This tab shows an overview of the selected study/paper [more details]
Reference

Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma.

Paper Id
COSP28262
Authors
Guo G,Gui Y,Gao S,Tang A,Hu X,Huang Y,Jia W,Li Z,He M,Sun L,Song P,Sun X,Zhao X,Yang S,Liang C,Wan S,Zhou F,Chen C,Zhu J,Li X,Jian M,Zhou L,Ye R,Huang P,Chen J,Jiang T,Liu X,Wang Y,Zou J,Jiang Z,Wu R,Wu S,Fan F,Zhang Z,Liu L,Yang R,Liu X,Wu H,Yin W,Zhao X,Liu Y,Peng H,Jiang B,Feng Q,Li C,Xie J,Lu J,Kristiansen K,Li Y,Zhang X,Li S,Wang J,Yang H,Cai Z and Wang J
Affiliation
Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen, China.
Journal
Nature genetics 2012;44(1):17-9
ISSN:1546-1718
PUBMED:22138691
Abstract
We sequenced whole exomes of ten clear cell renal cell carcinomas (ccRCCs) and performed a screen of ∼1,100 genes in 88 additional ccRCCs, from which we discovered 12 previously unidentified genes mutated at elevated frequencies in ccRCC. Notably, we detected frequent mutations in the ubiquitin-mediated proteolysis pathway (UMPP), and alterations in the UMPP were significantly associated with overexpression of HIF1α and HIF2α in the tumors (P = 0.01 and 0.04, respectively). Our findings highlight the potential contribution of UMPP to ccRCC tumorigenesis through the activation of the hypoxia regulatory network.
Paper Status
Curated
Genes Analysed
1185
Mutated Samples
81
Total No. of Samples
98
This tab shows genes with mutations in the selected study/paper [more details]
Genes Samples CDS Mutation AA Mutation
This tab shows genes without mutations in the selected study/paper [more details]
Non-Mutant Genes Gene Id (COSG)
This tab shows samples without mutations in the selected study/paper [more details]
Non-Mutant Samples Sample Id (COSS)
This tab shows mutated samples in the selected study/paper [more details]
Sample Name Mutation Count
This tab shows non coding variant in the selected study/paper [more details]
Sample ID Sample Name ID NCV Annotation Zygosity Chromosome Genome start Genome stop Genome version Strand WT seq Mut seq
This tab shows the gene expression and copy number variation data for this study. [more details]

Table Information

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The table currently shows only high value (numeric) copy number data. Copy number segments are excluded if the total copy number and minor allele values are unknown.

Click here to include all copy number data. For more detailed information about copy number data and gain/loss definitions click here.

Sample Gene Expression Expr Level (Z-Score)

Over Expressed; Z-Score > 2.0

Under Expressed; Z-Score < -2.0

Normal; Z-Score within the range -2.0 to 2.0

CN Type Minor Allele Copy Number CN Segment Posn. Average Ploidy

1. N/A represents cases where the average ploidy value is not available( mostly ICGC samples). For some TCGA samples where the minor allele information is not available the average ploidy value could not be calculated.

2. For TCGA samples, the ASCAT algorithm was used to calculate the average ploidy.

3. For CGP samples, the PICNIC algorithm was used to calculate the average ploidy.

CNV
This tab shows a summary table with counts (number of samples) for CNV gain/loss and under/over expression for all genes. [more details]

The results shown in this table are derived from all copy number data. This includes non-numeric data with descriptive definitions of gain/loss.

  Copy Number Expression
Gene Gain Loss Tested Over Under Tested
This tab shows the fusion mutations observed in this sample [more details]
Gene Sample Name Id Sample(COSS) CDS Mutation Somatic status Zygosity Validated Type