lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes

Bioinformatics
Yining Liu, Min Zhao

Abstract

Thousands of human long non-coding RNAs (lncRNAs) have been identified in cancers and played important roles in a wide range of tumorigenesis. However, the functions of vast majority of human lncRNAs are still elusive. Emerging studies revealed that the expression level of majority lncRNAs shows discordant expression pattern with their protein-coding gene neighbors in various model organisms. Therefore, it may be useful to infer lncRNAs' potential biological function in cancer development by more comprehensive functional views of co-expressed cancer genes beyond mere physical proximity of genes. To this aim, we performed thorough searches and analyses of the interactions between lncRNA and non-neighboring cancer genes and provide a comprehensive co-expression data resource, LnCaNet. In current version, LnCaNet contains the pre-computed 8 494 907 significant co-expression pairs of 9641 lncRNAs and 2544 well-classified cancer genes in 2922 matched TCGA samples. In detail, we integrated 10 cancer gene lists from public database and calculate the co-expression with all the lncRNAs in 11 TCGA cancer types separately. Based on the resulted 110 co-expression networks, we identified 17 common regulatory pairs related to extracellular s...Continue Reading

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Oct 16, 2012·Nucleic Acids Research·Min ZhaoZhongming Zhao
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Citations

Sep 12, 2016·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Yining LiuMin Zhao
Sep 7, 2016·BioMed Research International·Junyi LiYuan-Yuan Li
Feb 1, 2018·Scientific Reports·Chao RenWenjie Shu
Feb 6, 2018·Briefings in Bioinformatics·Junpeng ZhangJiuyong Li
Sep 25, 2018·Briefings in Functional Genomics·Xing ChenJian-Qiang Li
Jan 16, 2018·Stem Cells International·Fuquan ChenXinyi Lu
Mar 27, 2020·Frontiers in Bioengineering and Biotechnology·Jizhou ZhangShangwei Ning
Aug 6, 2019·Frontiers in Genetics·Daniele MercatelliFederico M Giorgi
Feb 3, 2021·Journal of Molecular Neuroscience : MN·Wu XuYa-Wen Pan
Jul 24, 2021·Database : the Journal of Biological Databases and Curation·Min ZhaoHong Qu

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