Whole miRNome-wide Differential Co-expression of MicroRNAs

Co-regulation of genes has been extensively analyzed, however, rather limited knowledge is available on co-regulations within the miRNome. We investigated differential co-expression of microRNAs (miRNAs) based on miRNome profiles of whole blood from 540 individuals. These include patients suffering...

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Main Authors:	Stäehler, Cord F., Keller, Andreas, Leidinger, Petra, Backes, Christina, Chandran, Anoop, Wischhusen, Jöerg, Meder, Benjamin, Meese, Eckart
Format:	Online
Language:	English
Published:	Elsevier 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054199/

id	pubmed-5054199
recordtype	oai_dc
spelling	pubmed-50541992016-10-14 Whole miRNome-wide Differential Co-expression of MicroRNAs Stäehler, Cord F. Keller, Andreas Leidinger, Petra Backes, Christina Chandran, Anoop Wischhusen, Jöerg Meder, Benjamin Meese, Eckart Original Research Co-regulation of genes has been extensively analyzed, however, rather limited knowledge is available on co-regulations within the miRNome. We investigated differential co-expression of microRNAs (miRNAs) based on miRNome profiles of whole blood from 540 individuals. These include patients suffering from different cancer and non-cancer diseases, and unaffected controls. Using hierarchical clustering, we found 9 significant clusters of co-expressed miRNAs containing 2–36 individual miRNAs. Through analyzing multiple sequencing alignments in the clusters, we found that co-expression of miRNAs is associated with both sequence similarity and genomic co-localization. We calculated correlations for all 371,953 pairs of miRNAs for all 540 individuals and identified 184 pairs of miRNAs with high correlation values. Out of these 184 pairs of miRNAs, 16 pairs (8.7%) were differentially co-expressed in unaffected controls, cancer patients and patients with non-cancer diseases. By computing correlated and anti-correlated miRNA pairs, we constructed a network with 184 putative co-regulations as edges and 100 miRNAs as nodes. Thereby, we detected specific clusters of miRNAs with high and low correlation values. Our approach represents the most comprehensive co-regulation analysis based on whole miRNome-wide expression profiling. Our findings further decrypt the interactions of miRNAs in normal and human pathological processes. Elsevier 2012-10 2012-08-23 /pmc/articles/PMC5054199/ /pubmed/23200138 http://dx.doi.org/10.1016/j.gpb.2012.08.003 Text en © 2012 Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. Published by Elsevier Ltd and Science Press. All rights reserved. http://creativecommons.org/licenses/by-nc-sa/3.0/ This is an open access article under the CC BY-NC-SA license (http://creativecommons.org/licenses/by-nc-sa/3.0/).
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Stäehler, Cord F. Keller, Andreas Leidinger, Petra Backes, Christina Chandran, Anoop Wischhusen, Jöerg Meder, Benjamin Meese, Eckart
spellingShingle	Stäehler, Cord F. Keller, Andreas Leidinger, Petra Backes, Christina Chandran, Anoop Wischhusen, Jöerg Meder, Benjamin Meese, Eckart Whole miRNome-wide Differential Co-expression of MicroRNAs
author_facet	Stäehler, Cord F. Keller, Andreas Leidinger, Petra Backes, Christina Chandran, Anoop Wischhusen, Jöerg Meder, Benjamin Meese, Eckart
author_sort	Stäehler, Cord F.
title	Whole miRNome-wide Differential Co-expression of MicroRNAs
title_short	Whole miRNome-wide Differential Co-expression of MicroRNAs
title_full	Whole miRNome-wide Differential Co-expression of MicroRNAs
title_fullStr	Whole miRNome-wide Differential Co-expression of MicroRNAs
title_full_unstemmed	Whole miRNome-wide Differential Co-expression of MicroRNAs
title_sort	whole mirnome-wide differential co-expression of micrornas
description	Co-regulation of genes has been extensively analyzed, however, rather limited knowledge is available on co-regulations within the miRNome. We investigated differential co-expression of microRNAs (miRNAs) based on miRNome profiles of whole blood from 540 individuals. These include patients suffering from different cancer and non-cancer diseases, and unaffected controls. Using hierarchical clustering, we found 9 significant clusters of co-expressed miRNAs containing 2–36 individual miRNAs. Through analyzing multiple sequencing alignments in the clusters, we found that co-expression of miRNAs is associated with both sequence similarity and genomic co-localization. We calculated correlations for all 371,953 pairs of miRNAs for all 540 individuals and identified 184 pairs of miRNAs with high correlation values. Out of these 184 pairs of miRNAs, 16 pairs (8.7%) were differentially co-expressed in unaffected controls, cancer patients and patients with non-cancer diseases. By computing correlated and anti-correlated miRNA pairs, we constructed a network with 184 putative co-regulations as edges and 100 miRNAs as nodes. Thereby, we detected specific clusters of miRNAs with high and low correlation values. Our approach represents the most comprehensive co-regulation analysis based on whole miRNome-wide expression profiling. Our findings further decrypt the interactions of miRNAs in normal and human pathological processes.
publisher	Elsevier
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054199/
_version_	1613676030929666048

Whole miRNome-wide Differential Co-expression of MicroRNAs

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