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Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer

DIR@IMTECH: CSIR-Institute of Microbial Technology

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Title Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer
 
Creator Bhalla, Sherry
Chaudhary, Kumardeep
Kumar, Ritesh
Sehgal, Manika
Kaur, Harpreet
Sharma, Suresh
Raghava, G.P.S.
 
Subject QR Microbiology
 
Description In this study, an attempt has been made to identify expression-based gene biomarkers that can discriminate early and late stage of clear cell renal cell carcinoma (ccRCC) patients. We have analyzed the gene expression of 523 samples to identify genes that are differentially expressed in the early and late stage of ccRCC. First, a threshold-based method has been developed, which attained a maximum accuracy of 71.12% with ROC 0.67 using single gene NR3C2. To improve the performance of threshold-based method, we combined two or more genes and achieved maximum accuracy of 70.19% with ROC of 0.74 using eight genes on the validation dataset. These eight genes include four underexpressed (NR3C2, ENAM, DNASE1L3, FRMPD2) and four overexpressed (PLEKHA9, MAP6D1, SMPD4, C11orf73) genes in the late stage of ccRCC. Second, models were developed using state-of-art techniques and achieved maximum accuracy of 72.64% and 0.81 ROC using 64 genes on validation dataset. Similar accuracy was obtained on 38 genes selected from subset of genes, involved in cancer hallmark biological processes. Our analysis further implied a need to develop gender-specific models for stage classification. A web server, CancerCSP, has been developed to predict stage of ccRCC using gene expression data derived from RNAseq experiments.
 
Publisher Nature Publishing Group
 
Date 2017
 
Type Article
PeerReviewed
 
Relation http://dx.doi.org/10.1038/srep44997
http://crdd.osdd.net/open/2031/
 
Identifier Bhalla, Sherry and Chaudhary, Kumardeep and Kumar, Ritesh and Sehgal, Manika and Kaur, Harpreet and Sharma, Suresh and Raghava, G.P.S. (2017) Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer. Scientific Reports, 7. ISSN 2045-2322