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The integrative knowledge base for miRNA-mRNA expression in colorectal cancer
ID Jevšinek Skok, Daša (Author), ID Hauptman, Nina (Author), ID Boštjančič, Emanuela (Author), ID Zidar, Nina (Author)

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Abstract
"miRNA colorectal cancer" (https://mirna-coadread.omics.si/) is a freely available web application for studying microRNA and mRNA expression and their correlation in colorectal cancer. To the best of our knowledge, "miRNA colorectal cancer" has the largest knowledge base of miRNA-target gene expressions and correlations in colorectal cancer, based on the largest available sample size from the same source of data. Data from high-throughput molecular profiling of 295 colon and rectum adenocarcinoma samples from The Cancer Genome Atlas was analyzed and integrated into our knowledge base. The objective of developing this web application was to help researchers to discover the behavior and role of miRNA-target gene interactions in colorectal cancer. For this purpose, results of differential expression and correlation analyses of miRNA and mRNA data collected in our knowledge base are available through web forms. To validate our knowledge base experimentally, we selected genes FN1, TGFB2, RND3, ZEB1 and ZEB2 and miRNAs hsa-miR-200a/b/c-3p, hsa-miR-141-3p and hsa-miR-429. Both approaches revealed a negative correlation between miRNA hsa-miR-200b/c-3p and its target gene FN1 and between hsa-miR-200a-3p and its target TGFB2, thus supporting the usefulness of the developed knowledge base.

Language:English
Keywords:web aplication, RNA expression, colorectal cancer, gene expression, knowledge base, cancer genome atlas, miRNA, mRNA, gene correlation, target genes
Work type:Article
Typology:1.01 - Original Scientific Article
Organization:MF - Faculty of Medicine
Publication status:Published
Publication version:Version of Record
Year:2019
Number of pages:9 str.
Numbering:Vol. 9, art. 18065
PID:20.500.12556/RUL-128787 This link opens in a new window
UDC:61
ISSN on article:2045-2322
DOI:10.1038/s41598-019-54358-w This link opens in a new window
COBISS.SI-ID:5920616 This link opens in a new window
Publication date in RUL:29.07.2021
Views:972
Downloads:182
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Record is a part of a journal

Title:Scientific reports
Shortened title:Sci. rep.
Publisher:Nature Publishing Group
ISSN:2045-2322
COBISS.SI-ID:18727432 This link opens in a new window

Licences

License:CC BY 4.0, Creative Commons Attribution 4.0 International
Link:http://creativecommons.org/licenses/by/4.0/
Description:This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
Licensing start date:02.12.2019

Projects

Funder:ARRS - Slovenian Research Agency
Project number:P3-0054
Name:Patologija in molekularna genetika

Funder:ARRS - Slovenian Research Agency
Project number:Z3-6797
Name:Identifikacija in potrditev novih kandidatnih metilacijsko specifičnih bio-označevalcev pri karcinomu debelega črevesja in danke

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