PERT-P100-PRM_VORINOSTAT

LinkedOmicsKB © 2022-2023 Zhang Lab

Basic information

Phenotype
PERT-P100-PRM_VORINOSTAT
Description
Enrichment score representing phosphorylation alterations after vorinostat. 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
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.

protein-8-6-4-20246metapBRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC
RNA-4-2024681012metapBRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC

Association of protein abundance of genes

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Signed p-values
Gene
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
No matching records found

* P-values for individual cohorts can be clicked to show the data plots. The rows in the table can be expanded to show results from other omics.

Gene set enrichment analysis

Submit genes and the common logarithm of the p-values of their association with PERT-P100-PRM_VORINOSTAT 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.

-3-2-101234567891011metapBRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC
Loading, please wait
Signed p-values
Gene
Protein
Site
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
No matching records found

* P-values for individual cohorts can be clicked to show the data plots.

Gene set enrichment analysis

Submit phosphorylation sites and the common logarithm of the p-values of their association with PERT-P100-PRM_VORINOSTAT to WebGestalt.