Regulatory Network Analysis of lncRNA-miRNA-mRNA

DELs (targeted studies) and DEMs (miRNAs associated with hub molecules among the top pathway and the targets reported at both mRNA and protein levels) were used to screen the experimentally validated interaction between them by DIANA-LncBase v3 (https://diana.e-ce.uth.gr/lncbasev3) (Karagkouni et al., 2020 (link)). Both the subunits of miRNA, i.e., “-3p” and “-5p” were considered for finding associated lncRNAs in those cases where the subunits were not specified. Then, lncRNA-miRNA and miRNA-mRNA co-expression pairs (positive relation) were then used to construct ceRNA interaction networks (lncRNA-miRNA-mRNA). The networks were visualized using Cytoscape. Another database, mirTarBase (mirtarbase.cuhk.edu.cn), containing more than three hundred and sixty thousand miRNA-mRNA interactions was then used to categorize the miRNA-mRNA interactions with strong evidence (Reporter assay/Western blot/qPCR) or less strong evidence (Microarray, NGS, pSILAC, CLIP-Seq and others).

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Saklani N., Chauhan V., Akhtar J., Upadhyay S.K., Sirdeshmukh R, & Gautam P. (2023). In silico analysis to identify novel ceRNA regulatory axes associated with gallbladder cancer. Frontiers in Genetics, 14, 1107614.

Publication 2023

Assay Clip seq Lncrna Microarray Mirna Mrna Protein Subunits Western blot

Corresponding Organization : National Institute of Pathology

Other organizations : Gautam Buddha University, Kumaun University, Manipal Academy of Higher Education, Institute of Bioinformatics

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Variable analysis

independent variables

DELs (targeted studies)
DEMs (miRNAs associated with hub molecules among the top pathway)

dependent variables

Experimentally validated interaction between DELs and DEMs
LncRNA-miRNA and miRNA-mRNA co-expression pairs (positive relation)
MiRNA-mRNA interactions with strong evidence (Reporter assay/Western blot/qPCR) or less strong evidence (Microarray, NGS, pSILAC, CLIP-Seq and others)

control variables

Both the subunits of miRNA, i.e., "-3p" and "-5p" were considered for finding associated lncRNAs in those cases where the subunits were not specified

controls

Positive controls not specified
Negative controls not specified

Annotations

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