ArticleCancer informatics2017
An Assessment of Database-Validated microRNA Target Genes in Normal Colonic Mucosa: Implications for Pathway Analysis.
Article in Cancer informatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- The p53-signaling pathway and colorectal cancer: Interactions between downstream p53 target genes and miRNAs.Genomics · 2019Article
- The functional role of miRNAs in colorectal cancer: insights from a large population-based study.Cancer biology & medicine · 2019Article
- The TGFβ-signaling pathway and colorectal cancer: associations between dysregulated genes and miRNAs.Journal of translational medicine · 2018Article
- Precision Medicine for CRC Patients in the Veteran Population: State-of-the-Art, Challenges and Research Directions.Digestive diseases and sciences · 2018Review
- Dysregulated genes and miRNAs in the apoptosis pathway in colorectal cancer patients.Apoptosis : an international journal on programmed cell death · 2018Article
- The PI3K/AKT signaling pathway: Associations of miRNAs with dysregulated gene expression in colorectal cancer.Molecular carcinogenesis · 2018Article
- The NF-κB signalling pathway in colorectal cancer: associations between dysregulated gene and miRNA expression.Journal of cancer research and clinical oncology · 2018Article
- Expression of Wnt-signaling pathway genes and their associations with miRNAs in colorectal cancer.Oncotarget · 2018Article
- The MAPK-Signaling Pathway in Colorectal Cancer: Dysregulated Genes and Their Association With MicroRNAs.Cancer informatics · 2018Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundDetermination of functional pathways regulated by microRNAs (miRNAs), while an essential step in developing therapeutics, is challenging. Some miRNAs have been studied extensively; others have limited information. In this study, we focus on 254 miRNAs previously identified as being associated with colorectal cancer and their database-identified validated target genes.
methodsWe use RNA-Seq data to evaluate messenger RNA (mRNA) expression for 157 subjects who also had miRNA expression data. In the replication phase of the study, we replicated associations between 254 miRNAs associated with colorectal cancer and mRNA expression of database-identified target genes in normal colonic mucosa. In the discovery phase of the study, we evaluated expression of 18 miR-NAs (those with 20 or fewer database-identified target genes along with miR-21-5p, miR-215-5p, and miR-124-3p which have more than 500 database-identified target genes) with expression of 17 434 mRNAs to identify new targets in colon tissue. Seed region matches between miRNA and newly identified targeted mRNA were used to help determine direct miRNA-mRNA associations.
resultsFrom the replication of the 121 miRNAs that had at least 1 database-identified target gene using mRNA expression methods, 97.9% were expressed in normal colonic mucosa. Of the 8622 target miRNA-mRNA associations identified in the database, 2658 (30.2%) were associated with gene expression in normal colonic mucosa after adjusting for multiple comparisons. Of the 133 miRNAs with database-identified target genes by non-mRNA expression methods, 97.2% were expressed in normal colonic mucosa. After adjustment for multiple comparisons, 2416 miRNA-mRNA associations remained significant (19.8%). Results from the discovery phase based on detailed examination of 18 miRNAs identified more than 80 000 miRNA-mRNA associations that had not previously linked to the miRNA. Of these miRNA-mRNA associations, 15.6% and 14.8% had seed matches for CRCh38 and CRCh37, respectively.
conclusionsOur data suggest that miRNA target gene databases are incomplete; pathways derived from these databases have similar deficiencies. Although we know a lot about several miRNAs, little is known about other miRNAs in terms of their targeted genes. We encourage others to use their data to continue to further identify and validate miRNA-targeted genes.
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