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miRactDB characterizes miRNA–gene relation switch between normal and cancer tissues across pan-cancer
- Source :
- Brief Bioinform
- Publication Year :
- 2020
- Publisher :
- Oxford University Press, 2020.
-
Abstract
- It has been increasingly accepted that microRNA (miRNA) can both activate and suppress gene expression, directly or indirectly, under particular circumstances. Yet, a systematic study on the switch in their interaction pattern between activation and suppression and between normal and cancer conditions based on multi-omics evidences is not available. We built miRactDB, a database for miRNA–gene interaction, at https://ccsm.uth.edu/miRactDB, to provide a versatile resource and platform for annotation and interpretation of miRNA–gene relations. We conducted a comprehensive investigation on miRNA–gene interactions and their biological implications across tissue types in both tumour and normal conditions, based on TCGA, CCLE and GTEx databases. We particularly explored the genetic and epigenetic mechanisms potentially contributing to the positive correlation, including identification of miRNA binding sites in the gene coding sequence (CDS) and promoter regions of partner genes. Integrative analysis based on this resource revealed that top-ranked genes derived from TCGA tumour and adjacent normal samples share an overwhelming part of biological processes, which are quite different than those from CCLE and GTEx. The most active miRNAs predicted to target CDS and promoter regions are largely overlapped. These findings corroborate that adjacent normal tissues might have undergone significant molecular transformations towards oncogenesis before phenotypic and histological change; and there probably exists a small yet critical set of miRNAs that profoundly influence various cancer hallmark processes. miRactDB provides a unique resource for the cancer and genomics communities to screen, prioritize and rationalize their candidates of miRNA–gene interactions, in both normal and cancer scenarios.
- Subjects :
- Carcinogenesis
Genomics
MiRNA binding
Computational biology
Biology
medicine.disease_cause
Epigenesis, Genetic
03 medical and health sciences
0302 clinical medicine
Neoplasms
microRNA
medicine
Coding region
Humans
Epigenetics
Promoter Regions, Genetic
Molecular Biology
Gene
030304 developmental biology
0303 health sciences
Binding Sites
Cancer
medicine.disease
Gene Expression Regulation, Neoplastic
MicroRNAs
030220 oncology & carcinogenesis
Problem Solving Protocol
Information Systems
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Brief Bioinform
- Accession number :
- edsair.doi.dedup.....a1d272ac17a1289067f3e445a87b5277