Kidney Renal Papillary Cell Carcinoma: Association of mutation, copy number alteration, and subtype markers with pathways<BR>(primary solid tumor cohort)

Kidney Renal Papillary Cell Carcinoma: Association of mutation, copy number alteration, and subtype markers with pathways
(primary solid tumor cohort)

Maintained by Spring Yingchun Liu (Broad Institute)

- Overview

+ Introduction

- Summary

There are 6 genes with significant mutation (Q value <= 0.1) and 306 genes with significant copy number alteration (Q value <= 0.25). The identified marker genes (Q value <= 0.01 or within top 2000) are 0 for subtype 1. Pathways significantly enriched with these genes (Q value <= 0.01) are identified :

1 pathways significantly enriched with genes with copy number alteration or mutation.

0 pathways significantly enriched with marker genes of gene expression subtype 1

- Results

+ The top five pathways enriched with genes with copy number alteration or mutation

Pathway	Nof Genes	Nof CNV_Mut	Enrichment	P value	Q value
KEGG_RNA_DEGRADATION	55	8	3.3	0	0.0005
BIOCARTA_ATRBRCA_PATHWAY	21	3	3.2	0.0036	0.57
KEGG_SPLICEOSOME	126	6	1.8	0.0069	0.57
KEGG_ENDOCYTOSIS	183	8	1.6	0.0053	0.57
KEGG_RIBOSOME	87	5	2	0.0093	0.59

+ The top five pathways enriched with marker genes of gene expression subtype 1

Pathway	Nof Genes	Enrichment	P value	Q value
BIOCARTA_RELA_PATHWAY	16	NaN	1	1
BIOCARTA_NO1_PATHWAY	31	NaN	1	1
BIOCARTA_CSK_PATHWAY	24	NaN	1	1
BIOCARTA_AMI_PATHWAY	20	NaN	1	1
BIOCARTA_ARAP_PATHWAY	18	NaN	1	1

+ Methods & Data

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