Basic information
- Phenotype
- PERT-PSP_NOCODAZOLE
- Description
- Enrichment score representing phosphorylation alterations in response to nocodazole. The score was calculated using PTM-SEA on the phosphoproteomics data.
- Source
- https://proteomics.broadapps.org/ptmsigdb/
- Method
- Phosphosite signature scores were calculated using the PTMsigDB v1.9.0 database and the ssGSEA2.0 R package (PMID: 30563849). The parameters were the same as those used for Hallmark pathway activity (sample.norm.type="rank", weight=0.75, statistic="area.under.RES", nperm=1000, min.overlap=10). Phosphoproteomics data were filtered to the fifteenmer phosphosites with complete data across all samples within a cohort. If there were multiple rows with complete data for identical fifteenmers, one row was selected at random. Each site was z-score transformed. Activity scores are normalized enrichment scores from ssGSEA.
- Genes
-
- ANAPC1 S688
- CDC16 S560
- CDC23 T562
- CDCA8 S219
- CDK1 T161
- CKAP4 S17
- COPA S173
- CSNK2B S209
- DLG1 S158
- EIF2A S506
- FOXK2 S428
- GORASP2 T225
- GORASP2 T222
- H1-4 T146
- H2AX S140
- HNRNPU S59
- IARS1 S1047
- ILF3 T592
- JUN S63
- LIG1 S76
- MAD1L1 S428
- MAP4 S787
- MYO1C S408
- NCKAP5L S440
- NPM1 S254
- NPM1 T199
- NUP98 S612
- NUP98 S839
- PPP1R12A T696
- PSMA5 S16
- PTPN2 S304
- RANGAP1 S428
- RBM4 S86
- RIC8A S502
- RMI1 S284
- RPL12 S38
- RPS6KB1 S447
- RPS6KB1 T444
- SIRT2 S368
- SQSTM1 T269
- SQSTM1 S272
- STMN1 S16
- STMN1 S25
- STMN1 S38
- STMN1 S63
- TMPO S424
- TOP1 S112
- TP53 S315
- VIM S56
- 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 PERT-PSP_NOCODAZOLE 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 PERT-PSP_NOCODAZOLE to WebGestalt.