Co-expression Network Analysis of Human lncRNAs and Cancer Genes
We used gene co-expression network analysis to functionally annotate long noncoding RNAs (lncRNAs) and identify their potential cancer associations. The integrated microarray data set from our previous study was used to extract the expression profiles of 1,865 lncRNAs. Known cancer genes were compil...
Main Authors: | , |
---|---|
Format: | Article |
Language: | English |
Published: |
SAGE Publishing
2014-01-01
|
Series: | Cancer Informatics |
Online Access: | https://doi.org/10.4137/CIN.S14070 |
id |
doaj-7ba04da42a954631b82aafdb188ee20f |
---|---|
record_format |
Article |
spelling |
doaj-7ba04da42a954631b82aafdb188ee20f2020-11-25T03:15:36ZengSAGE PublishingCancer Informatics1176-93512014-01-0113s510.4137/CIN.S14070Co-expression Network Analysis of Human lncRNAs and Cancer GenesSteven B. Cogill0Liangjiang Wang1Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.We used gene co-expression network analysis to functionally annotate long noncoding RNAs (lncRNAs) and identify their potential cancer associations. The integrated microarray data set from our previous study was used to extract the expression profiles of 1,865 lncRNAs. Known cancer genes were compiled from the Catalogue of Somatic Mutations in Cancer and UniProt databases. Co-expression analysis identified a list of previously uncharacterized lncRNAs that showed significant correlation in expression with core cancer genes. To further annotate the lncRNAs, we performed a weighted gene co-expression network analysis, which resulted in 37 co-expression modules. Three biologically interesting modules were analyzed in depth. Two of the modules showed relatively high expression in blood and brain tissues, whereas the third module was found to be downregulated in blood cells. Hub lncRNA genes and enriched functional annotation terms were identified within the modules. The results suggest the utility of this approach as well as potential roles of uncharacterized lncRNAs in leukemia and neuroblastoma.https://doi.org/10.4137/CIN.S14070 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Steven B. Cogill Liangjiang Wang |
spellingShingle |
Steven B. Cogill Liangjiang Wang Co-expression Network Analysis of Human lncRNAs and Cancer Genes Cancer Informatics |
author_facet |
Steven B. Cogill Liangjiang Wang |
author_sort |
Steven B. Cogill |
title |
Co-expression Network Analysis of Human lncRNAs and Cancer Genes |
title_short |
Co-expression Network Analysis of Human lncRNAs and Cancer Genes |
title_full |
Co-expression Network Analysis of Human lncRNAs and Cancer Genes |
title_fullStr |
Co-expression Network Analysis of Human lncRNAs and Cancer Genes |
title_full_unstemmed |
Co-expression Network Analysis of Human lncRNAs and Cancer Genes |
title_sort |
co-expression network analysis of human lncrnas and cancer genes |
publisher |
SAGE Publishing |
series |
Cancer Informatics |
issn |
1176-9351 |
publishDate |
2014-01-01 |
description |
We used gene co-expression network analysis to functionally annotate long noncoding RNAs (lncRNAs) and identify their potential cancer associations. The integrated microarray data set from our previous study was used to extract the expression profiles of 1,865 lncRNAs. Known cancer genes were compiled from the Catalogue of Somatic Mutations in Cancer and UniProt databases. Co-expression analysis identified a list of previously uncharacterized lncRNAs that showed significant correlation in expression with core cancer genes. To further annotate the lncRNAs, we performed a weighted gene co-expression network analysis, which resulted in 37 co-expression modules. Three biologically interesting modules were analyzed in depth. Two of the modules showed relatively high expression in blood and brain tissues, whereas the third module was found to be downregulated in blood cells. Hub lncRNA genes and enriched functional annotation terms were identified within the modules. The results suggest the utility of this approach as well as potential roles of uncharacterized lncRNAs in leukemia and neuroblastoma. |
url |
https://doi.org/10.4137/CIN.S14070 |
work_keys_str_mv |
AT stevenbcogill coexpressionnetworkanalysisofhumanlncrnasandcancergenes AT liangjiangwang coexpressionnetworkanalysisofhumanlncrnasandcancergenes |
_version_ |
1724638478709293056 |