Phenotype: KINASE-PSP

Basic information

Phenotype

KINASE-PSP_AMPKA1/PRKAA1

Description

Enrichment score representing kinase activity of AMPK alpha 1. 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

PFKFB2 S466

PFKFB3 S461

PIAS1 S510

PPP1R12C S452

PRKAA1 S496

PRKAB1 S108

RPTOR S722

SNX17 S437

TBC1D1 S237

USP10 S76

YAP1 S61

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

* 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 KINASE-PSP_AMPKA1/PRKAA1 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

* 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 KINASE-PSP_AMPKA1/PRKAA1 to WebGestalt.