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Bioinformation. 2019 Nov 10;15(10):772-779. doi: 10.6026/97320630015772. eCollection 2019.

Detection and analysis of stable and flexible genes towards a genome signature framework in cancer.

Author information

1
International Burch University Sarajevo, Francuske Revolucije BB, 71210 Sarajevo.
2
Sarajevo School of Science and Technology, Hrasnicka Cesta 3a, 71210 Sarajevo.
3
The University of Leipzig, Faculty of Physics and Earth Science, Peter Debye Institute for Soft Matter Physics, LinnestraBe 5, 04103 Leipzig, Germany.

Abstract

Comparison and detection of stable cancer genes across cancer types is of interest. The gene expression data of 6 different cancer types (colon, breast, lung, ovarian, brain and renal) and a control group from The Cancer Genome Atlas (TCGA) database were used in this study. The comparison of gene expression data together with the calculation standard deviations of such data was completed using a statistical model for the detection of stable genes. Genes having similar expression (referred as flexible genes) pattern to the control group in four out of six cancer types are PATE, NEUROD4 and TRAFD1. Moreover, 13 genes showed low difference compared to the control group with low standard deviation across cancer types (referred as stable genes). Among them, genes GDF2, KCNT1 and RNF151 showed consistent low expression while ODF4, OR5I1, MYOG and OR2B11 showed consistent high expression. Thus, the detection and analysis of stable and flexible cancer genes help towards the design and development of a framework (outline) for specific genome signature (biomarker) in cancer.

KEYWORDS:

Cancer; cancer types; flexible; gene expression; model; pattern analysis; stable; statistics

Conflict of interest statement

The authors declare that they have no conflict of interests.

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