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Combinatorial Chemistry & High Throughput Screening

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ISSN (Print): 1386-2073
ISSN (Online): 1875-5402

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Research Article

Enrichment of Up-regulated and Down-regulated Gene Clusters Using Gene Ontology, miRNAs and lncRNAs in Colorectal Cancer

Author(s): Fahimeh Fattahi, Jafar Kiani, Mohsen Khosravi, Somayeh Vafaei, Asghar Mohammadi, Zahra Madjd* and Mohammad Najafi*

Volume 22, Issue 8, 2019

Page: [534 - 545] Pages: 12

DOI: 10.2174/1386207321666191010114149

Price: $65

Abstract

Aim and Objective: It is interesting to find the gene signatures of cancer stages based on the omics data. The aim of study was to evaluate and to enrich the array data using gene ontology and ncRNA databases in colorectal cancer.

Methods: The human colorectal cancer data were obtained from the GEO databank. The downregulated and up-regulated genes were identified after scoring, weighing and merging of the gene data. The clusters with high-score edges were determined from gene networks. The miRNAs related to the gene clusters were identified and enriched. Furthermore, the long non-coding RNA (lncRNA) networks were predicted with a central core for miRNAs.

Results: Based on cluster enrichment, genes related to peptide receptor activity (1.26E-08), LBD domain binding (3.71E-07), rRNA processing (2.61E-34), chemokine (4.58E-19), peptide receptor (1.16E-19) and ECM organization (3.82E-16) were found. Furthermore, the clusters related to the non-coding RNAs, including hsa-miR-27b-5p, hsa-miR-155-5p, hsa-miR-125b-5p, hsa-miR-21-5p, hsa-miR-30e-5p, hsa-miR-588, hsa-miR-29-3p, LINC01234, LINC01029, LINC00917, LINC00668 and CASC11 were found.

Conclusion: The comprehensive bioinformatics analyses provided the gene networks related to some non-coding RNAs that might help in understanding the molecular mechanisms in CRC.

Keywords: Network, miRNA, lncRNA, online gene expression omnibus, gene ontology, omics data.

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