LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data

Jiang, Qinghua; Ma, Rui; Wang, Jixuan; Wu, Xiaoliang; Jin, Shuilin; Peng, Jiajie; Tan, Renjie; Zhang, Tianjiao; Yu, Li; Wang, Yadong

doi:10.1186/1471-2164-16-s3-s2

Cited by 126 publications

(98 citation statements)

References 43 publications

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“…These lncRNA and mRNA target sequences were merged from multiple databases, such as 23,898 from GENCODE (V19) (24), 14,353 from Human LincRNA Catalog (25), 7760 from RefSeq, 5627 from UCSC (http://genome.ucsc.edu/), 13,701 from NRED (ncRNA Expression Database, http://nred.matticklab.com/cgi-bin/ncrnadb.pl), 21,488 from LNCipedia (http://www.lncipedia.org/), 1038 from H-InvDB (http://www.h-invitational.jp/hinv/ahg-db/news.jsp), 3019 from lncRNAs-a (Enhancer-like) (25), 1053 from Antisense ncRNA pipeline (26), 407 Hox ncRNAs, 962 UCRs (27), and 848 from Chen Ruisheng lab (Institute of Biophysics, Chinese Academy of Science, http://www.ibp.cas.cn/nRNA). Each RNA sequence was detected by probes and repeated twice.…”

Section: Methodsmentioning

confidence: 99%

The Potential Roles of Long Noncoding RNAs (lncRNA) in Glioblastoma Development

Liu

Mitra

Zhao

et al. 2016

Molecular Cancer Therapeutics

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Long non-coding RNA (lncRNA) may contribute to the initiation and progression of tumor. In this study, we first systematically compared lncRNA and mRNA expression between GBM and paired normal brain tissues using microarray data. We found 27 lncRNA and 82 mRNA significantly up-regulated in GBM, as well as 198 lncRNA and 285 mRNA significantly down-regulated in GBM. We identified 138 co-expressed lncRNA-mRNA pairs from these differentially expressed lncRNA and genes. Subsequent pathway analysis of the lncRNA-paired genes indicated that EphrinB-EPHB, p75-mediated signaling, TNF alpha/NF-κB, and ErbB2/ErbB3 signaling pathways might be altered in GBM. Specifically, lncRNA RAMP2-AS1 had significant decrease of expression in GBM tissues and showed co-expressional relationship with NOTCH3, an important tumor promoter in many neoplastic diseases. Our follow up experiment indicated that (1) an overexpression of RAMP2-AS1 reduced GBM cell proliferation in vitro and also reduced GBM xenograft tumors in vivo; (2) NOTCH3 and RAMP2-AS1 co-expression rescued the inhibitory action of RAMP2-AS1 in glioblastoma cells; and (3) RNA pull-down assay revealed a direct interaction of RAMP2-AS1 with DHC10, which may consequently inhibit, as we hypothesize, the expression of NOTCH3 and its downstream signaling molecule HES1 in GBM. Taken together, our data revealed that lncRNA expression profile in GBM tissue was significantly altered; and RAMP2-AS1 might play a tumor suppressive role in GBM through an indirect inhibition of NOTCH3. Our results provided some insights into understanding the key roles of lncRNA-mRNA co-regulation in human GBM and the mechanisms responsible for GBM progression and pathogenesis.

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Section: Methodsmentioning

confidence: 99%

The Potential Roles of Long Noncoding RNAs (lncRNA) in Glioblastoma Development

Liu

Mitra

Zhao

et al. 2016

Molecular Cancer Therapeutics

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“…We applied lncRNA2 function 17 software which include functional annotation of 9625 human lncRNA genes to annotate the DEIs. All nodes in Gene Ontology (GO) and a total of 4380 function pathways were included in this functional pathway.…”

Section: Go Annotation and Kegg Pathway Analysismentioning

confidence: 99%

“…Data of all the 634 oncogenes were from COSMIC data set, 17,18 which included information of somatic mutation associated with all kinds of cancers. The whole 1452 tumor suppressor gene data were extracted from TSGene data set and TAG data set.…”

Section: Collection Of Oncogenes and Tumor Suppressor Genes (Tsgs)mentioning

confidence: 99%

Co-expression network analysis of long noncoding RNAs (IncRNAs) and cancer genes revealsSFTA1P and CASC2abnormalities in lung squamous cell carcinoma

Huang

et al. 2017

Cancer Biology & Therapy

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Lung squamous cell carcinoma(LSCC) is the most common and aggressive lung tumor with poor clinical outcome. Previously studies showed that deregulation of long noncoding RNAs (lncRNAs) were involved in LSCC. We intended to figure out the role of lncRNAs in the regulation process of cancer-related genes and pathways they are involved. Data of 552 samples, including 501 cancer samples and 51 normal ones, were extracted from The Cancer Genome Atlas (TCGA). Differentially expressed lncRNAs (DEIs) were screened out (FDR<0.05, jlogFCj>1) and then followed by GO ontology and KEGG annotation analysis. Oncogenes from COSMIC data set and Tumor suppressor genes (TSGs) from TSGene data set were collected and analyzed by gene Set Enrichment Analysis (GSEA) . The differentially expressed oncogenes and tumor supressor gene (TSGs) were obtained and co-expression analysis was conducted to generate co-expression lncRNA-gene pairs, which can be helpful in figuring out the role of lncRNA in the regulation of oncogenes and tumor suppressor genes. A total of 31 lncRNAs with low expression levels and 37 lncRNAs with high expression levels were screened out and most of them were enriched in pathways such as meiosis, male gamete generation, defensins. Of note, SFTA1P and CASC2 were found to be related with most of the oncogenes and TSGs by co-expression analysis. We suggested SFTA1P and CASC2 played important role in the regulation of both oncogene and TSGs during the carcinogenesis of LSCC and have the potential to be applied in future diagnosis, prognostic process and target therapy of LSCC.

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“…Several databases have been developed to curate computationally predicted and experimentally veriied lncRNAs, such as LncRNAdb [194], GENCODE [137], lncRNAtor [7], lncRNome [195], NONCODE [135], lncRNAWiki [134], LncRNA2Function [143] and starBase v2.0 [196]. LncRNAdb was the irst lncRNA database [194] and its updated version (LncRNAdb v2.0) integrates lncRNAs reported in livestock species (catle, sheep, pig, horse and chicken) [131].…”

Section: Functional Inference Of Lncrnamentioning

confidence: 99%

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

Ngoc¹,

Dudemaine²,

Fomenky³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

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The recent remarkable development of transcriptomics technologies, especially next generation sequencing technologies, allows deeper exploration of the hidden landscapes of complex traits and creates great opportunities to improve livestock productivity and welfare. Non-coding RNAs (ncRNAs), RNA molecules that are not translated into proteins, are key transcriptional regulators of health and production traits, thus, transcriptomics analyses of ncRNAs are important for a beter understanding of the regulatory architecture of livestock phenotypes. In this chapter, we present an overview of common frameworks for generating and processing RNA sequence data to obtain ncRNA transcripts. Then, we review common approaches for analyzing ncRNA transcriptome data and present current state of the art methods for identiication of ncRNAs and functional inference of identiied ncRNAs, with emphasis on tools for livestock species. We also discuss future challenges and perspectives for ncRNA transcriptome data analysis in livestock species.

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LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data

Cited by 126 publications

References 43 publications

The Potential Roles of Long Noncoding RNAs (lncRNA) in Glioblastoma Development

The Potential Roles of Long Noncoding RNAs (lncRNA) in Glioblastoma Development

Co-expression network analysis of long noncoding RNAs (IncRNAs) and cancer genes revealsSFTA1P and CASC2abnormalities in lung squamous cell carcinoma

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

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