURP, SKA1, NEK2, CENPM, CENPN, ERCC6L, MAD2L1, KIF18A, CDT1, BIRC5, EZH2, TTK, NCAPG, AURKB, AURKA, CCNB1
+
condensed chromosome, centromeric region
+
GO:0000779
+		189.04.8e-09CDC20, CENPE, NDC80, HJURP, SKA1, NEK2, CENPM, CENPN, ERCC6L, MAD2L1, KIF18A, CDT1, BIRC5, TTK, NCAPG, AURKB, AURKA, CCNB1
+
spindle
+
GO:0005819
+		2613.04.8e-09CDCA8, CDC20, KIF23, CENPE, ASPM, DLGAP5, SKA1, NUSAP1, TPX2, TACC3, NEK2, CDK1, MAD2L1, KIF18A, BIRC5, KIF11, TRAT1, TTK, AURKB, PRC1, KIFC1, KIF18B, KIF20A, AURKA, CCNB1, KIF4A
+
mitotic spindle
+
GO:0072686
+		189.04.8e-09KIF23, CENPE, ASPM, DLGAP5, SKA1, NUSAP1, TPX2, TACC3, CDK1, MAD2L1, KIF18A, KIF11, TRAT1, AURKB, PRC1, KIFC1, KIF18B, AURKA
+
condensed chromosome
+
GO:0000793
+		2110.04.8e-09CDC20, CENPE, NDC80, TOP2A, NCAPH, HJURP, SKA1, NEK2, CENPM, CENPN, ERCC6L, MAD2L1, KIF18A, CDT1, BIRC5, TTK, NCAPG, AURKB, CHEK1, AURKA, CCNB1
+
chromosomal region
+
GO:0098687
+		2512.04.8e-09CDCA8, CDC20, CENPE, NDC80, TOP2A, HJURP, SKA1, NEK2, CENPM, RAD51AP1, CENPN, CDK1, ERCC6L, MAD2L1, KIF18A, CDT1, BIRC5, EZH2, TTK, NCAPG, AURKB, CHEK1, AURKA, CCNB1, MCM5
+
kinetochore
+
GO:0000776
+		178.54.8e-09CDC20, CENPE, NDC80, HJURP, SKA1, NEK2, CENPM, CENPN, ERCC6L, MAD2L1, KIF18A, CDT1, BIRC5, TTK, AURKB, AURKA, CCNB1
+
spindle microtubule
+
GO:0005876
+		105.03.1e-06CENPE, SKA1, CDK1, KIF18A, KIF11, AURKB, PRC1, KIF18B, AURKA, KIF4A
+
microtubule associated complex
+
GO:0005875
+		126.01.1e-05CDCA8, KIF23, KIF18A, BIRC5, KIF11, AURKB, KIFC1, KIF18B, KIF20A, AURKA, KIF4A, DNALI1
+
mitotic spindle midzone
+
GO:1990023
+		52.51.3e-05CENPE, KIF18A, AURKB, PRC1, KIF18B
Cluster_2
+
Cell cycle
+
hsa04061
+		1514.01.1e-078318, 991, 9133, 10403, 890, 983, 4085, 81620, 7272, 9212, 1111, 9319, 891, 4174, 9232
+
external encapsulating structure
+
hsa03320
+		2512.03.9e-06MMP1, S100A9, S100A8, MARCO, S100A7, ADAMDEC1, MMP12, COL16A1, ADIPOQ, FCGBP, ANXA9, MMP28, OMD, COMP, COL17A1, CILP, CCN5, NDP, MATN3, CHAD, TPSB2, ASPN, LRRC17, MFAP4, OGN
+
extracellular matrix
+
hsa04110
+		2512.03.9e-06MMP1, S100A9, S100A8, MARCO, S100A7, ADAMDEC1, MMP12, COL16A1, ADIPOQ, FCGBP, ANXA9, MMP28, OMD, COMP, COL17A1, CILP, CCN5, NDP, MATN3, CHAD, TPSB2, ASPN, LRRC17, MFAP4, OGN
+
collagen-containing extracellular matrix
+
GO:0030312
+		189.04.6e-04S100A9, S100A8, MARCO, S100A7, ADAMDEC1, COL16A1, ADIPOQ, ANXA9, MMP28, COMP, COL17A1, CILP, NDP, MATN3, TPSB2, ASPN, MFAP4, OGN
+
Oocyte meiosis
+
GO:0031012
+		109.46.3e-04991, 9133, 983, 4085, 51806, 6790, 891, 9232, 3708, 5241
+
Cellular senescence
+
GO:0062023
+		109.41.2e-032305, 4605, 9133, 890, 983, 51806, 1111, 891, 776, 3708
+
nuclear chromosome
+
hsa04114
+		115.52.4e-03CDC45, MCM10, TOP2A, NCAPH, NEK2, GINS1, BIRC5, NCAPG, GINS2, CHEK1, MCM5
+
Motor proteins
+
hsa04218
+		109.44.2e-039493, 1062, 81930, 3832, 3833, 146909, 10112, 24137, 4629, 7802
+
Progesterone-mediated oocyte maturation
+
GO:0000228
+		76.61.1e-029133, 890, 983, 4085, 6790, 891, 5241
Cluster_11
+
Viral protein interaction with cytokine and cytokine receptor
+
hsa04814
+		87.51.3e-033627, 10563, 6373, 4283, 6362, 6355, 9547, 1524
Cluster_12
+
PPAR signaling pathway
+
hsa04914
+		76.61.4e-034312, 9415, 9370, 5105, 2167, 3158, 5346
+
+
+
+

Example2: Merging GSEA results from GO + KEGG +

+

Like before, we should generate a list contains 2 GSEA +results.

+
+ego3 <- gseGO(geneList     = geneList,
+              OrgDb        = org.Hs.eg.db,
+              ont          = "CC",
+              minGSSize    = 100,
+              maxGSSize    = 500,
+              pvalueCutoff = 0.05) |> setReadable(OrgDb = org.Hs.eg.db,keyType = "ENTREZID")
+#> preparing geneSet collections...
+#> GSEA analysis...
+#> Warning in fgseaMultilevel(pathways = pathways, stats = stats, minSize =
+#> minSize, : For some pathways, in reality P-values are less than 1e-10. You can
+#> set the `eps` argument to zero for better estimation.
+#> leading edge analysis...
+#> done...
+kk3 <- gseKEGG(gene         = geneList,
+                 organism     = 'hsa',
+                 pvalueCutoff = 0.05) |> setReadable(OrgDb = org.Hs.eg.db,keyType = "ENTREZID")
+#> preparing geneSet collections...
+#> GSEA analysis...
+#> Warning in fgseaMultilevel(pathways = pathways, stats = stats, minSize =
+#> minSize, : For some pathways, in reality P-values are less than 1e-10. You can
+#> set the `eps` argument to zero for better estimation.
+#> leading edge analysis...
+#> done...
+gsea_result_list<-list(ego3,kk3)
+str(ora_result_list,max.level = 1)
+#> List of 2
+#>  $ :Formal class 'enrichResult' [package "DOSE"] with 15 slots
+#>  $ :Formal class 'enrichResult' [package "DOSE"] with 15 slots
+

Then, go to EnrichGT()!

+
+gsea_result_list_egt<-gsea_result_list |> EnrichGT()
+#> 
+#> ── EnrichGT message: ───────────────────────────────────────────────────────────
+#> ℹ Too many clusters! Try with max as ncol/10...
+#> use force=T to forbid the self-check
+#> Joining with `by = join_by(ID)`
+

+
+gsea_result_list_egt@gt_object
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Parse form: gsea_result_list
Split into 10 Clusters. Generated by github@zhimingye/EnrichGT
DescriptionabsNESPadjcore_enrichment
Cluster_1
+
condensed chromosome, centromeric region
+
GO:0000779
+		2.7221.4e-09CDC20, CENPE, NDC80, HJURP, SKA1, NEK2, CENPM, CENPN, ERCC6L, MAD2L1, KIF18A, CDT1, BIRC5, TTK, NCAPG, AURKB, AURKA, CCNB1, KIF2C, PLK1, BUB1B, ZWINT, CENPU, SPC25, SPAG5, CENPI, NCAPD2, CENPA, BUB1, CENPF, ZWILCH, CEBPB, DSN1, KNTC1, FIRRM, NCAPD3
+
chromosome, centromeric region
+
GO:0000775
+		2.6701.4e-09CDCA8, CDC20, CENPE, NDC80, TOP2A, HJURP, SKA1, NEK2, CENPM, CENPN, ERCC6L, MAD2L1, KIF18A, CDT1, BIRC5, EZH2, TTK, NCAPG, AURKB, AURKA, CCNB1, KIF2C, PLK1, BUB1B, ZWINT, CENPU, SPC25, SPAG5, DSCC1, CENPI, OIP5, HELLS, NCAPD2, CENPA, BUB1, CENPF, ZWILCH, CEBPB, H2BC11, DSN1, KNTC1, FIRRM, NCAPD3
+
kinetochore
+
GO:0000776
+		2.6701.4e-09CDC20, CENPE, NDC80, HJURP, SKA1, NEK2, CENPM, CENPN, ERCC6L, MAD2L1, KIF18A, CDT1, BIRC5, TTK, AURKB, AURKA, CCNB1, KIF2C, PLK1, BUB1B, ZWINT, CENPU, SPC25, SPAG5, CENPI, BUB1, CENPF, ZWILCH, DSN1, KNTC1, FIRRM
+
condensed chromosome
+
GO:0000793
+		2.5111.4e-09CDC20, CENPE, NDC80, TOP2A, NCAPH, HJURP, SKA1, NEK2, CENPM, CENPN, ERCC6L, MAD2L1, KIF18A, CDT1, BIRC5, TTK, NCAPG, AURKB, CHEK1, AURKA, CCNB1, KIF2C, PLK1, BUB1B, ZWINT, CENPU, SPC25, SPAG5, CENPI, RAD51, MKI67, NCAPD2, CENPA, BUB1, CENPF, ZWILCH, BLM, CEBPB, NCAPG2, HMGB2, DSN1, KNTC1, FIRRM, NCAPD3, SMC4, RCC1
+
mitotic spindle
+
GO:0072686
+		2.3601.4e-09KIF23, CENPE, ASPM, DLGAP5, SKA1, NUSAP1, TPX2, TACC3, CDK1, MAD2L1, KIF18A, KIF11, TRAT1, AURKB, PRC1, KIFC1, KIF18B, AURKA, CDC6, PLK1, RACGAP1, SPAG5, ECT2, ESPL1, HAUS6, ODAM, GPSM2, PYCR3
+
spindle
+
GO:0005819
+		2.2111.4e-09CDCA8, CDC20, KIF23, CENPE, ASPM, DLGAP5, SKA1, NUSAP1, TPX2, TACC3, NEK2, CDK1, MAD2L1, KIF18A, BIRC5, KIF11, TRAT1, TTK, AURKB, PRC1, KIFC1, KIF18B, KIF20A, AURKA, CCNB1, KIF4A, KIF14, HMMR, KIF2C, SHCBP1, CDC6, PLK1, RACGAP1, BUB1B, SPAG5, ECT2, ESPL1, KIF15, HAUS6, ODAM, GPSM2, CDC25B, PYCR3, CENPF, FBXO5, ZWILCH, SAC3D1, CDC7, DSN1, KIF20B, KNTC1, FIRRM, SLC25A5, PTPN7, CD180, WDR62, BORA, RAD21, TUBB, ACOT13, MICAL3, AUNIP, PSRC1, RMDN1, TUBG1, TUBB3, CIAO2B
+
midbody
+
GO:0030496
+		2.1002.6e-08CDCA8, KIF23, CENPE, ASPM, CEP55, NEK2, CDK1, BIRC5, AURKB, PRC1, KIF20A, AURKA, KIF4A, KIF14, SHCBP1, PLK1, RACGAP1, SPAG5, ECT2
+
microtubule
+
GO:0005874
+		1.6976.6e-06KIF23, CENPE, ASPM, SKA1, NUSAP1, TPX2, NEK2, CDK1, KIF18A, BIRC5, KIF11, AURKB, PRC1, KIFC1, KIF18B, KIF20A, AURKA, KIF4A, KIF14, KIF2C, PLK1, RACGAP1, GTSE1, SPAG5, KIF15, HAUS6, MX1, RIBC2, CCT5, TTLL4, NDRG1, ZWILCH, TTLL7, CLIP4, STMN1, TUBA4A, TEKT2, KIF20B, KNTC1, CCT6A, CFAP20, TUBA4B, CCT2, MX2, TUBA1C, KCNAB2, CDK2AP2, TUBB, DNM1L, PSRC1, TCP11L1, RMDN1, TUBG1, TUBB3
+
centrosome
+
GO:0005813
+		1.5662.8e-05CDC45, CDC20, KIF23, CCNB2, NDC80, ASPM, CEP55, DLGAP5, SKA1, TACC3, NEK2, CDK1, TRAT1, AURKB, CHODL, CHEK1, DTL, AURKA, CCNB1, HMMR, KIF2C, PLK1, CENPU, SPAG5, TAP1, ESPL1, CCNE1, KIF15, PCLAF, PLK4, HAUS6, CCNE2, CTSC, GPSM2, LCK, CCT5, CDC25B, CTAG2, RPP25, STIL, CENPF, LHCGR, PCNA, NDRG1, NUP93, E2F1, SAC3D1, PSMB5, FANCE, TBC1D31, RLBP1, RANBP1, CCDC88C, SNX10, KIF20B
+
spindle pole
+
GO:0000922
+		1.9074.0e-05CDC20, ASPM, DLGAP5, TPX2, TACC3, NEK2, MAD2L1, KIF11, AURKB, PRC1, AURKA, CCNB1, CDC6, PLK1, SPAG5, GPSM2, CDC25B, CENPF, DSN1, KIF20B, KNTC1, WDR62, RAD21, AUNIP, PSRC1, RMDN1, TUBG1, SPDL1
Cluster_2
+
chromosomal region
+
hsa04657
+		2.5541.4e-09CDCA8, CDC20, CENPE, NDC80, TOP2A, HJURP, SKA1, NEK2, CENPM, RAD51AP1, CENPN, CDK1, ERCC6L, MAD2L1, KIF18A, CDT1, BIRC5, EZH2, TTK, NCAPG, AURKB, CHEK1, AURKA, CCNB1, MCM5, MCM2, KIF2C, PLK1, BUB1B, ZWINT, CENPU, SPC25, SPAG5, DSCC1, CENPI, RAD51, ORC1, OIP5, HELLS, MCM6, MCM4, FEN1, NCAPD2, CENPA, BUB1, CENPF, PCNA, RECQL4, ZWILCH, MACROH2A2, BLM, DNA2, CEBPB, H2BC11, MCM7, DSN1, MSH2, KNTC1, FIRRM, NCAPD3, HDAC2, PPP1CA, SMC4, MCM3, POLD1, RAD21, CHEK2, ERCC4, ZNF276, SPDL1, SEC13, NBN, MIS18A, ACTL6A, H2BC3, DNMT3A, PARP1, SUV39H1, KDM1A, DNMT1, H2AX, RANGAP1, INCENP, CBX3, CENPQ, POLE3, GAR1, XRCC3
+
nuclear chromosome
+
hsa04061
+		2.5531.4e-09CDC45, MCM10, TOP2A, NCAPH, NEK2, GINS1, BIRC5, NCAPG, GINS2, CHEK1, MCM5, MCM2, PLK1, RAD51, ORC6, ORC1, MCM6, MCM4, TIPIN, NCAPD2, GINS4, ANP32E, PCNA, GINS3, MACROH2A2, BLM, NCAPG2, POLE2, POLA2, MCM7, SINHCAF, PRIM1, NCAPD3, HDAC2, WDHD1, RUVBL1, SMC4, RCC1, PRIM2, MCM3, POLD1, RAD21, TUBG1, SMC2, TIMELESS, UCHL5, ACTL6A, EXOSC9, PARP1, SUV39H1, RRS1, H2AX, INCENP, POLD2, POLE3, BAZ1A, TTN, RPA3
+
DNA replication
+
hsa05323
+		2.3791.7e-05MCM5, MCM2, MCM6, MCM4, FEN1, RFC4, PCNA, RNASEH2A, DNA2, POLE2, POLA2, MCM7, RFC2, PRIM1, PRIM2, MCM3, POLD1, RFC3, POLD2, POLE3, RPA3
+
chromosome, telomeric region
+
hsa04064
+		1.8901.1e-04RAD51AP1, CDK1, EZH2, CHEK1, MCM5, MCM2, RAD51, ORC1, MCM6, MCM4, FEN1, PCNA, RECQL4, MACROH2A2, BLM, DNA2, MCM7, MSH2, HDAC2, PPP1CA, MCM3, POLD1, CHEK2, ERCC4, NBN, H2BC3, PARP1, KDM1A, H2AX, CBX3, GAR1, XRCC3, H3-4
+
Mismatch repair
+
hsa04060
+		1.7144.2e-02EXO1, RFC4, PCNA, MSH2, RFC2, MSH6, POLD1, RFC3, POLD2, RPA3, LIG1, RFC5
+
Base excision repair
+
hsa04062
+		1.6064.5e-02FEN1, RFC4, PCNA, NEIL3, POLE2, RFC2, POLD1, UNG, RFC3, PARP1, POLD2, POLE3, TDG, LIG1, RFC5, PARP2, APEX1, TDP1
Cluster_3
+
collagen-containing extracellular matrix
+
hsa04668
+		2.1821.4e-09LOXL2, SOD3, COL4A6, NID1, LAMA4, EGFL7, TNC, GDF10, SERPINA3, COL6A1, COL11A1, WNT5A, IGFBP7, THSD4, VWF, COL18A1, CRELD1, CCN2, COL2A1, COL15A1, ADAMTS20, LTBP4, CD151, EDIL3, LTBP3, MGP, WNT2B, PXDN, TGFB2, LAMB1, RARRES2, GPC1, CTSF, SPP2, COL1A2, PRG4, CTSG, SERPINF1, LUM, ANG, EFEMP2, SEMA3B, COL1A1, TIMP3, PRELP, NID2, FBLN5, COL21A1, ANGPTL2, COL6A3, COL8A1, MMRN1, SRPX, ITIH5, CDH13, SHH, MFAP5, PCOLCE, FBLN1, COL3A1, ANGPTL7, COL5A3, COL5A2, WNT5B, MMRN2, THBS2, ADAMTS5, EFEMP1, MMP2, FBLN2, COL7A1, CCN3, MYOC, CXCL12, EMILIN1, HPX, HSPG2, VCAN, COL5A1, COL6A2, LAMA2, LOXL1, MXRA5, LAMA3, LTBP2, SPARC, MEGF9, COL8A2, TGFB1I1, COLQ, BGN, CLU, F13A1, SPON1, GPC4, ECM2, AEBP1, HTRA1, POSTN, DPT, COLEC12, FMOD, MST1, F3, TNN, TGFB3, SERPINA5, CPA3, LAMB2, SPARCL1, COL10A1, FBN1, DCN, LRRC15, BCAM, TPSAB1, COL4A5, AZGP1, THBS4, ELN, COL14A1, COL16A1, ADIPOQ, ANXA9, MMP28, COMP, COL17A1, CILP, NDP, MATN3, TPSB2, ASPN, MFAP4, OGN
+
external encapsulating structure
+
GO:0098687
+		2.1131.4e-09CD248, LAMA4, EGFL7, TNC, GDF10, SERPINA3, COL6A1, COL11A1, MMP26, WNT5A, OVGP1, IGFBP7, THSD4, VWF, COL18A1, CRELD1, NDNF, CCN4, CCN2, COL2A1, COL15A1, MMP3, ADAMTS20, LTBP4, CD151, EDIL3, LTBP3, MGP, IGFALS, WNT2B, FGF1, PXDN, OLFML2A, LRRTM4, TGFB2, LAMB1, MMP13, RARRES2, GPC1, CTSF, SPP2, COL1A2, PRG4, CTSG, SERPINF1, LUM, ANG, EFEMP2, SEMA3B, COL1A1, TIMP3, PRELP, NID2, FBLN5, COL21A1, ANGPTL2, COL6A3, COL8A1, MUC6, MMRN1, SRPX, ITIH5, CDH13, SHH, MFAP5, PCOLCE, FBLN1, COL3A1, ANGPTL7, COL5A3, MMP10, COL5A2, WNT5B, OLFML2B, MMRN2, THBS2, ADAMTS5, EFEMP1, MMP2, FBLN2, COL7A1, CCN3, LRIG1, WNT11, MYOC, CXCL12, EMILIN1, HPX, HSPG2, TIMP4, VCAN, COL5A1, COL6A2, LAMA2, LOXL1, MXRA5, LAMA3, LTBP2, CRISPLD2, SPARC, MEGF9, COL8A2, TGFB1I1, COLQ, BGN, CLU, WNT4, F13A1, SPON1, GPC4, ECM2, LRRC32, AEBP1, HTRA1, POSTN, DPT, COLEC12, FMOD, MST1, ANOS1, LRRN3, F3, TNN, TGFB3, SNED1, SERPINA5, CPA3, LAMB2, TNFRSF11B, SPARCL1, COL10A1, FBN1, DCN, LRRC15, BCAM, TPSAB1, COL4A5, AZGP1, THBS4, KERA, ELN, COL14A1, COL16A1, ADIPOQ, FCGBP, ANXA9, MMP28, OMD, COMP, COL17A1, CILP, CCN5, NDP, MATN3, CHAD, TPSB2, ASPN, LRRC17, MFAP4, OGN
+
extracellular matrix
+
GO:0000228
+		2.1131.4e-09CD248, LAMA4, EGFL7, TNC, GDF10, SERPINA3, COL6A1, COL11A1, MMP26, WNT5A, OVGP1, IGFBP7, THSD4, VWF, COL18A1, CRELD1, NDNF, CCN4, CCN2, COL2A1, COL15A1, MMP3, ADAMTS20, LTBP4, CD151, EDIL3, LTBP3, MGP, IGFALS, WNT2B, FGF1, PXDN, OLFML2A, LRRTM4, TGFB2, LAMB1, MMP13, RARRES2, GPC1, CTSF, SPP2, COL1A2, PRG4, CTSG, SERPINF1, LUM, ANG, EFEMP2, SEMA3B, COL1A1, TIMP3, PRELP, NID2, FBLN5, COL21A1, ANGPTL2, COL6A3, COL8A1, MUC6, MMRN1, SRPX, ITIH5, CDH13, SHH, MFAP5, PCOLCE, FBLN1, COL3A1, ANGPTL7, COL5A3, MMP10, COL5A2, WNT5B, OLFML2B, MMRN2, THBS2, ADAMTS5, EFEMP1, MMP2, FBLN2, COL7A1, CCN3, LRIG1, WNT11, MYOC, CXCL12, EMILIN1, HPX, HSPG2, TIMP4, VCAN, COL5A1, COL6A2, LAMA2, LOXL1, MXRA5, LAMA3, LTBP2, CRISPLD2, SPARC, MEGF9, COL8A2, TGFB1I1, COLQ, BGN, CLU, WNT4, F13A1, SPON1, GPC4, ECM2, LRRC32, AEBP1, HTRA1, POSTN, DPT, COLEC12, FMOD, MST1, ANOS1, LRRN3, F3, TNN, TGFB3, SNED1, SERPINA5, CPA3, LAMB2, TNFRSF11B, SPARCL1, COL10A1, FBN1, DCN, LRRC15, BCAM, TPSAB1, COL4A5, AZGP1, THBS4, KERA, ELN, COL14A1, COL16A1, ADIPOQ, FCGBP, ANXA9, MMP28, OMD, COMP, COL17A1, CILP, CCN5, NDP, MATN3, CHAD, TPSB2, ASPN, LRRC17, MFAP4, OGN
+
endoplasmic reticulum lumen
+
hsa03030
+		1.6987.4e-05SIL1, CASQ2, TNC, BACE1, COL6A1, COL11A1, MIA3, ESD, WNT5A, FLT3, WFS1, PROC, IGFBP7, COL18A1, ARSJ, COL2A1, COL15A1, FSTL3, CASQ1, SLC27A2, BCHE, LAMB1, HRC, SPP2, COL1A2, ERO1B, EDEM3, GOLM1, ARSD, COL1A1, COL21A1, COL6A3, COL8A1, SHH, COL3A1, COL5A3, FSTL1, COL5A2, WNT5B, ADAMTS5, PDGFC, CHRDL1, COL7A1, GAS6, CST3, VCAN, COL5A1, COL6A2, COL8A2, AFP, CLU, WNT4, ALB, SPON1, PRSS23, MXRA8, LAMB2, IGFBP4, SPARCL1, COL10A1, FBN1, COL4A5, COL14A1, PDGFD, COL16A1, COL17A1, BMP4, MATN3, STC2
+
Protein digestion and absorption
+
GO:0000781
+		1.9224.1e-04COL4A6, PRCP, COL6A1, COL11A1, COL18A1, ATP1B2, COL2A1, COL15A1, COL1A2, ATP1B1, COL1A1, COL21A1, MME, COL6A3, COL8A1, COL3A1, COL5A3, COL5A2, ATP1A2, COL7A1, CPB1, COL5A1, COL6A2, COL8A2, SLC7A8, CPA3, COL10A1, COL4A5, SLC1A1, ELN, COL14A1, COL16A1, COL17A1
+
Focal adhesion
+
hsa03430
+		1.7269.5e-04MAPK3, PGF, VEGFC, CTNNB1, MYL5, TLN2, EMP2, THBS3, PIK3R1, COL4A6, PIP5K1C, LAMA4, TNC, HGF, COL6A1, ARHGAP5, KDR, VWF, BCL2, ITGAV, COL2A1, ITGA3, CCND1, LAMB1, DOCK1, EMP1, COL1A2, COL1A1, COL6A3, MYL9, PARVA, FLNB, THBS2, SHC2, PDGFC, ITGB5, IGF1R, PDGFRB, CAV1, COL6A2, LAMA2, LAMA3, TNN, LAMB2, COL4A5, ITGA7, THBS4, IGF1, VAV3, PDGFD, COMP, CHAD
+
Cytoskeleton in muscle cells
+
hsa03410
+		1.6562.4e-03ITGA1, TPM2, SPTBN5, THBS1, MYBPC1, COL9A2, TNNT2, SDC4, SGCB, MYBPH, MYOM2, ACTG2, AMPD1, MYL5, TLN2, THBS3, TNNT1, CAPN3, COL4A6, NID1, COL6A1, COL11A1, ITGAV, ATP1B2, TPM1, MYH10, PDLIM1, ITGA3, SSPN, FLNC, SGCE, PDLIM2, SPTAN1, COL1A2, MYH7B, SPTBN4, ATP1B1, COL1A1, NID2, COL6A3, MYL9, SYNE1, FBLN1, COL3A1, COL5A3, COL5A2, THBS2, ATP1A2, MYOZ3, FBLN2, SGCD, ITGB5, MYOT, FHL1, HSPG2, VCAN, COL5A1, COL6A2, LAMA2, BGN, LMOD1, FBN1, DCN, COL4A5, ITGA7, THBS4, ELN, MYH11, COMP
+
sarcolemma
+
GO:0062023
+		1.7113.3e-03CACNB2, PPP3CB, KRT19, SGCB, PPP3CA, SCN2A, FLOT1, CAPN3, SLC9A1, COL6A1, UTRN, SLC30A1, PRKG1, SSPN, FLNC, SLC8B1, CASQ1, SGCE, AHNAK, SRI, KCND3, ATP1B1, COL6A3, AQP1, ATP1A2, CACNG4, AHNAK2, SGCD, RTN2, MYOT, IGF1R, ABCC8, CAV1, COL6A2, CACNA1C, LAMA2, SYNC, BGN, TGFB3, FXYD1, CACNA1D
+
PI3K-Akt signaling pathway
+
GO:0030312
+		1.4541.4e-02BDNF, FGF7, THBS3, G6PC3, PRKAA2, PIK3R1, STK11, COL4A6, TEK, LAMA4, TNC, HGF, COL6A1, MYB, KDR, CDKN1B, CREB3L1, IFNA4, INSR, CHRM2, FLT3, EIF4B, VWF, BCL2, ITGAV, EFNA1, F2R, COL2A1, NGFR, ITGA3, CCND1, FGFR3, TSC1, FGF1, NGF, LAMB1, LPAR1, COL1A2, COL1A1, LPAR4, EPOR, COL6A3, FGF2, GNG12, PRLR, THBS2, LPAR6, PDGFC, ITGB5, KITLG, IGF1R, NTF3, PDGFRB, COL6A2, LAMA2, GHR, LAMA3, FGF18, MAGI1, NTRK2, IKBKB, GNG11, TNN, LAMB2, MAGI2, IRS1, COL4A5, ITGA7, THBS4, IGF1, PDGFD, COMP, PCK1, ERBB4, CHAD
+
ECM-receptor interaction
+
GO:0031012
+		1.6891.5e-02THBS3, COL4A6, LAMA4, TNC, COL6A1, VWF, ITGAV, CD36, COL2A1, ITGA3, SV2A, LAMB1, COL1A2, COL1A1, COL6A3, THBS2, ITGB5, HSPG2, COL6A2, LAMA2, LAMA3, TNN, LAMB2, COL4A5, ITGA7, THBS4, COMP, CHAD
Cluster_4
+
Proteasome
+
GO:0005788
+		2.4727.9e-07PSMA7, PSMD3, PSMB9, PSMB5, IFNG, PSMD7, ADRM1, PSME2, PSMB3, PSMA4, PSMB2, PSMA3, PSMA5, PSMB7, PSMD14, PSME4, SEM1, PSMB10, PSMD8, PSMC3, PSMD2, PSMB4, PSMC4, PSMA2, PSMB6, PSMD12, POMP, PSMA1
+
Biosynthesis of amino acids
+
hsa04974
+		2.2234.9e-05PSAT1, PHGDH, CBS, ASS1, PFKP, ASNS, PYCR3, SHMT2, TKT, PSPH, IDH2, TPI1, BCAT1, GAPDH, PGK1, ENO1, PGAM1, PYCR1, TALDO1, ACO2, PKM, IDH3A, SDS, GOT1, RPIA, IDH3G, PRPS2, IDH1, PGK2, PRPS1L1, ENO3, PFKL, ARG2, ALDH18A1
+
Ribosome biogenesis in eukaryotes
+
hsa04510
+		2.1174.1e-04GTPBP4, RPP25, RPP40, RBM28, RRP7A, PWP2, EMG1, POP7, NXT1, EIF6, GAR1, GNL2, REXO5, RAN, POP4, RPP38, NOP10, CSNK2B, WDR43, TCOF1, POP1, SNU13, FBL, RPP30, UTP18, NHP2, IMP4, UTP6, XPO1, NAT10, NXF3, REXO2, WDR3, HEATR1, NVL, NMD3, CSNK2A2, RCL1, NXT2, LSG1, BMS1
+
mitochondrial protein-containing complex
+
hsa04820
+		1.5529.5e-04PDK1, MRPS17, MRPL15, MRPL13, CYC1, COX5A, MRPL12, MRPS33, SLC25A5, MRPL48, MRPS12, TOMM22, HSD17B10, NDUFS6, NDUFA9, PPIF, DLAT, MRPS7, MRPL42, UQCR10, TIMM17A, UQCRFS1, IDH3A, TIMM44, MRPS15, PDHA1, FXN, CHCHD3, MRPL3, TOMM40, APOO, MCCC1, NDUFS5, ATP5MC3, NDUFV1, ATP5MF, ATP5F1B, COX7B, NDUFB2, GADD45GIP1, TIMM23, NDUFA6, ATP5F1C, IDH3G, MRPS18A, MRPL11, NDUFB11, MRPL2, MPC2, COX8A, PDHA2, MRPL20, COX5B, TIMM8A, PDHX, MRPL9, AGK, TOMM70, TIMM17B, NDUFS1, SAMM50, MFN1, MRPL17, NDUFA4, NDUFA8, MRPL19, DAP3, TIMM8B, ATP5MC1, NDUFA1, COX6B1, CLPX, MRPL33, TIMM13, MRPL18, MRPL4, POLG, SDHA, MRPL35, NDUFB6, SUPV3L1, MRPL39, NDUFS3, MCUB, MRPS11, MRPS2, NDUFB5, PHB2, ATP5PF, COX6A1, UQCRB, NDUFB4, MRPS34, UQCRC1, MRPL44, ATP5PD, ATP5F1E, BAX, VDAC1, MRPL23, PAM16, COX4I1, MRPL58, MRPS16, COX7A2L
+
Drug metabolism - cytochrome P450
+
GO:0042383
+		1.8217.9e-03CYP3A4, CYP2E1, CYP2C8, CYP2A7, ALDH3B2, GSTM5, FMO3, UGT2B15, CYP2A6, HPGDS, AOX1, GSTM4, ADH1C, GSTM2, GSTM1, GSTT2, GSTT1, MAOA, GSTM3, MAOB, ADH1B, FMO5
+
Prion disease
+
hsa04151
+		1.4988.1e-03CCL5, C1QB, C1QA, PSMA7, PSMD3, PSMB5, TUBA4A, CYBA, CYC1, PSMD7, STIP1, NCF2, COX5A, ADRM1, PSMB3, CYCS, CACNA1S, SLC25A5, PSMA4, TUBA1C, PSMB2, PSMA3, PSMA5, PSMB7, TUBB, PSMD14, TUBB3, NDUFS6, MAPK13, NCF4, RAC2, SEM1, NDUFA9, PPIF, TUBB4B, UQCR10, UQCRFS1, PSMD8, TUBA1B, ATF4, PSMC3, TNF, IL6, PSMD2, NDUFS5, ATP5MC3, GRIN2D, NDUFV1, PSMB4, RYR2, ATP5F1B, PSMC4, C8G, COX7B, NDUFB2, CYBB, PSMA2, TUBB1, HSPA6, NDUFA6, ATP5F1C, CSNK2B, MAPK1, RYR1, PSMB6, NDUFB11, PRKACB, COX8A, COX5B, VDAC2, PSMD12, PSMA1, C9, GSK3B, MAPK12, NDUFS1, NDUFA4, DDIT3, NDUFA8, PSMD1, MAPK14, IL1A, ATP5MC1, NDUFA1, COX6B1, C8A, PRKACG, CASP3
+
Nucleocytoplasmic transport
+
hsa04512
+		1.7119.5e-03MAGOHB, KPNA2, NUP93, XPOT, NUP155, MAGOH, CSE1L, SEC13, NUP205, NDC1, EIF4A3, NXT1, NUP62, RANGAP1, RAN, IPO4, NUP88, NUP85, NUP50, RAE1, NUP42, UPF2, DDX19A, NCBP1, AHCTF1, NUP153, SEH1L, XPO4, SUMO4, NUP107, TNPO3, THOC5, XPO1, KPNA5, NUP37, KPNB1, NUP58, NXF3, KPNA3, SUMO3, NMD3, IPO13, SUMO2, NXT2, NUP188, TNPO2, KPNA1, XPO6
+
HIF-1 signaling pathway
+
hsa03050
+		1.7049.9e-03PDK1, EIF4EBP1, ANGPT4, TFRC, PFKP, LDHB, HK3, LDHC, IFNG, PLCG2, HMOX1, GAPDH, PGK1, ENO1, VHL, SLC2A1, VEGFA, ELOC, PDHA1, MAP2K1, RBX1, IL6, LTBR, HIF1A, HK2, EGFR, CYBB, MAP2K2, EGF, SERPINE1, RPS6KB2, MAPK1, PRKCA, PDHA2, IL6R, LDHA, PRKCG, PGK2, NPPA, ENO3, EIF4E2, PFKL, EIF4E, EGLN1
+
transport vesicle
+
hsa01230
+		1.4211.4e-02SCAP, DEFA6, RAB5B, CD59, CA4, TRIM9, SLC35G2, RAB13, GOSR1, RAB3A, AP1AR, SYPL1, SEC24B, ATP7A, PPT1, TGOLN2, RAB40A, NRSN2, DMXL2, PENK, SLC2A4, ATP8A1, RAB11FIP5, RAB40C, COPZ1, GABRA2, BCL2L1, TRIP11, ATP6V0A1, PTPRS, ATP6V1G2, SYNRG, TH, NPTX1, MFF, APH1B, SEC16A, GRIA1, UNC13A, RAB40B, SNCA, OPRD1, SPRED2, KCNQ1, VAMP3, SEC23A, SYNGR4, PLEKHF2, AP1G2, TMEM168, BDNF, SCGN, UNC13B, ATP2B1, SCAMP1, ICA1, IQSEC1, BACE1, OVGP1, WFS1, SEC31B, RAB40AL, DBH, SNCAIP, SSPN, FGFR3, RPH3AL, RAB26, DGKI, VAMP1, VAMP2, SEPTIN8, MCTP1, SV2A, PTPRN2, PDCD6, NGF, DPYSL3, ROGDI, SYTL2, DOC2A, CLBA1, MME, RAB27B, AMPH, MYOF, IL33, SORL1, SREBF1, ABCC8, NTF3, CRISPLD2, SYNDIG1, GABBR1, CPE, SLC18A2, BGN, SYT1, NTS, SLC4A8, COPZ2, CPA3, IGF1, MYRIP, ITPR1, SYT17, HLA-DQA1, LAMP5
+
Bladder cancer
+
hsa03008
+		1.7961.5e-02MMP1, MMP9, CXCL8, MYC, E2F1, CDKN2A, E2F3, CDK4, UPK3A, VEGFA, CDH1, MAP2K1, TYMP, EGFR, MAP2K2, EGF, MAPK1, DAPK1, NRAS
Cluster_5
+
cytoplasmic region
+
GO:0098798
+		1.6481.5e-03DCTN1, SPTBN5, ZC3H14, UNC13A, WDR11, MAP1A, CALY, DNAH2, HSPB1, AP3M2, NME7, MAP2K4, CTNNB1, DNAH7, KIF3B, CFAP45, UNC13B, IFT70A, PCLO, GLI1, SPEF1, PURA, NEK4, PRKCZ, FABP2, TRAK2, PKD2, ATG14, CLASP2, DYNC2LI1, NEFL, IFT140, STXBP1, RAB27B, NME8, NUMA1, CEP162, BBS1, DNAI4, TRAK1, TOGARAM1, DYNC2H1, PIERCE1, SPATA7, GLI3, KIF5C, SYBU, DRC3, SPAG6, EFHC1, MAK, DNAI7, MAPT, DNALI1
+
plasma membrane bounded cell projection cytoplasm
+
hsa00982
+		1.6206.2e-03WDR11, MAP1A, CALY, DNAH2, HSPB1, AP3M2, NME7, MAP2K4, DNAH7, KIF3B, CFAP45, IFT70A, GLI1, SPEF1, PURA, NEK4, TRAK2, ATG14, DYNC2LI1, NEFL, IFT140, RAB27B, NME8, CEP162, BBS1, DNAI4, TRAK1, TOGARAM1, DYNC2H1, PIERCE1, SPATA7, GLI3, KIF5C, SYBU, DRC3, SPAG6, EFHC1, MAK, DNAI7, MAPT, DNALI1
+
motile cilium
+
hsa05020
+		1.5719.7e-03DNAH7, IFT46, OXCT2, CFAP45, TSGA10, GK2, SPEF1, SCNN1A, CUL3, ABHD2, SPATA6, CFAP44, DNAAF11, IQCA1, CCR6, PKD2, SEPTIN10, IFT88, ATP1B1, DYNC2LI1, NME8, BBS1, WDR19, SPATA6L, DNAI4, BBS4, DYNC2H1, DRC3, SPAG6, SLC26A3, NME5, GSTM3, MAK, CFAP69, DNALI1
+
cilium
+
hsa03013
+		1.4011.1e-02TTBK2, VPS13A, PCDHB13, GNAQ, PDE6B, NME7, TMEM80, AHI1, BBS10, DNAH7, KIF3B, MAP1B, JADE1, CEP41, CCP110, IFT46, OXCT2, CFAP45, CDC14A, IFT70A, TSGA10, GLI1, NPR2, DZIP1, GK2, NEDD9, SPEF1, AGBL2, SCNN1A, CUL3, CEP290, FAM149B1, NEK4, ABHD2, UNC119B, DLG5, BBS9, SPATA6, ALMS1, NPY2R, CFAP44, DNAAF11, BBIP1, IQCA1, CCR6, CLXN, PKD2, ATG14, CEP15, C1orf115, IFT22, SEPTIN10, IFT88, FLCN, ATP1B1, ANKMY2, DYNC2LI1, TTC23, PJA2, PCM1, DLEC1, IFT140, GRK4, NME8, CEP162, BBS1, WDR19, SPATA6L, DNAI4, BBOF1, PRKAR2B, BBS4, CCDC68, ALPK1, TOGARAM1, MYOC, CAV1, VCAN, MACIR, DYNC2H1, PIERCE1, DYNC2I1, SPATA7, GLI3, KIF5C, CPLANE1, EVC, DRC3, MXRA8, SPAG6, SLC26A3, EFHC1, LZTFL1, MAGI2, NME5, GSTM3, MAK, TBX3, DNAI7, MYRIP, CCDC170, CFAP69, DNALI1
Cluster_6
+
specific granule
+
hsa04066
+		1.6374.2e-03CAMP, HPSE, ORM1, LYZ, GGH, CRISP3, LCN2, MS4A3, SLPI, ILF2, CYBA, AOC1, LAIR1, OLFM4, SLC2A3, CHI3L1, ELANE, DOCK2, CD53, ITGB2, ATP11A, KCNAB2, PTX3, CEACAM8, CXCL1, PDXK, BPI, TMC6, CD33, RAP2B, CTSD, PLAUR, ALDH3B1, CHIT1, TRPM2, CYBB, PTPRJ, SLCO4C1, TNFRSF1B, CHRNB4
+
vesicle lumen
+
GO:0030133
+		1.3921.1e-02S100A9, S100A8, S100A7, CAMP, S100P, HPSE, ORM1, LYZ, GGH, CRISP3, CTSW, LCN2, CTSC, PRDX4, PADI2, PRSS2, PSMD3, BIN2, HK3, SLPI, SERPINB3, ILF2, PNP, GPI, AOC1, PTGES2, PSMD7, GSTP1, OLFM4, DSN1, PLAC8, FABP5, APRT, CHI3L1, S100A12, ELANE, CCT2, DOCK2, PSMA5, PSMB7, PGAM1, PTX3, TUBB, SRGN, ADA, PSMD14, CXCL1, FCN1, PDXK, CSTB, GDI2, BPI, VEGFA, PKM, PYGB, TUBB4B
+
cytoplasmic vesicle lumen
+
hsa05219
+		1.3981.1e-02S100A9, S100A8, S100A7, CAMP, S100P, HPSE, ORM1, LYZ, GGH, CRISP3, CTSW, LCN2, CTSC, PRDX4, PADI2, PRSS2, PSMD3, BIN2, HK3, SLPI, SERPINB3, ILF2, PNP, GPI, AOC1, PTGES2, PSMD7, GSTP1, OLFM4, DSN1, PLAC8, FABP5, APRT, CHI3L1, S100A12, ELANE, CCT2, DOCK2, PSMA5, PSMB7, PGAM1, PTX3, TUBB, SRGN, ADA, PSMD14, CXCL1, FCN1, PDXK, CSTB, GDI2, BPI, VEGFA, PKM, PYGB, TUBB4B
+
secretory granule lumen
+
GO:0099568
+		1.3931.6e-02S100A9, S100A8, S100A7, CAMP, S100P, HPSE, ORM1, LYZ, GGH, CRISP3, CTSW, LCN2, CTSC, PRDX4, PADI2, PRSS2, PSMD3, BIN2, HK3, SLPI, SERPINB3, ILF2, PNP, GPI, AOC1, PTGES2, PSMD7, GSTP1, OLFM4, DSN1, PLAC8, FABP5, APRT, CHI3L1, S100A12, ELANE, CCT2, DOCK2, PSMA5, PSMB7, PGAM1, PTX3, TUBB, SRGN, PSMD14, CXCL1, FCN1, PDXK, CSTB, GDI2, BPI, VEGFA, PKM, PYGB, TUBB4B
+
primary lysosome
+
GO:0032838
+		1.4761.9e-02S100A7, LYZ, GGH, CTSC, PADI2, PRSS2, SERPINB3, PTGES2, DSN1, PLAC8, LPCAT1, FABP5, SYNGR1, VNN1, ELANE, CCT2, TUBB, CEACAM8, GDI2, BPI, PYGB, TUBB4B, RAB3D, CPNE1, VCP, RNASE2, SLCO4C1, GALNS, LAMP2, ARSB, MAPK1, PRDX6, CTSA, FRK, DDOST, C3AR1, CKAP4, PSMD1, STX3, ACTR2, MAN2B1, TOLLIP, HEBP2, GRN, GM2A, MAGT1, FTL, GCA, MNDA
+
azurophil granule
+
GO:0031514
+		1.4761.9e-02S100A7, LYZ, GGH, CTSC, PADI2, PRSS2, SERPINB3, PTGES2, DSN1, PLAC8, LPCAT1, FABP5, SYNGR1, VNN1, ELANE, CCT2, TUBB, CEACAM8, GDI2, BPI, PYGB, TUBB4B, RAB3D, CPNE1, VCP, RNASE2, SLCO4C1, GALNS, LAMP2, ARSB, MAPK1, PRDX6, CTSA, FRK, DDOST, C3AR1, CKAP4, PSMD1, STX3, ACTR2, MAN2B1, TOLLIP, HEBP2, GRN, GM2A, MAGT1, FTL, GCA, MNDA
+
tertiary granule
+
GO:0005929
+		1.3784.1e-02CAMP, MMP9, ORM1, LYZ, GGH, CRISP3, PKP1, ILF2, PRSS3, CYBA, CTSS, LAIR1, OLFM4, SLC2A3, CD300A, LILRB2, CD53, ITGB2, ATP11A, FCER1G, KCNAB2, PTX3, CEACAM8, CXCL1, CSTB, TMC6, CD33, RAP2B, CTSD, CR1, CHIT1, TRPM2, CYBB, NCKAP1L, PTAFR, CHRNB4, LAMP2
Cluster_7
+
neuron to neuron synapse
+
GO:0042581
+		1.4351.1e-02USP8, DNM3, ITGA8, SLC8A1, PKP4, LRFN3, ADD3, HOMER2, PLPPR4, GRIA1, PLXNC1, NLGN1, RPL14, SEPTIN11, PRKN, OPRD1, SORCS3, GRIK1, CACNG5, ADCY1, ADD1, CTNNB1, MAP1B, PLEKHA5, PCLO, FLRT3, IQSEC1, BACE1, GRM5, NECTIN3, CHRM2, DLG5, SLC30A1, PRKCZ, ATP1B2, NLGN4Y, IQSEC3, NGFR, GRIP1, AKAP9, SIPA1L1, ARHGAP32, CAMK2N1, RTN1, TSC1, DGKI, MPDZ, ROGDI, LIN7A, CPEB3, LRRTM2, NEFH, PJA2, SPOCK1, PALM, SYNPO, CAP2, CACNG4, DCLK1, CTNND2, CACNA1C, SYNDIG1, NTRK2, RAPGEF4, SYT1, SLC4A8, GRIA2, MAGI2, ADRA2A, CLSTN2, SLC1A1, ITPR1, PSD3, NLGN4X, ERBB4, PTPRT
+
asymmetric synapse
+
GO:0031983
+		1.4302.1e-02PTPRS, USP8, DNM3, ITGA8, SLC8A1, PKP4, LRFN3, ADD3, HOMER2, PLPPR4, GRIA1, PLXNC1, NLGN1, RPL14, PRKN, OPRD1, SORCS3, GRIK1, CACNG5, ADCY1, ADD1, CTNNB1, MAP1B, PLEKHA5, PCLO, FLRT3, IQSEC1, GRM5, NECTIN3, CHRM2, DLG5, SLC30A1, PRKCZ, NLGN4Y, IQSEC3, NGFR, GRIP1, AKAP9, SIPA1L1, ARHGAP32, CAMK2N1, RTN1, TSC1, DGKI, MPDZ, LIN7A, CPEB3, LRRTM2, NEFH, PJA2, SPOCK1, PALM, SYNPO, CAP2, CACNG4, DCLK1, CTNND2, CACNA1C, SYNDIG1, NTRK2, SLC4A8, GRIA2, MAGI2, ADRA2A, CLSTN2, SLC1A1, ITPR1, PSD3, NLGN4X, ERBB4, PTPRT
+
postsynaptic specialization
+
GO:0060205
+		1.3702.8e-02USP8, DNM3, ITGA8, SLC8A1, PKP4, LRFN3, ADD3, HOMER2, PLPPR4, GRIA1, NLGN1, RPL14, SEPTIN11, PRKN, OPRD1, SORCS3, GRIK1, CACNG5, ADCY1, ADD1, CTNNB1, MAP1B, PLEKHA5, ERBIN, PCLO, FLRT3, IQSEC1, GRM5, NECTIN3, DLG5, SLC30A1, PRKCZ, NLGN4Y, IQSEC3, NGFR, GRIP1, AKAP9, SIPA1L1, ARHGAP32, CAMK2N1, RTN1, TSC1, DGKI, MPDZ, LIN7A, CPEB3, KCND3, LRRTM2, CHRNB1, NEFH, PJA2, SPOCK1, PALM, SYNPO, KCND2, CAP2, CACNG4, DCLK1, CTNND2, CACNA1C, SYNDIG1, NTRK2, GRIA2, MAGI2, ADRA2A, CLSTN2, GLRB, ITPR1, PSD3, NLGN4X, ERBB4, PTPRT
+
postsynaptic density
+
GO:0034774
+		1.3734.6e-02PTPRS, USP8, DNM3, ITGA8, SLC8A1, PKP4, LRFN3, ADD3, HOMER2, PLPPR4, GRIA1, NLGN1, RPL14, PRKN, OPRD1, SORCS3, GRIK1, CACNG5, ADCY1, ADD1, CTNNB1, MAP1B, PLEKHA5, PCLO, FLRT3, IQSEC1, GRM5, NECTIN3, DLG5, SLC30A1, PRKCZ, NLGN4Y, IQSEC3, NGFR, GRIP1, AKAP9, SIPA1L1, ARHGAP32, CAMK2N1, RTN1, TSC1, DGKI, MPDZ, LIN7A, CPEB3, LRRTM2, NEFH, PJA2, SPOCK1, PALM, SYNPO, CAP2, CACNG4, DCLK1, CTNND2, CACNA1C, SYNDIG1, NTRK2, GRIA2, MAGI2, ADRA2A, CLSTN2, ITPR1, PSD3, NLGN4X, ERBB4, PTPRT
Cluster_8
+
Epstein-Barr virus infection
+
GO:0005766
+		1.9301.5e-05CXCL10, CCNA2, TAP1, ISG15, CCNE1, CCNE2, SKP2, STAT1, HLA-DRB4, HLA-DOB, MYC, CD3G, PSMD3, E2F1, IRAK1, CD247, CD3D, LYN, OAS1, RUNX3, OAS3, PSMD7, PLCG2, ADRM1, HDAC2, CYCS, E2F3, BAK1, CDK4, BID, CD3E, ICAM1, OAS2, PSMD14, RIGI, NFKBIB, MAPK13, SEM1, TNFAIP3, TAP2, CD19, PSMD8, IFNA21, SYK, PSMC3, NFKBIE, TNF, IL6, TLR2, PSMD2, FCER2, FADD, HLA-DQB1, PSMC4, TRAF2, RELB, HLA-G, CR2, CD40, EIF2AK2, NFKBIA, BCL2L11, SAP30, HLA-F, IRF9, IKBKE, CHUK, PSMD12, MAPK12, HLA-DMB, CALR, MAP2K3, PDIA3, HLA-DMA, PSMD1, MAPK14
+
Neutrophil extracellular trap formation
+
GO:0042582
+		1.9034.1e-04CAMP, AQP9, TLR8, CLEC7A, H2AZ1, H2BC12, MACROH2A2, H2BC11, H3C10, CYBA, FPR3, PLCG2, NCF2, H2AC25, HDAC2, H2AC17, SLC25A5, ELANE, ITGB2, H2BC9, MAPK13, NCF4, RAC2, PPIF, CLCN5, SELPLG, H2BC3, SYK, MAP2K1, H2AX, TLR2, CR1, H3-4, CYBB, CASP1, MAP2K2, CLCN4, C5AR1, FCGR3B, H2AC4, MAPK1, HDAC9, ITGA2B, PRKCA, PRKCG, VDAC2, H2AC14, MAPK12
+
Primary immunodeficiency
+
GO:0070820
+		2.0672.3e-03ICOS, TAP1, LCK, IL2RG, IL7R, CD3D, CD40LG, CD8A, PTPRC, CD3E, ADA, UNG, TAP2, CD19
+
Human immunodeficiency virus 1 infection
+
GO:0098984
+		1.6392.5e-03CCNB2, APOBEC3B, CDK1, CALML5, CHEK1, CCNB1, TAP1, APOBEC3A, CD3G, IRAK1, CD247, CD3D, PLCG2, CYCS, CALML4, BAK1, CDC25C, SAMHD1, BID, CCR5, CD3E, MAPK13, GNGT1, RAC2, TAP2, ELOC, IFNA21, MAP2K1, TNF, RBX1, TLR2, CXCR4, FADD, AP1S1, TRAF2, HLA-G, AP1G1, APOBEC3G, GNG5, FASLG, TNFRSF1B, MAP2K2, APOBEC3C, RPS6KB2, DDB1, MAPK1, NFKBIA, HLA-F, PRKCA, NRAS, CUL1, PRKCG, GNG4, CHUK, LIMK1, MAPK12, APOBEC3F, CALR, MAP2K3, PDIA3, NFATC3, AP1B1, MAPK14, GNB3, CASP3, PTK2, PAK1, HLA-B, GNAI1, PPP3R1, PRKCB, MYD88
+
Tuberculosis
+
GO:0032279
+		1.6344.1e-03CAMP, CALML5, STAT1, CLEC7A, HLA-DRB4, HLA-DOB, RIPK2, IRAK1, CEBPG, CEBPB, IFNG, CTSS, CORO1A, CYP27B1, ATP6V0A4, CYCS, CALML4, SPHK1, HSPD1, BID, ITGB2, TLR1, FCER1G, LBP, MRC1, MAPK13, CD14, ATP6V0B, IFNA21, SYK, TNF, CTSD, IL6, TLR2, CR1, FADD, CARD9, HLA-DQB1, CASP10, FCGR2B, RFXANK, LAMP2, FCGR3B, IL10RA, MAPK1, IL12B, FCGR2C, IL12A, MAPK12, ATP6V0D1, TLR6, HLA-DMB, HLA-DMA, MAPK14, IL1A
+
Antigen processing and presentation
+
GO:0099572
+		1.8445.2e-03TAP1, KLRC3, HLA-DRB4, HLA-DOB, IFI30, KIR2DS1, IFNG, CTSS, KLRD1, CD8A, KIR2DL3, LGMN, KLRC4, PSME2, KIR2DS5, CTSL, KIR3DL3, TAP2, TNF, HLA-DQB1, RFXANK, HLA-G, HSPA6, HLA-F, KIR2DL4, HLA-DMB, CALR, PDIA3, HLA-DMA, HSP90AB1, CTSB, HLA-DRA, HLA-B, CD8B, HSPA5, CD4, KIR2DL2
+
T cell receptor signaling pathway
+
GO:0014069
+		1.6647.0e-03ICOS, CTLA4, LCK, PPP2R3B, CD3G, CD247, CD3D, IFNG, CD40LG, ITK, CD8A, CDK4, PTPRC, CD3E, LCP2, CD28, NFKBIB, MAPK13, PRKCQ, NCK1, MAP2K1, NFKBIE, TNF, PDCD1, NCK2, RASGRP1, MAP2K2, GRAP2, MAPK1, SOS1, NFKBIA, NRAS, CHUK, IL2, GSK3B, MAPK12, NFATC3, MAPK14, TEC, PPP2R2B, MAP3K8, PAK1, CD8B, PPP3R1, GRB2
+
Natural killer cell mediated cytotoxicity
+
hsa05169
+		1.6937.9e-03GZMB, LCK, PRF1, KLRC3, CD247, KIR2DS1, IFNG, PLCG2, KLRD1, KIR2DL3, ULBP2, KIR2DS5, BID, ITGB2, NCR3, ICAM1, SH2D1A, CD48, LCP2, FCER1G, RAC2, KIR3DL3, IFNA21, SYK, MAP2K1, TNF, HLA-G, FASLG, TYROBP, MAP2K2, FCGR3B, MAPK1, SOS1, MICB, NCR1, PRKCA, NRAS, PRKCG, CD244, CASP3, TNFRSF10B, PAK1, HLA-B, IFNAR2, PPP3R1, PRKCB, GRB2, IFNA1, KIR2DL2
+
Toll-like receptor signaling pathway
+
hsa04613
+		1.6797.9e-03CXCL10, CXCL11, CXCL9, CXCL8, CCL5, STAT1, TLR8, CCL4, IRAK1, CD86, TLR1, SPP1, LBP, MAPK13, CD14, IFNA21, MAP2K1, TNF, IL6, TLR2, FADD, MAP2K2, CD40, MAPK1, NFKBIA, IRF9, IKBKE, IL12B, CHUK, IL12A, MAPK12, TLR6, MAP2K3, IRF5, MAPK14
+
Graft-versus-host disease
+
hsa05340
+		1.8401.5e-02GZMB, PRF1, HLA-DRB4, HLA-DOB, IFNG, KLRD1, KIR2DL3, CD86, CD28, KIR3DL3, TNF, IL6, HLA-DQB1, HLA-G, FASLG, HLA-F, IL2, HLA-DMB, HLA-DMA, IL1A, HLA-DRA, HLA-B, KIR2DL2, HLA-C, HLA-DOA, CD80, HLA-A
Cluster_9
+
Cell cycle
+
hsa05170
+		2.8523.4e-08CDC45, CDC20, CCNB2, NDC80, CCNA2, CDK1, MAD2L1, CDT1, TTK, AURKB, CHEK1, TRIP13, CCNB1, MCM5, PTTG1, MCM2, CDC25A, CDC6, PLK1, BUB1B, ESPL1, CCNE1, ORC6, ORC1, CCNE2, MCM6, MCM4, DBF4, SKP2, CDC25B, BUB1, MYC, PCNA, FBXO5, E2F1, CDKN2A, CDC7, MCM7, SFN, HDAC2, E2F3, CDKN2C, PKMYT1, CDC25C, CDK4, MCM3, RAD21, CHEK2, TFDP1, E2F5
+
Human T-cell leukemia virus 1 infection
+
hsa05152
+		1.7244.5e-04CDC20, CCNB2, CCNA2, MAD2L1, IL1R2, CHEK1, PTTG1, FOSL1, BUB1B, ESPL1, CCNE1, MMP7, CCNE2, LCK, IL2RA, HLA-DRB4, HLA-DOB, MYC, IL2RG, CD3G, E2F1, CDKN2A, CD3D, ADCY8, ELK4, RANBP1, VAC14, E2F3, CDKN2C, FDPS, SLC25A5, CDK4, ITGB2, CD3E, ICAM1, CHEK2, TSPO, IL15, SLC2A1, IL15RA, ATF4, MAP2K1, TNF, CDKN2B, IL6, LTA, LTBR, ANAPC10, HLA-DQB1, RAN, RELB, EGR2, HLA-G
+
Cellular senescence
+
hsa04612
+		1.7619.9e-04FOXM1, MYBL2, CCNB2, CCNA2, CDK1, CALML5, CHEK1, CCNB1, CDC25A, CXCL8, EIF4EBP1, CCNE1, CCNE2, MYC, E2F1, CDKN2A, MRAS, E2F3, PPP1CA, CALML4, SLC25A5, CDK4, CHEK2, E2F5
+
Oocyte meiosis
+
hsa04660
+		1.7894.1e-03CDC20, CCNB2, CDK1, MAD2L1, CALML5, AURKA, CCNB1, PTTG1, PLK1, ESPL1, CCNE1, CCNE2, BUB1, FBXO5, ADCY8, PPP1CA, CALML4, PKMYT1, CDC25C
+
p53 signaling pathway
+
hsa04650
+		1.8176.6e-03CCNB2, RRM2, CDK1, CHEK1, CCNB1, GTSE1, CCNE1, CCNE2, SERPINB5, CDKN2A, SFN, CYCS, CDK4, BID, ADGRB1, CHEK2
+
Viral carcinogenesis
+
hsa04620
+		1.5371.3e-02CDC20, CCNA2, CDK1, CHEK1, CCNE1, CCNE2, SKP2, H2BC12, CCR8, CDKN2A, H2BC11, LYN, GTF2A1, RANBP1, VAC14, HDAC2, BAK1, CDK4, CCR5, H2BC9, YWHAZ, PKM, H2BC3, ATF4, SYK, CDKN2B, LTBR, TRAF2, EGR2, HLA-G, RBL1, EIF2AK2, DDB1, MAPK1, HDAC9, NFKBIA, PRKACB, HLA-F, UBR4, TRAF1, IRF9, PMAIP1, NRAS, CCR3, GTF2E1, SCRIB, ATP6V0D1, GTF2A2, YWHAQ, YWHAH, TBPL1, PRKACG, CASP3, CCR4, SRC, HLA-B, MAD1L1
+
Progesterone-mediated oocyte maturation
+
hsa05332
+		1.6681.8e-02CCNB2, CCNA2, CDK1, MAD2L1, AURKA, CCNB1, CDC25A, PLK1, CDC25B, BUB1, ADCY8, PKMYT1, CDC25C
Cluster_10
+
IL-17 signaling pathway
+
hsa04110
+		2.2271.7e-05MMP1, S100A9, S100A8, S100A7, CXCL10, CXCL3, CCL20, FOSL1, MMP9, CXCL8, LCN2, CCL2, MUC5B, CEBPB, CCL7, IFNG, CCL17, CXCL5, CXCL1, TRAF4, MAPK13, TNFAIP3, ELAVL1, TNF, IL6, FADD, PTGS2, TRAF2, IL13, CCL11, MAPK1, NFKBIA, IKBKE, CHUK, GSK3B, MAPK12, MAPK6, IL17B, MAPK14, HSP90B1, IL25, HSP90AB1
+
Viral protein interaction with cytokine and cytokine receptor
+
hsa05166
+		1.9764.1e-04CXCL10, CXCL13, CXCL11, CXCL9, CCL18, CCL8, CXCL3, CCL20, CXCL8, CCL5, IL2RA, CCR1, CCL2, IL2RG, CCL4, CCR8, CCR7, IL24, CCL7, CCL17, CCR5, CCL22, XCL1, CXCL5, CXCL1, IL18RAP, CCL16, CCL13, TNF, IL19, IL6, LTA, CXCR4, LTBR
+
Rheumatoid arthritis
+
hsa04218
+		1.9565.9e-04MMP1, CXCL3, CCL20, CXCL8, TNFRSF11A, CTLA4, CCL5, CCL2, HLA-DRB4, HLA-DOB, LTB, IFNG, ATP6V0A4, CD86, ITGB2, ICAM1, CXCL5, CTSL, IL15, CXCL1, CD28, VEGFA, ATP6V0B, TNF, IL6, TLR2, HLA-DQB1, ATP6V1F, ATP6V1B1
+
NF-kappa B signaling pathway
+
hsa04114
+		1.9009.9e-04BCL2A1, CXCL3, CXCL8, TNFRSF11A, LCK, CCL4, BIRC3, IRAK1, LTB, LYN, VCAM1, CD40LG, PLCG2, ICAM1, CXCL1, RIGI, LBP, TNFAIP3, PRKCQ, CCL13, CD14, PARP1, SYK, TNF, LTA, PTGS2, LTBR, TRAF2, RELB, CD40, CSNK2B, NFKBIA, TRAF1
+
Cytokine-cytokine receptor interaction
+
hsa04115
+		1.5642.3e-03CXCL10, CXCL13, CXCL11, CXCL9, CCL18, IL1R2, CCL8, CXCL3, CCL20, IL12RB2, CXCL8, TNFRSF11A, CCL5, CXCR6, IL2RA, CCR1, CCL2, IL2RG, CCL4, CCR8, CCR7, GDF5, IL24, LTB, IL7, IL7R, CCL7, TNFRSF17, IFNG, CD40LG, TNFRSF21, IL21R, CSF2RB, IL32, CCL17, CCR5, IL27RA, CCL22, XCL1, CXCL5, IL15, CXCL1, IL18RAP, CD27, CCL16, GDF11, EBI3, IFNW1, CCL13, IFNA21, IL15RA, CRLF2, TNF, IL19, IL6, LTA, CXCR4, LTBR, IL1RL2, IL1RAP, CX3CL1, IL13, TNFRSF4, CXCR3, BMP7, FASLG, TNFRSF1B, CD40, CSF2RA, IL10RA, CCL11, IL36G, IL6R, IL9, IL12B, IL2, XCR1, CCR2, INHA, CCR3, IL12A, IL2RB, IL11
+
Chemokine signaling pathway
+
hsa05203
+		1.6493.9e-03CXCL10, CXCL13, CXCL11, CXCL9, CCL18, CCL8, CXCL3, CCL20, CXCL8, CCL5, CXCR6, CCR1, STAT1, CCL2, CCL4, HCK, CCR8, CCR7, LYN, CCL7, ADCY8, PLCG2, ITK, CCL17, DOCK2, CCR5, CCL22, XCL1, CXCL5, CXCL1, ARRB2, NFKBIB, GNGT1, CCL16, RAC2
+
TNF signaling pathway
+
hsa04914
+		1.6826.4e-03CXCL10, CXCL3, CCL20, MMP9, CCL5, CCL2, BIRC3, CEBPB, VCAM1, ICAM1, CXCL5, IL15, IRF1, CXCL1, DNM1L, MAPK13, TNFAIP3, ATF4, MAP2K1, TNF, IL6, LTA, ITCH, FADD, PTGS2, CASP10, TRAF2, CX3CL1, SOCS3, TNFRSF1B, MAPK1, NFKBIA, TRAF1
+
+
+
+

Session Info +

+
+sessioninfo::session_info()
+#> ─ Session info ───────────────────────────────────────────────────────────────
+#>  setting  value
+#>  version  R version 4.3.3 (2024-02-29)
+#>  os       macOS 15.0
+#>  system   aarch64, darwin20
+#>  ui       X11
+#>  language en
+#>  collate  en_US.UTF-8
+#>  ctype    en_US.UTF-8
+#>  tz       Asia/Shanghai
+#>  date     2024-10-09
+#>  pandoc   3.1.11 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
+#> 
+#> ─ Packages ───────────────────────────────────────────────────────────────────
+#>  package          * version    date (UTC) lib source
+#>  AnnotationDbi    * 1.64.1     2023-11-02 [1] Bioconductor
+#>  ape                5.7-1      2023-03-13 [1] CRAN (R 4.3.0)
+#>  aplot              0.2.2      2023-10-06 [1] CRAN (R 4.3.1)
+#>  Biobase          * 2.62.0     2023-10-26 [1] Bioconductor
+#>  BiocGenerics     * 0.48.1     2023-11-02 [1] Bioconductor
+#>  BiocParallel       1.36.0     2023-10-26 [1] Bioconductor
+#>  Biostrings         2.70.2     2024-01-30 [1] Bioconductor 3.18 (R 4.3.2)
+#>  bit                4.0.5      2022-11-15 [1] CRAN (R 4.3.0)
+#>  bit64              4.0.5      2020-08-30 [1] CRAN (R 4.3.0)
+#>  bitops             1.0-7      2021-04-24 [1] CRAN (R 4.3.0)
+#>  blob               1.2.4      2023-03-17 [1] CRAN (R 4.3.0)
+#>  bslib              0.6.1      2023-11-28 [1] CRAN (R 4.3.1)
+#>  cachem             1.0.8      2023-05-01 [1] CRAN (R 4.3.0)
+#>  cli              * 3.6.3      2024-06-21 [1] CRAN (R 4.3.3)
+#>  clusterProfiler  * 4.10.1     2024-03-09 [1] Bioconductor 3.18 (R 4.3.3)
+#>  codetools          0.2-19     2023-02-01 [1] CRAN (R 4.3.3)
+#>  colorspace         2.1-0      2023-01-23 [1] CRAN (R 4.3.0)
+#>  cowplot            1.1.3      2024-01-22 [1] CRAN (R 4.3.1)
+#>  crayon             1.5.2      2022-09-29 [1] CRAN (R 4.3.0)
+#>  data.table         1.15.4     2024-03-30 [1] CRAN (R 4.3.1)
+#>  DBI                1.2.2      2024-02-16 [1] CRAN (R 4.3.1)
+#>  desc               1.4.3      2023-12-10 [1] CRAN (R 4.3.1)
+#>  digest             0.6.35     2024-03-11 [1] CRAN (R 4.3.1)
+#>  DOSE               3.28.2     2023-12-12 [1] Bioconductor 3.18 (R 4.3.2)
+#>  dplyr            * 1.1.4      2023-11-17 [1] CRAN (R 4.3.1)
+#>  EnrichGT         * 0.2.5      2024-10-09 [1] local
+#>  enrichplot         1.22.0     2023-11-06 [1] Bioconductor
+#>  evaluate           0.23       2023-11-01 [1] CRAN (R 4.3.1)
+#>  fansi              1.0.6      2023-12-08 [1] CRAN (R 4.3.1)
+#>  farver             2.1.1      2022-07-06 [1] CRAN (R 4.3.0)
+#>  fastmap            1.1.1      2023-02-24 [1] CRAN (R 4.3.0)
+#>  fastmatch          1.1-4      2023-08-18 [1] CRAN (R 4.3.0)
+#>  fgsea              1.28.0     2023-10-26 [1] Bioconductor
+#>  float              0.3-2      2023-12-10 [1] CRAN (R 4.3.1)
+#>  fontawesome        0.5.2      2023-08-19 [1] CRAN (R 4.3.0)
+#>  forcats          * 1.0.0      2023-01-29 [1] CRAN (R 4.3.0)
+#>  fs                 1.6.3      2023-07-20 [1] CRAN (R 4.3.0)
+#>  generics           0.1.3      2022-07-05 [1] CRAN (R 4.3.0)
+#>  GenomeInfoDb       1.38.7     2024-03-09 [1] Bioconductor 3.18 (R 4.3.3)
+#>  GenomeInfoDbData   1.2.11     2024-03-18 [1] Bioconductor
+#>  ggforce            0.4.2      2024-02-19 [1] CRAN (R 4.3.1)
+#>  ggfun              0.1.4      2024-01-19 [1] CRAN (R 4.3.1)
+#>  ggplot2          * 3.5.0      2024-02-23 [1] CRAN (R 4.3.1)
+#>  ggplotify          0.1.2      2023-08-09 [1] CRAN (R 4.3.0)
+#>  ggraph             2.2.1      2024-03-07 [1] CRAN (R 4.3.1)
+#>  ggrepel            0.9.5      2024-01-10 [1] CRAN (R 4.3.1)
+#>  ggtree             3.10.1     2024-02-27 [1] Bioconductor 3.18 (R 4.3.2)
+#>  glue               1.7.0      2024-01-09 [1] CRAN (R 4.3.1)
+#>  GO.db              3.18.0     2024-03-18 [1] Bioconductor
+#>  GOSemSim           2.28.1     2024-01-20 [1] Bioconductor 3.18 (R 4.3.2)
+#>  graphlayouts       1.1.1      2024-03-09 [1] CRAN (R 4.3.1)
+#>  gridExtra          2.3        2017-09-09 [1] CRAN (R 4.3.0)
+#>  gridGraphics       0.5-1      2020-12-13 [1] CRAN (R 4.3.0)
+#>  gson               0.1.0      2023-03-07 [1] CRAN (R 4.3.0)
+#>  gt               * 0.11.0     2024-07-09 [1] CRAN (R 4.3.3)
+#>  gtable             0.3.4      2023-08-21 [1] CRAN (R 4.3.0)
+#>  HDO.db             0.99.1     2024-03-18 [1] Bioconductor
+#>  highr              0.10       2022-12-22 [1] CRAN (R 4.3.0)
+#>  hms                1.1.3      2023-03-21 [1] CRAN (R 4.3.0)
+#>  htmltools          0.5.7      2023-11-03 [1] CRAN (R 4.3.1)
+#>  httr               1.4.7      2023-08-15 [1] CRAN (R 4.3.0)
+#>  igraph             2.0.3      2024-03-13 [1] CRAN (R 4.3.1)
+#>  IRanges          * 2.36.0     2023-10-26 [1] Bioconductor
+#>  jquerylib          0.1.4      2021-04-26 [1] CRAN (R 4.3.0)
+#>  jsonlite           1.8.8      2023-12-04 [1] CRAN (R 4.3.1)
+#>  KEGGREST           1.42.0     2023-10-26 [1] Bioconductor
+#>  knitr              1.45       2023-10-30 [1] CRAN (R 4.3.1)
+#>  lattice            0.22-5     2023-10-24 [1] CRAN (R 4.3.3)
+#>  lazyeval           0.2.2      2019-03-15 [1] CRAN (R 4.3.0)
+#>  lgr                0.4.4      2022-09-05 [1] CRAN (R 4.3.0)
+#>  lifecycle          1.0.4      2023-11-07 [1] CRAN (R 4.3.1)
+#>  lubridate        * 1.9.3      2023-09-27 [1] CRAN (R 4.3.1)
+#>  magrittr           2.0.3      2022-03-30 [1] CRAN (R 4.3.0)
+#>  MASS               7.3-60.0.1 2024-01-13 [1] CRAN (R 4.3.3)
+#>  Matrix             1.6-5      2024-01-11 [1] CRAN (R 4.3.3)
+#>  memoise            2.0.1      2021-11-26 [1] CRAN (R 4.3.0)
+#>  mlapi              0.1.1      2022-04-24 [1] CRAN (R 4.3.0)
+#>  munsell            0.5.0      2018-06-12 [1] CRAN (R 4.3.0)
+#>  nlme               3.1-164    2023-11-27 [1] CRAN (R 4.3.3)
+#>  org.Hs.eg.db     * 3.18.0     2024-03-18 [1] Bioconductor
+#>  patchwork          1.2.0      2024-01-08 [1] CRAN (R 4.3.1)
+#>  pillar             1.9.0      2023-03-22 [1] CRAN (R 4.3.0)
+#>  pkgconfig          2.0.3      2019-09-22 [1] CRAN (R 4.3.0)
+#>  pkgdown            2.0.7      2022-12-14 [1] CRAN (R 4.3.0)
+#>  plyr               1.8.9      2023-10-02 [1] CRAN (R 4.3.1)
+#>  png                0.1-8      2022-11-29 [1] CRAN (R 4.3.0)
+#>  polyclip           1.10-6     2023-09-27 [1] CRAN (R 4.3.1)
+#>  proxy            * 0.4-27     2022-06-09 [1] CRAN (R 4.3.0)
+#>  purrr            * 1.0.2      2023-08-10 [1] CRAN (R 4.3.0)
+#>  qvalue             2.34.0     2023-10-26 [1] Bioconductor
+#>  R6                 2.5.1      2021-08-19 [1] CRAN (R 4.3.0)
+#>  ragg               1.3.0      2024-03-13 [1] CRAN (R 4.3.1)
+#>  RColorBrewer       1.1-3      2022-04-03 [1] CRAN (R 4.3.0)
+#>  Rcpp               1.0.12     2024-01-09 [1] CRAN (R 4.3.1)
+#>  RCurl              1.98-1.14  2024-01-09 [1] CRAN (R 4.3.1)
+#>  readr            * 2.1.5      2024-01-10 [1] CRAN (R 4.3.1)
+#>  reshape2           1.4.4      2020-04-09 [1] CRAN (R 4.3.0)
+#>  RhpcBLASctl        0.23-42    2023-02-11 [1] CRAN (R 4.3.0)
+#>  rlang              1.1.3      2024-01-10 [1] CRAN (R 4.3.1)
+#>  rmarkdown          2.26       2024-03-05 [1] CRAN (R 4.3.1)
+#>  rsparse            0.5.2      2024-06-28 [1] CRAN (R 4.3.3)
+#>  RSQLite            2.3.5      2024-01-21 [1] CRAN (R 4.3.1)
+#>  rstudioapi         0.15.0     2023-07-07 [1] CRAN (R 4.3.0)
+#>  S4Vectors        * 0.40.2     2023-11-25 [1] Bioconductor 3.18 (R 4.3.2)
+#>  sass               0.4.9      2024-03-15 [1] CRAN (R 4.3.1)
+#>  scales             1.3.0      2023-11-28 [1] CRAN (R 4.3.1)
+#>  scatterpie         0.2.1      2023-06-07 [1] CRAN (R 4.3.0)
+#>  sessioninfo        1.2.2      2021-12-06 [1] CRAN (R 4.3.0)
+#>  shadowtext         0.1.3      2024-01-19 [1] CRAN (R 4.3.1)
+#>  stringi            1.8.3      2023-12-11 [1] CRAN (R 4.3.1)
+#>  stringr          * 1.5.1      2023-11-14 [1] CRAN (R 4.3.1)
+#>  systemfonts        1.1.0      2024-05-15 [1] CRAN (R 4.3.3)
+#>  text2vec         * 0.6.4      2023-11-09 [1] CRAN (R 4.3.1)
+#>  textshaping        0.3.7      2023-10-09 [1] CRAN (R 4.3.1)
+#>  tibble           * 3.2.1      2023-03-20 [1] CRAN (R 4.3.0)
+#>  tidygraph          1.3.1      2024-01-30 [1] CRAN (R 4.3.1)
+#>  tidyr            * 1.3.1      2024-01-24 [1] CRAN (R 4.3.1)
+#>  tidyselect         1.2.1      2024-03-11 [1] CRAN (R 4.3.1)
+#>  tidytree           0.4.6      2023-12-12 [1] CRAN (R 4.3.1)
+#>  tidyverse        * 2.0.0      2023-02-22 [1] CRAN (R 4.3.0)
+#>  timechange         0.3.0      2024-01-18 [1] CRAN (R 4.3.1)
+#>  treeio             1.26.0     2023-11-06 [1] Bioconductor
+#>  tweenr             2.0.3      2024-02-26 [1] CRAN (R 4.3.1)
+#>  tzdb               0.4.0      2023-05-12 [1] CRAN (R 4.3.0)
+#>  utf8               1.2.4      2023-10-22 [1] CRAN (R 4.3.1)
+#>  vctrs              0.6.5      2023-12-01 [1] CRAN (R 4.3.1)
+#>  viridis            0.6.5      2024-01-29 [1] CRAN (R 4.3.1)
+#>  viridisLite        0.4.2      2023-05-02 [1] CRAN (R 4.3.0)
+#>  withr              3.0.0      2024-01-16 [1] CRAN (R 4.3.1)
+#>  xfun               0.42       2024-02-08 [1] CRAN (R 4.3.1)
+#>  xml2               1.3.6      2023-12-04 [1] CRAN (R 4.3.1)
+#>  XVector            0.42.0     2023-10-26 [1] Bioconductor
+#>  yaml               2.3.8      2023-12-11 [1] CRAN (R 4.3.1)
+#>  yulab.utils        0.1.4      2024-01-28 [1] CRAN (R 4.3.1)
+#>  zlibbioc           1.48.0     2023-10-26 [1] Bioconductor
+#> 
+#>  [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
+#> 
+#> ──────────────────────────────────────────────────────────────────────────────
+
+
+
+ + + + +
+ + + + + + + diff --git a/articles/c_fusing_files/figure-html/unnamed-chunk-4-1.png b/articles/c_fusing_files/figure-html/unnamed-chunk-4-1.png new file mode 100644 index 0000000..055727f Binary files /dev/null and b/articles/c_fusing_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/articles/c_fusing_files/figure-html/unnamed-chunk-6-1.png b/articles/c_fusing_files/figure-html/unnamed-chunk-6-1.png new file mode 100644 index 0000000..f8c0e69 Binary files /dev/null and b/articles/c_fusing_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/articles/c_gsea.html b/articles/c_gsea.html index 56c84cf..98484b5 100644 --- a/articles/c_gsea.html +++ b/articles/c_gsea.html @@ -26,7 +26,7 @@ EnrichGT - 0.2.3 + 0.2.5