» Articles » PMID: 29108255

Comprehensive Bioinformatics Analysis of the Characterization and Determination Underlying Mechanisms of Over-expression and Co-expression of Genes Residing on 20q in Colorectal Cancer

Overview
Journal Oncotarget
Specialty Oncology
Date 2017 Nov 8
PMID 29108255
Citations 7
Authors
Affiliations
Soon will be listed here.
Abstract

The Long arm of chromosome 20 (20q) is closely related to the development of colorectal cancer, so identifying the expression profile of genes on 20q through a comprehensive overview is indispensable. In this article, preliminar experimental data, several available databases and bioinformatics tools such as the Cancer Genome Atlas, the Encyclopedia of DNA Elements, the JASPAR database and starBase were combined to analyze the correlation between genes and chromosomal aberrations, microRNA and transcription factors, as well as to explore the expression feature and potential regulative mechanism. The results showed that the most frequently unregulated genes in colorectal cancer arelocated on chromosome 20q, present a significant CNA-mRNA correlation.Furthermore, the genes with mRNA overexpression showed co-expression features and tended to be clustered within the same genomic neighborhoods. Then, several genes were selected to carry out further analysis and demonstrated that shared transcription factors, a conserved bidirectional promoter, and competition for a limited pool of microRNAin the 3'UTR of mRNA may be the underlying mechanisms behind the co-expression of physically adjacent genes.Finally, the databases, Lentivirus shRNA, and qPCR were used to find that these adjacent genes with co-expression cooperatively participated in the same biological pathways associated with the pathogenesis and development of colorectal cancer.

Citing Articles

The N6-Methyladenosine (m6A) Methylation Gene  Reveals a Potential Diagnostic Role for Gastric Cancer.

Liu T, Yang S, Cheng Y, Kong X, Du D, Wang X Cancer Manag Res. 2020; 12:11953-11964.

PMID: 33244271 PMC: 7685380. DOI: 10.2147/CMAR.S279370.


PLAGL2 and POFUT1 are regulated by an evolutionarily conserved bidirectional promoter and are collaboratively involved in colorectal cancer by maintaining stemness.

Li D, Lin C, Li N, Du Y, Yang C, Bai Y EBioMedicine. 2019; 45:124-138.

PMID: 31279780 PMC: 6642334. DOI: 10.1016/j.ebiom.2019.06.051.


Study of Promoter Methylation Patterns of HOXA2, HOXA5, and HOXA6 and Its Clinicopathological Characteristics in Colorectal Cancer.

Li D, Bai Y, Feng Z, Li W, Yang C, Guo Y Front Oncol. 2019; 9:394.

PMID: 31165042 PMC: 6536611. DOI: 10.3389/fonc.2019.00394.


YTHDF1 Regulates Tumorigenicity and Cancer Stem Cell-Like Activity in Human Colorectal Carcinoma.

Bai Y, Yang C, Wu R, Huang L, Song S, Li W Front Oncol. 2019; 9:332.

PMID: 31131257 PMC: 6509179. DOI: 10.3389/fonc.2019.00332.


Overexpression of NELFCD promotes colorectal cancer cells proliferation, migration, and invasion.

Song S, Li D, Yang C, Yan P, Bai Y, Zhang Y Onco Targets Ther. 2018; 11:8741-8750.

PMID: 30584332 PMC: 6287418. DOI: 10.2147/OTT.S186266.


References
1.
Mathelier A, Fornes O, Arenillas D, Chen C, Denay G, Lee J . JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2015; 44(D1):D110-5. PMC: 4702842. DOI: 10.1093/nar/gkv1176. View

2.
Lozupone F, Borghi M, Marzoli F, Azzarito T, Matarrese P, Iessi E . TM9SF4 is a novel V-ATPase-interacting protein that modulates tumor pH alterations associated with drug resistance and invasiveness of colon cancer cells. Oncogene. 2015; 34(40):5163-74. DOI: 10.1038/onc.2014.437. View

3.
Li J, Liu S, Zhou H, Qu L, Yang J . starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2013; 42(Database issue):D92-7. PMC: 3964941. DOI: 10.1093/nar/gkt1248. View

4.
Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson S . GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics. 2010; 26(22):2927-8. PMC: 2971582. DOI: 10.1093/bioinformatics/btq562. View

5.
Tay Y, Rinn J, Pandolfi P . The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014; 505(7483):344-52. PMC: 4113481. DOI: 10.1038/nature12986. View