Basic information
- Phenotype
- HALLMARK_BILE_ACID_METABOLISM
- Description
- Enrichment score representing genes involved in bile acid metabolism. The score was calculated using ssGSEA on the RNA data (Z-score transformed coding genes with expression in at least 50% of the samples in a cohort).
- Source
- http://www.gsea-msigdb.org/gsea/msigdb/cards/HALLMARK_BILE_ACID_METABOLISM.html
- Method
- Single sample gene set enrichment analysis (ssGSEA) was performed for each cancer type using gene-wise Z-scores of the RNA expression data (RSEM) for the MSigDB Hallmark gene sets v7.0 (PMID: 26771021) via the ssGSEA2.0 R package (PMID: 30563849). RNA data were filtered to coding genes with < 50% 0 expression. (Parameters: sample.norm.type="rank", weight=0.75, statistic="area.under.RES", nperm=1000, min.overlap=10). Pathway activity scores are normalized enrichment scores from ssGSEA.
- Genes
-
- ABCA2
- ABCA3
- ABCA4
- ABCA5
- ABCA6
- ABCA8
- ABCA9
- ABCD1
- ABCD2
- ABCD3
- ABCG4
- ABCG8
- ACSL1
- ACSL5
- AGXT
- AKR1D1
- ALDH1A1
- ALDH8A1
- ALDH9A1
- AMACR
- APOA1
- AQP9
- AR
- ATXN1
- BBOX1
- BCAR3
- BMP6
- CAT
- CH25H
- CROT
- CYP27A1
- CYP39A1
- CYP46A1
- CYP7A1
- CYP7B1
- CYP8B1
- DHCR24
- DIO1
- DIO2
- EFHC1
- EPHX2
- FADS1
- FADS2
- FDXR
- GC
- GCLM
- GNMT
- GNPAT
- GSTK1
- HACL1
- HAO1
- HSD17B11
- HSD17B4
- HSD17B6
- HSD3B1
- HSD3B7
- IDH1
- IDH2
- IDI1
- ISOC1
- KLF1
- LCK
- LIPE
- LONP2
- MLYCD
- NEDD4
- NPC1
- NR0B2
- NR1H4
- NR1I2
- NR3C2
- NUDT12
- OPTN
- PAOX
- PECR
- PEX1
- PEX11A
- PEX11G
- PEX12
- PEX13
- PEX16
- PEX19
- PEX26
- PEX6
- PEX7
- PFKM
- PHYH
- PIPOX
- PNPLA8
- PRDX5
- PXMP2
- RBP1
- RETSAT
- RXRA
- RXRG
- SCP2
- SERPINA6
- SLC22A18
- SLC23A1
- SLC23A2
- SLC27A2
- SLC27A5
- SLC29A1
- SLC35B2
- SLCO1A2
- SOAT2
- SOD1
- SULT1B1
- SULT2B1
- TFCP2L1
- TTR
- More...
Gene association
Number of significant genes with P-value ≤ 10-6 for each cohorts are summarized in bar plots. The scatter plot highlights significant associations diven by protein rather than mRNA abundance.
Association of protein abundance of genes
| Signed p-values | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | Meta P | BRCA | CCRCC | COAD | GBM | HNSCC | LSCC | LUAD | OV | PDAC | UCEC |
Gene set enrichment analysis
Submit genes and the common logarithm of the p-values of their association with HALLMARK_BILE_ACID_METABOLISM to WebGestalt.
Phosphosite association
Number of significant genes with P-value ≤ 10-6 for each cohorts are summarized in the bar plot. The scatter plot highlights significant associations diven by phosphorylation rather than protein abundance.
| Signed p-values | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | Protein | Site | Meta P | BRCA | CCRCC | COAD | GBM | HNSCC | LSCC | LUAD | OV | PDAC | UCEC |
Gene set enrichment analysis
Submit phosphorylation sites and the common logarithm of the p-values of their association with HALLMARK_BILE_ACID_METABOLISM to WebGestalt.