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

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.

SUBMITTER: Liu Z

PROVIDER: S-EPMC6141275 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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

Liu Zhi Z Dai Juncheng J Shen Hongbing H

Data in brief 20180626

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 exp ...[more]

PMID: 30229065

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Project description:The senescence-accelerated mouse prone 8 (SAMP8) mouse model is a useful model for investigating the fundamental mechanisms involved in the age-related learning and memory deficits of Alzheimer's disease (AD), while the SAM/resistant 1 (SAMR1) mouse model shows normal features. Recent evidence has shown that long non-coding RNAs (lncRNAs) may play an important role in AD pathogenesis. However, a comprehensive and systematic understanding of the function of AD-related lncRNAs and their associated nearby coding genes in AD is still lacking. In this study, we collected the hippocampus, the main area of AD pathological processes, of SAMP8 and SAMR1 animals and performed microarray analysis to identify aberrantly expressed lncRNAs and their associated nearby coding genes, which may contribute to AD pathogenesis. We identified 3,112 differentially expressed lncRNAs and 3,191 differentially expressed mRNAs in SAMP8 mice compared to SAMR1 mice. More than 70% of the deregulated lncRNAs were intergenic and exon sense-overlapping lncRNAs. Gene Ontology (GO) and pathway analyses of the AD-related transcripts were also performed and are described in detail, which imply that metabolic process reprograming was likely related to AD. Furthermore, six lncRNAs and six mRNAs were selected for further validation of the microarray results using quantitative PCR, and the results were consistent with the findings from the microarray. Moreover, we analyzed 780 lincRNAs (also called long "intergenic" non-coding RNAs) and their associated nearby coding genes. Among these lincRNAs, AK158400 had the most genes nearby (n = 13), all of which belonged to the histone cluster 1 family, suggesting regulation of the nucleosome structure of the chromosomal fiber by affecting nearby genes during AD progression. In addition, we also identified 97 aberrant antisense lncRNAs and their associated coding genes. It is likely that these dysregulated lncRNAs and their associated nearby coding genes play a role in the development and/or progression of AD.

Dataset Information

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

Publications

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

Similar Datasets

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