Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq study

Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq study

Among all the sequencing techniques, RNA sequencing (RNA-seq) has galloped with pace adopting the profiling of transcriptomic data in almost every biological analytics area like gene regulation study, development biology and clinical research. Recently the discovery of differentially expressed genes...

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Main Authors: Rashmi Tripathi, Apoorva Soni, Pritish Kumar Varadwaj
Format: Article
Language:English
Published: KeAi Communications Co., Ltd. 2016-10-01
Series:Non-coding RNA Research
Online Access:http://www.sciencedirect.com/science/article/pii/S246805401630004X
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spelling doaj-6c242ca13a2144bab17d2b6163e351a12021-02-02T01:18:59ZengKeAi Communications Co., Ltd.Non-coding RNA Research2468-05402016-10-01113542Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq studyRashmi Tripathi0Apoorva Soni1Pritish Kumar Varadwaj2Department of Bioinformatics, Indian Institute of Information Technology, Allahabad, U.P, IndiaDepartment of Molecular and Cellular Engineering, Sam Higginbottom Institute of Agriculture, Technology and Sciences, Allahabad, U.P, IndiaDepartment of Bioinformatics, Indian Institute of Information Technology, Allahabad, U.P, India; Corresponding author.Among all the sequencing techniques, RNA sequencing (RNA-seq) has galloped with pace adopting the profiling of transcriptomic data in almost every biological analytics area like gene regulation study, development biology and clinical research. Recently the discovery of differentially expressed genes across different conditions has outshone the barrier of genetic & epigenetic regulations. The present work identified and analyzed differentially expressed novel long non-coding RNAs (lncRNAs) for breast cancer. A complex computational pipeline was adopted for the study which includes analysis of 18498 differentially expressed genes with 4114 up-regulated and 3475 down-regulated transcripts. The overexpression of lnc-MTAP (CDKN2B-AS1), lnc-PCP4 (DSCAM-S1), and lnc-FAM (H19) in breast cells suggests that these lncRNAs may have significant role to play in breast cancer. These results validated the relevance of the dysregulation pattern in cancer cells due to the presence of lncRNAs. The study further opens a new scope for experimental analysis to confirm the aberrant expression pattern of these lncRNAs which may act as potential bio-markers for the diagnosis and early detection of breast cancer. Keywords: RNA sequencing, Transcriptomics, Differentially expressed genes, Long non-coding RNAs (lncRNAs), Breast cancer, Dysregulationhttp://www.sciencedirect.com/science/article/pii/S246805401630004X
collection DOAJ
language English
format Article
sources DOAJ
author Rashmi Tripathi
Apoorva Soni
Pritish Kumar Varadwaj
spellingShingle Rashmi Tripathi
Apoorva Soni
Pritish Kumar Varadwaj
Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq study
Non-coding RNA Research
author_facet Rashmi Tripathi
Apoorva Soni
Pritish Kumar Varadwaj
author_sort Rashmi Tripathi
title Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq study
title_short Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq study
title_full Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq study
title_fullStr Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq study
title_full_unstemmed Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq study
title_sort integrated analysis of dysregulated lncrna expression in breast cancer cell identified by rna-seq study
publisher KeAi Communications Co., Ltd.
series Non-coding RNA Research
issn 2468-0540
publishDate 2016-10-01
description Among all the sequencing techniques, RNA sequencing (RNA-seq) has galloped with pace adopting the profiling of transcriptomic data in almost every biological analytics area like gene regulation study, development biology and clinical research. Recently the discovery of differentially expressed genes across different conditions has outshone the barrier of genetic & epigenetic regulations. The present work identified and analyzed differentially expressed novel long non-coding RNAs (lncRNAs) for breast cancer. A complex computational pipeline was adopted for the study which includes analysis of 18498 differentially expressed genes with 4114 up-regulated and 3475 down-regulated transcripts. The overexpression of lnc-MTAP (CDKN2B-AS1), lnc-PCP4 (DSCAM-S1), and lnc-FAM (H19) in breast cells suggests that these lncRNAs may have significant role to play in breast cancer. These results validated the relevance of the dysregulation pattern in cancer cells due to the presence of lncRNAs. The study further opens a new scope for experimental analysis to confirm the aberrant expression pattern of these lncRNAs which may act as potential bio-markers for the diagnosis and early detection of breast cancer. Keywords: RNA sequencing, Transcriptomics, Differentially expressed genes, Long non-coding RNAs (lncRNAs), Breast cancer, Dysregulation
url http://www.sciencedirect.com/science/article/pii/S246805401630004X
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AT apoorvasoni integratedanalysisofdysregulatedlncrnaexpressioninbreastcancercellidentifiedbyrnaseqstudy
AT pritishkumarvaradwaj integratedanalysisofdysregulatedlncrnaexpressioninbreastcancercellidentifiedbyrnaseqstudy
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