Dataset for regulation between lncRNAs and their nearby protein-coding genes in human cancers

Data in Brief
Zhi LiuHongbing Shen

Abstract

This article contains data related to the research article entitled "Systematic analysis reveals long noncoding RNAs regulating neighboring transcription factors in human cancers" (Liu et al., 2018 in press) [1]. Long noncoding RNAs (lncRNAs) are proposed to play essential roles in modulating the expression of the nearby loci. In this study, we systematically investigated the relationship between lncRNAs and their neighboring genes based on the genomic location of genes and the transcriptome expression profiles from TCGA samples across 12 tumor types. Position conservation analysis was applied to find lncRNAs conserved by position across vertebrate species. Gene ontology and enrichment analysis identified TF genes as a specific type of protein-coding genes that adjacent to highly positionally conserved lncRNA. The expression correlation of lncRNAs and their adjacent TFs were assessed across tumors to define significant co-expressed lncRNA-TF pairs, and a causal inference test (CIT) was used to infer the causal regulation of lncRNA on its nearby TF genes. A list of candidate lncRNA/TF regulation pairs in tumors was provided.

Citations

Jul 22, 2020·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Hui ZhaoGuanghong Zheng
Jun 28, 2020·Digestive Diseases and Sciences·Zhi-Feng Jiang, Lin Zhang
May 13, 2019·Molecular Immunology·Swati DahariyaRavi Kumar Gutti

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

EnsemblCompara
NONCODE

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