Get Start
getStart.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/EnrichGTGet Start
Enrich the enriched result (enrich^2)
First enrich genes by clusterProfiler…
ego <- enrichGO(gene = gene,
universe = names(geneList),
OrgDb = org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
pvalueCutoff = 0.5,
qvalueCutoff = 0.5,
readable = TRUE)Then, run obj |> EnrichGT() !
obj <- ego |> EnrichGT()
#> ℹ =====[SUGGESTION]=====
#> You are passing an object from GO Enrichment.
#> Please ensure that `obj |> clusterProfiler::simplify()` is executed, to pre-simplify result,
#> For better enriched result.
#> Loading required package: text2vec
#>
#> Attaching package: 'text2vec'
#> The following object is masked from 'package:BiocGenerics':
#>
#> normalize
obj@gt_object| Parse form: ego | ||||
| Split into 17 Clusters. Generated by github@zhimingye/EnrichGT | ||||
| Description | Count | PCT | Padj | geneID |
|---|---|---|---|---|
| Cluster_1 | ||||
|
nuclear chromosome segregation
GO:0098813
|
33 | 17.0 | 6.7e-18 | CDCA8, CDC20, KIF23, CENPE, MYBL2, CCNB2, NDC80, TOP2A, NCAPH, ASPM, DLGAP5, UBE2C, NUSAP1, TPX2, TACC3, NEK2, CDK1, MAD2L1, KIF18A, CDT1, BIRC5, KIF11, TTK, NCAPG, AURKB, TRIP13, PRC1, KIFC1, KIF18B, AURKA, CCNB1, KIF4A, PTTG1 |
|
chromosome segregation
GO:0007059
|
37 | 19.0 | 6.7e-18 | CDCA8, CDC20, KIF23, CENPE, MYBL2, CCNB2, NDC80, TOP2A, NCAPH, ASPM, DLGAP5, UBE2C, HJURP, SKA1, NUSAP1, TPX2, TACC3, NEK2, CENPM, CENPN, CDK1, MAD2L1, KIF18A, CDT1, BIRC5, KIF11, TTK, NCAPG, AURKB, TRIP13, PRC1, KIFC1, KIF18B, AURKA, CCNB1, KIF4A, PTTG1 |
|
mitotic sister chromatid segregation
GO:0000070
|
27 | 14.0 | 2.1e-17 | CDCA8, CDC20, KIF23, CENPE, MYBL2, NDC80, NCAPH, DLGAP5, UBE2C, NUSAP1, TPX2, NEK2, CDK1, MAD2L1, KIF18A, CDT1, BIRC5, KIF11, TTK, NCAPG, AURKB, TRIP13, PRC1, KIFC1, KIF18B, CCNB1, KIF4A |
|
sister chromatid segregation
GO:0000819
|
29 | 15.0 | 2.2e-17 | CDCA8, CDC20, KIF23, CENPE, MYBL2, NDC80, TOP2A, NCAPH, DLGAP5, UBE2C, NUSAP1, TPX2, TACC3, NEK2, CDK1, MAD2L1, KIF18A, CDT1, BIRC5, KIF11, TTK, NCAPG, AURKB, TRIP13, PRC1, KIFC1, KIF18B, CCNB1, KIF4A |
|
mitotic nuclear division
GO:0140014
|
31 | 16.0 | 4.1e-17 | CDCA8, CDC20, KIF23, CENPE, MYBL2, NDC80, NCAPH, DLGAP5, UBE2C, NUSAP1, TPX2, NEK2, UBE2S, CDK1, MAD2L1, KIF18A, CDT1, BIRC5, KIF11, TTK, NCAPG, AURKB, CHEK1, TRIP13, PRC1, KIFC1, KIF18B, AURKA, CCNB1, KIF4A, BMP4 |
|
nuclear division
GO:0000280
|
36 | 18.0 | 5.3e-17 | CDCA8, CDC20, KIF23, CENPE, MYBL2, CCNB2, NDC80, TOP2A, NCAPH, ASPM, DLGAP5, UBE2C, NUSAP1, TPX2, NEK2, RAD51AP1, UBE2S, CDK1, MAD2L1, KIF18A, CDT1, BIRC5, KIF11, TTK, NCAPG, AURKB, CHEK1, TRIP13, PRC1, KIFC1, KIF18B, AURKA, CCNB1, KIF4A, PTTG1, BMP4 |
|
organelle fission
GO:0048285
|
37 | 19.0 | 1.7e-16 | CDCA8, CDC20, KIF23, CENPE, MYBL2, CCNB2, NDC80, TOP2A, NCAPH, ASPM, DLGAP5, UBE2C, NUSAP1, TPX2, NEK2, RAD51AP1, UBE2S, CDK1, MAD2L1, KIF18A, CDT1, BIRC5, KIF11, TTK, NCAPG, AURKB, CHEK1, TRIP13, PRC1, KIFC1, KIF18B, AURKA, CCNB1, KIF4A, PTTG1, BMP4, MAPT |
|
microtubule cytoskeleton organization involved in mitosis
GO:1902850
|
23 | 12.0 | 1.9e-14 | CDCA8, CDC20, KIF23, CENPE, MYBL2, NDC80, DLGAP5, NUSAP1, TPX2, TACC3, NEK2, CDK1, MAD2L1, PAX6, BIRC5, KIF11, TTK, AURKB, PRC1, KIFC1, AURKA, CCNB1, KIF4A |
|
chromosome organization
GO:0051276
|
38 | 19.0 | 1.4e-13 | CDC45, CDCA8, CDC20, KIF23, CENPE, MYBL2, NDC80, TOP2A, NCAPH, DLGAP5, UBE2C, HJURP, NUSAP1, TPX2, TACC3, NEK2, CENPN, CDK1, MAD2L1, GINS1, KIF18A, CDT1, BIRC5, KIF11, EZH2, TTK, NCAPG, AURKB, GINS2, TRIP13, PRC1, KIFC1, KIF18B, CCNB1, KIF4A, MCM5, PTTG1, MAPT |
|
cell division
GO:0051301
|
37 | 19.0 | 2.5e-12 | CDCA8, CDC20, KIF23, CENPE, CCNB2, NDC80, TOP2A, NCAPH, E2F8, ASPM, CEP55, UBE2C, SKA1, NUSAP1, CDCA3, TPX2, TACC3, NEK2, UBE2S, CCNA2, CDK1, ERCC6L, MAD2L1, PAX6, CDT1, BIRC5, KIF11, NCAPG, AURKB, PRC1, KIFC1, KIF18B, KIF20A, AURKA, CCNB1, KIF4A, PTTG1 |
| Cluster_2 | ||||
|
female meiotic nuclear division
GO:0007143
|
7 | 3.6 | 1.0e-05 | CCNB2, NDC80, TOP2A, NCAPH, TTK, TRIP13, AURKA |
|
meiotic nuclear division
GO:0140013
|
12 | 6.1 | 5.4e-05 | CDC20, CCNB2, NDC80, TOP2A, NCAPH, ASPM, RAD51AP1, KIF18A, TTK, TRIP13, AURKA, PTTG1 |
|
meiotic cell cycle process
GO:1903046
|
12 | 6.1 | 1.8e-04 | CDC20, CCNB2, NDC80, TOP2A, NCAPH, ASPM, RAD51AP1, KIF18A, TTK, TRIP13, AURKA, PTTG1 |
|
meiotic chromosome segregation
GO:0045132
|
8 | 4.1 | 2.3e-04 | CCNB2, NDC80, NCAPH, ASPM, TTK, TRIP13, AURKA, PTTG1 |
|
meiotic cell cycle
GO:0051321
|
13 | 6.6 | 5.8e-04 | CDC20, CCNB2, NDC80, TOP2A, NCAPH, ASPM, NEK2, RAD51AP1, KIF18A, TTK, TRIP13, AURKA, PTTG1 |
|
DNA replication
GO:0006260
|
14 | 7.1 | 8.8e-04 | CDC45, MCM10, E2F8, RRM2, CCNA2, CDK1, GINS1, CDT1, GINS2, CHAF1B, CHEK1, DTL, MCM5, DACH1 |
|
meiosis I cell cycle process
GO:0061982
|
8 | 4.1 | 3.2e-03 | CDC20, CCNB2, NDC80, TOP2A, RAD51AP1, TRIP13, AURKA, PTTG1 |
|
female gamete generation
GO:0007292
|
9 | 4.6 | 3.3e-03 | CCNB2, NDC80, TOP2A, NCAPH, ASPM, TTK, TRIP13, AURKA, PGR |
|
meiosis I
GO:0007127
|
7 | 3.6 | 1.1e-02 | CCNB2, NDC80, TOP2A, RAD51AP1, TRIP13, AURKA, PTTG1 |
|
cell cycle DNA replication
GO:0044786
|
5 | 2.6 | 1.2e-02 | CDC45, E2F8, GINS1, CDT1, DACH1 |
| Cluster_3 | ||||
|
antimicrobial humoral immune response mediated by antimicrobial peptide
GO:0061844
|
9 | 4.6 | 4.4e-05 | S100A9, S100A7, CXCL10, CXCL13, CXCL11, CAMP, CXCL9, GNLY, CXCL14 |
|
antimicrobial humoral response
GO:0019730
|
10 | 5.1 | 1.2e-04 | S100A9, S100A7, CXCL10, CXCL13, CXCL11, CAMP, CXCL9, GNLY, RNASE4, CXCL14 |
|
chemokine-mediated signaling pathway
GO:0070098
|
8 | 4.1 | 2.3e-03 | CXCL10, CXCL13, CXCL11, CXCL9, CCL18, CCL8, ACKR1, CX3CR1 |
|
lymphocyte chemotaxis
GO:0048247
|
6 | 3.1 | 3.3e-03 | S100A7, CXCL10, CXCL13, CXCL11, CCL18, CCL8 |
|
granulocyte chemotaxis
GO:0071621
|
9 | 4.6 | 3.5e-03 | S100A9, S100A8, S100A7, CXCL10, CXCL13, CXCL11, CXCL9, CCL18, CCL8 |
|
response to chemokine
GO:1990868
|
8 | 4.1 | 3.8e-03 | CXCL10, CXCL13, CXCL11, CXCL9, CCL18, CCL8, ACKR1, CX3CR1 |
|
cellular response to chemokine
GO:1990869
|
8 | 4.1 | 3.8e-03 | CXCL10, CXCL13, CXCL11, CXCL9, CCL18, CCL8, ACKR1, CX3CR1 |
|
humoral immune response
GO:0006959
|
12 | 6.1 | 4.0e-03 | S100A9, S100A7, CXCL10, CXCL13, CXCL11, CAMP, CXCL9, GNLY, RNASE4, C7, CXCL14, GATA3 |
|
neutrophil chemotaxis
GO:0030593
|
8 | 4.1 | 4.2e-03 | S100A9, S100A8, CXCL10, CXCL13, CXCL11, CXCL9, CCL18, CCL8 |
|
response to molecule of bacterial origin
GO:0002237
|
15 | 7.7 | 4.6e-03 | S100A9, S100A8, S100A7, CXCL10, CXCL13, CXCL11, SLC7A5, CAMP, CXCL9, INAVA, IDO1, MAOB, PCK1, HMGCS2, CX3CR1 |
| Cluster_4 | ||||
|
cell cycle G2/M phase transition
GO:0044839
|
11 | 5.6 | 3.6e-04 | FOXM1, MELK, CCNB2, NDC80, CCNA2, CDK1, AURKB, CHEK1, DTL, AURKA, CCNB1 |
|
G2/M transition of mitotic cell cycle
GO:0000086
|
9 | 4.6 | 3.9e-03 | FOXM1, MELK, CCNA2, CDK1, AURKB, CHEK1, DTL, AURKA, CCNB1 |
| Cluster_8 | ||||
|
microtubule-based movement
GO:0007018
|
12 | 6.1 | 3.1e-02 | KIF23, CENPE, DLGAP5, KIF18A, KIF11, KIFC1, KIF18B, KIF20A, KIF4A, MAPT, TRIM58, CFAP69 |
For further guidance, see other Articles.
Session info
sessioninfo::session_info()
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