NDLI: Identification of differentially expressed lncRNAs and mRNAs in luminal-B breast cancer by RNA-sequencing

Content Provider	Springer Nature : BioMed Central
Author	Yuan, Cheng-Liang Jiang, Xiang-Mei Yi, Ying E, Jian-Fei Zhang, Nai-Dan Luo, Xue Zou, Ning Wei, Wei Liu, Ying-Ying
Abstract	Background Luminal B cancers show much worse outcomes compared to luminal A. This present study aims to screen key lncRNAs and mRNAs correlated with luminal-B breast cancer. Methods Luminal-B breast cancer tissue samples and adjacent tissue samples were obtained from 4 patients with luminal-B breast cancer. To obtain differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) between luminal-B breast cancer tumor tissues and adjacent tissues, RNA-sequencing and bioinformatics analysis were performed. Functional annotation of DEmRNAs and protein-protein interaction networks (PPI) construction were performed. DEmRNAs transcribed within a 100 kb window up- or down-stream of DElncRNAs were searched, which were defined as cis nearby-targeted DEmRNAs of DElncRNAs. DElncRNA-DEmRNA co-expression networks were performed. The mRNA and lncRNA expression profiles were downloaded from The Cancer Genome Atlas (TCGA) database to validate the expression patterns of selected DEmRNAs and DElncRNAs. Results A total of 1178 DEmRNAs and 273 DElncRNAs between luminal-B breast cancer tumor tissues and adjacent tissues were obtained. Hematopoietic cell lineage, Cytokine-cytokine receptor interaction, Cell adhesion molecules (CAMs) and Primary immunodeficiency were significantly enriched KEGG pathways in luminal-B breast cancer. FN1, EGFR, JAK3, TUBB3 and PTPRC were five hub proteins of the PPI networks. A total of 99 DElncRNAs-nearby-targeted DEmRNA pairs and 1878 DElncRNA-DEmRNA co-expression pairs were obtained. Gene expression results validated in TCGA database were consistent with our RNA-sequencing results, generally. Conclusion This study determined key genes and lncRNAs involved in luminal-B breast cancer, which expected to present a new avenue for the diagnosis and treatment of luminal-B breast cancer.
Related Links	https://bmccancer.biomedcentral.com/counter/pdf/10.1186/s12885-019-6395-5.pdf
Ending Page	12
Page Count	12
Starting Page	1
File Format	HTM / HTML
ISSN	14712407
DOI	10.1186/s12885-019-6395-5
Journal	BMC Cancer
Issue Number	1
Volume Number	19
Language	English
Publisher	BioMed Central
Publisher Date	2019-12-03
Access Restriction	Open
Subject Keyword	Cancer Research Oncology Surgical Oncology Health Promotion and Disease Prevention Biomedicine Medicine Public Health Luminal-B breast cancer mRNA Long non-coding RNA (lncRNA) RNA-sequencing Medicine/Public Health
Content Type	Text
Resource Type	Article
Subject	Cancer Research Oncology Genetics
Journal Impact Factor	3.4/2023
5-Year Journal Impact Factor	3.8/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Transcriptome profiling and co-expression network analysis of lncRNAs and mRNAs in colorectal cancer by RNA sequencing

The emerging roles of long non-coding RNA (lncRNA) H19 in gynecologic cancers

BC200 overexpression contributes to luminal and triple negative breast cancer pathogenesis

Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

Long non-coding RNA AC087388.1 as a novel biomarker in colorectal cancer

Identification of differentially expressed microRNAs in human male breast cancer

Reconstruction of lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveals functional lncRNAs in skin cutaneous melanoma

Precision treatment exploration of breast cancer based on heterogeneity analysis of lncRNAs at the single-cell level

Distinct 5-methylcytosine profiles of LncRNA in breast cancer brain metastasis

Identification of differentially expressed lncRNAs and mRNAs in luminal-B breast cancer by RNA-sequencing

Similar Documents

Transcriptome profiling and co-expression network analysis of lncRNAs and mRNAs in colorectal cancer by RNA sequencing

The emerging roles of long non-coding RNA (lncRNA) H19 in gynecologic cancers

BC200 overexpression contributes to luminal and triple negative breast cancer pathogenesis

Identification of methylation sites and signature genes with prognostic value for luminal breast cancer

Long non-coding RNA AC087388.1 as a novel biomarker in colorectal cancer

Identification of differentially expressed microRNAs in human male breast cancer

Reconstruction of lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveals functional lncRNAs in skin cutaneous melanoma

Precision treatment exploration of breast cancer based on heterogeneity analysis of lncRNAs at the single-cell level

Distinct 5-methylcytosine profiles of LncRNA in breast cancer brain metastasis

Identification of differentially expressed lncRNAs and mRNAs in luminal-B breast cancer by RNA-sequencing