miRConnect: identifying effector genes of miRNAs and miRNA families in cancer cells.

micro(mi)RNAs are small non-coding RNAs that negatively regulate expression of most mRNAs. They are powerful regulators of various differentiation stages, and the expression of genes that either negatively or positively correlate with expressed miRNAs is expected to hold information on the biologica...

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Autores principales:	Youjia Hua, Shiwei Duan, Andrea E Murmann, Niels Larsen, Jørgen Kjems, Anders H Lund, Marcus E Peter
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3634f0c5ed6c447a90cb4767685a3a41
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spelling	oai:doaj.org-article:3634f0c5ed6c447a90cb4767685a3a412021-11-18T07:35:44ZmiRConnect: identifying effector genes of miRNAs and miRNA families in cancer cells.1932-620310.1371/journal.pone.0026521https://doaj.org/article/3634f0c5ed6c447a90cb4767685a3a412011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22046300/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203micro(mi)RNAs are small non-coding RNAs that negatively regulate expression of most mRNAs. They are powerful regulators of various differentiation stages, and the expression of genes that either negatively or positively correlate with expressed miRNAs is expected to hold information on the biological state of the cell and, hence, of the function of the expressed miRNAs. We have compared the large amount of available gene array data on the steady state system of the NCI60 cell lines to two different data sets containing information on the expression of 583 individual miRNAs. In addition, we have generated custom data sets containing expression information of 54 miRNA families sharing the same seed match. We have developed a novel strategy for correlating miRNAs with individual genes based on a summed Pearson Correlation Coefficient (sPCC) that mimics an in silico titration experiment. By focusing on the genes that correlate with the expression of miRNAs without necessarily being direct targets of miRNAs, we have clustered miRNAs into different functional groups. This has resulted in the identification of three novel miRNAs that are linked to the epithelial-to-mesenchymal transition (EMT) in addition to the known EMT regulators of the miR-200 miRNA family. In addition, an analysis of gene signatures associated with EMT, c-MYC activity, and ribosomal protein gene expression allowed us to assign different activities to each of the functional clusters of miRNAs. All correlation data are available via a web interface that allows investigators to identify genes whose expression correlates with the expression of single miRNAs or entire miRNA families. miRConnect.org will aid in identifying pathways regulated by miRNAs without requiring specific knowledge of miRNA targets.Youjia HuaShiwei DuanAndrea E MurmannNiels LarsenJørgen KjemsAnders H LundMarcus E PeterPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 10, p e26521 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Youjia Hua Shiwei Duan Andrea E Murmann Niels Larsen Jørgen Kjems Anders H Lund Marcus E Peter miRConnect: identifying effector genes of miRNAs and miRNA families in cancer cells.
description	micro(mi)RNAs are small non-coding RNAs that negatively regulate expression of most mRNAs. They are powerful regulators of various differentiation stages, and the expression of genes that either negatively or positively correlate with expressed miRNAs is expected to hold information on the biological state of the cell and, hence, of the function of the expressed miRNAs. We have compared the large amount of available gene array data on the steady state system of the NCI60 cell lines to two different data sets containing information on the expression of 583 individual miRNAs. In addition, we have generated custom data sets containing expression information of 54 miRNA families sharing the same seed match. We have developed a novel strategy for correlating miRNAs with individual genes based on a summed Pearson Correlation Coefficient (sPCC) that mimics an in silico titration experiment. By focusing on the genes that correlate with the expression of miRNAs without necessarily being direct targets of miRNAs, we have clustered miRNAs into different functional groups. This has resulted in the identification of three novel miRNAs that are linked to the epithelial-to-mesenchymal transition (EMT) in addition to the known EMT regulators of the miR-200 miRNA family. In addition, an analysis of gene signatures associated with EMT, c-MYC activity, and ribosomal protein gene expression allowed us to assign different activities to each of the functional clusters of miRNAs. All correlation data are available via a web interface that allows investigators to identify genes whose expression correlates with the expression of single miRNAs or entire miRNA families. miRConnect.org will aid in identifying pathways regulated by miRNAs without requiring specific knowledge of miRNA targets.
format	article
author	Youjia Hua Shiwei Duan Andrea E Murmann Niels Larsen Jørgen Kjems Anders H Lund Marcus E Peter
author_facet	Youjia Hua Shiwei Duan Andrea E Murmann Niels Larsen Jørgen Kjems Anders H Lund Marcus E Peter
author_sort	Youjia Hua
title	miRConnect: identifying effector genes of miRNAs and miRNA families in cancer cells.
title_short	miRConnect: identifying effector genes of miRNAs and miRNA families in cancer cells.
title_full	miRConnect: identifying effector genes of miRNAs and miRNA families in cancer cells.
title_fullStr	miRConnect: identifying effector genes of miRNAs and miRNA families in cancer cells.
title_full_unstemmed	miRConnect: identifying effector genes of miRNAs and miRNA families in cancer cells.
title_sort	mirconnect: identifying effector genes of mirnas and mirna families in cancer cells.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/3634f0c5ed6c447a90cb4767685a3a41
work_keys_str_mv	AT youjiahua mirconnectidentifyingeffectorgenesofmirnasandmirnafamiliesincancercells AT shiweiduan mirconnectidentifyingeffectorgenesofmirnasandmirnafamiliesincancercells AT andreaemurmann mirconnectidentifyingeffectorgenesofmirnasandmirnafamiliesincancercells AT nielslarsen mirconnectidentifyingeffectorgenesofmirnasandmirnafamiliesincancercells AT jørgenkjems mirconnectidentifyingeffectorgenesofmirnasandmirnafamiliesincancercells AT andershlund mirconnectidentifyingeffectorgenesofmirnasandmirnafamiliesincancercells AT marcusepeter mirconnectidentifyingeffectorgenesofmirnasandmirnafamiliesincancercells
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miRConnect: identifying effector genes of miRNAs and miRNA families in cancer cells.

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