Statistical analysis of differential gene expression in colorectal cancer using CLEAR-test

• Published in: Journal of biological regulators and homeostatic agents Vol. 25; no. 2; p. 279
• Main Authors: Mazurek, U, Owczarek, A, Nowakowska-Zajdel, E, Wierzgon, J, Grochowska-Niedworok, E, Kokot, T, Muc-Wierzgon, M
• Format: Journal Article
• Language: English
• Published: Italy 01-04-2011
• Subjects: Adenocarcinoma - genetics; Adenocarcinoma - metabolism; Adenocarcinoma - pathology; Algorithms; Cluster Analysis; Colon - metabolism; Colon - pathology; Colorectal Neoplasms - genetics; Colorectal Neoplasms - metabolism; Colorectal Neoplasms - pathology; Data Interpretation, Statistical; Gene Expression Profiling - methods; Gene Expression Profiling - statistics & numerical data; Gene Expression Regulation, Neoplastic; Humans; Neoplasm Staging - methods
• ISSN: 0393-974X

CLEAR test provides a novel method of analysis by combining inference for differential expression and variability. Frozen tumor specimens from 14 (3 coded Stage I, 5 Stage II, 2 Stage III and 4 Stage IV) colon cancer patients were obtained. Archived primary tumor samples were collected at the time of surgery and normal colon mucosae (controls specimens) were also collected. The studied transcriptomes were clustered using hierarchical agglomeration with Ward's method and Tchebychev distance. The separable groups of transcriptomes were classified as high clinical stage of adenocarcinoma (HCS; stages II-IV), low clinical stage of adenocarcinoma (LCS; stages I and 3 controls), and two normal colon mucosae (controls N1 and N2). The results of the CLEAR-test algorithm in normal colon specimens and adenocarcinoma specimens with low and high clinical stage showed 50 most and 50 least significant genes. The list of differential genes (p<0.01) in normal colon specimens and adenocarcinoma specimens with low and high clinical stage presented 58 genes.