Journal Article

The exploration of disease-specific gene regulatory networks in esophageal carcinoma and stomach adenocarcinoma

Qin, Guimin, Liu, Jiayan, Yang, Luqiong, Ma, Yuying, Huo, Qiuyan

2019

Overview

Background Feed-forward loops (FFLs), consisting of miRNAs, transcription factors (TFs) and their common target genes, have been validated to be important for the initialization and development of complex diseases, including cancer. Esophageal Carcinoma (ESCA) and Stomach Adenocarcinoma (STAD) are two types of malignant tumors in the digestive tract. Understanding common and distinct molecular mechanisms of ESCA and STAD is extremely crucial. Results In this paper, we presented a computational framework to explore common and distinct FFLs, and molecular biomarkers for ESCA and STAD. We identified FFLs by combining regulation pairs and RNA-seq data. Then we constructed disease-specific co-expression networks based on the FFLs identified. We also used random walk with restart (RWR) on disease-specific co-expression networks to prioritize candidate molecules. We identified 148 and 242 FFLs for these two types of cancer, respectively. And we found that one TF, E2F3 was related to ESCA, two genes, DTNA and KCNMA1 were related to STAD, while one TF ESR1 and one gene KIT were associated with both of the two types of cancer. Conclusions This proposed computational framework predicted disease-related biomolecules effectively and discovered the correlation between two types of cancers, which helped develop the diagnostic and therapeutic strategies of Esophageal Carcinoma and Stomach Adenocarcinoma.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Adenocarcinoma / Adenocarcinoma - genetics / Algorithms / Area Under Curve / Bioinformatics / Biological markers / Biomarkers / Biomedical and Life Sciences / Biomolecules / Biotechnology / Cancer / Cancer genetics / Carcinoma / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Computer applications / Diagnostic systems / Disease / DNA binding proteins / DNA methylation / Esophageal cancer / Esophageal carcinoma / Esophageal Neoplasms - genetics / Esophagus / ESR1 protein / Feed-forward loop / Gastric cancer / Gastrointestinal tract / Gene expression / Gene Expression Profiling / Gene Expression Regulation, Neoplastic / Gene Regulatory Networks / Genes / Genetic aspects / Genetic research / Humans / Life Sciences / Medical research / Microarrays / MicroRNA / MicroRNAs - genetics / MicroRNAs - metabolism / Molecular mechanism / Molecular modelling / Networks / Oncogenes / Probability / PubMed / Random walk / Random walk with restart / Researchers / Ribonucleic acid / RNA / Stomach / Stomach adenocarcinoma / Stomach Neoplasms - genetics / Transcription (Genetics) / Transcription factors / Transcription Factors - genetics / Transcription Factors - metabolism / Tumors