Platform-independent gene expression signature differentiates sessile serrated adenomas/polyps and hyperplastic polyps of the colon

BMC Medical Genomics
Yasir RahmatallahGalina Glazko

Abstract

Sessile serrated adenomas/polyps are distinguished from hyperplastic colonic polyps subjectively by their endoscopic appearance and histological morphology. However, hyperplastic and sessile serrated polyps can have overlapping morphological features resulting in sessile serrated polyps diagnosed as hyperplastic. While sessile serrated polyps can progress into colon cancer, hyperplastic polyps have virtually no risk for colon cancer. Objective measures, differentiating these types of polyps would improve cancer prevention and treatment outcome. RNA-seq training data set and Affimetrix, Illumina testing data sets were obtained from Gene Expression Omnibus (GEO). RNA-seq single-end reads were filtered with FastX toolkit. Read mapping to the human genome, gene abundance estimation, and differential expression analysis were performed with Tophat-Cufflinks pipeline. Background correction, normalization, and probe summarization steps for Affimetrix arrays were performed using the robust multi-array method (RMA). For Illumina arrays, log2-scale expression data was obtained from GEO. Pathway analysis was implemented using Bioconductor package GSAR. To build a platform-independent molecular classifier that accurately differentiates sess...Continue Reading

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Citations

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Datasets Mentioned

BETA
GSE43841
GSE10714
GSE45270

Methods Mentioned

BETA
biopsy
gene array
reverse transcription PCR
RNA-seq
biopsies
GTPase

Related Concepts

CHFR protein, human
TRIB2 protein, human
GBP2 protein, human
Poly-ADP-Ribose Binding Proteins
Adenoma, Trabecular
Malignant Tumor of Colon
Colonic Polyps
Hyperplasia
Neoplasm Proteins
Receptor Down-Regulation

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