FARNA: knowledgebase of inferred functions of non-coding RNA transcripts

Handle URI:
http://hdl.handle.net/10754/622041
Title:
FARNA: knowledgebase of inferred functions of non-coding RNA transcripts
Authors:
Alam, Tanvir ( 0000-0003-4844-0171 ) ; Uludag, Mahmut ( 0000-0001-8482-2172 ) ; Essack, Magbubah ( 0000-0003-2709-5356 ) ; Salhi, Adil; Ashoor, Haitham ( 0000-0003-2527-0317 ) ; Hanks, John B.; Kapfer, Craig Eric; Mineta, Katsuhiko ( 0000-0002-4727-045X ) ; Gojobori, Takashi ( 0000-0001-7850-1743 ) ; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Abstract:
Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, we present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcripts (2,734 microRNA and 7,555 long ncRNA) in 119 tissues and 177 primary cells of human. Since transcription factors (TFs) and TF co-factors (TcoFs) are crucial components of regulatory machinery for activation of gene transcription, cellular processes and diseases in which TFs and TcoFs are involved suggest functions of the transcripts they regulate. In FARNA, functions of a transcript are inferred from TFs and TcoFs whose genes co-express with the transcript controlled by these TFs and TcoFs in a considered cell/tissue. Transcripts were annotated using statistically enriched GO terms, pathways and diseases across cells/tissues based on guilt-by-association principle. Expression profiles across cells/tissues based on Cap Analysis of Gene Expression (CAGE) are provided. FARNA, having the most comprehensive function annotation of considered ncRNAs across widest spectrum of human cells/tissues, has a potential to greatly contribute to our understanding of ncRNA roles and their regulatory mechanisms in human. FARNA can be accessed at: http://cbrc.kaust.edu.sa/farna
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Alam T, Uludag M, Essack M, Salhi A, Ashoor H, et al. (2016) FARNA: knowledgebase of inferred functions of non-coding RNA transcripts. Nucleic Acids Research: gkw973. Available: http://dx.doi.org/10.1093/nar/gkw973.
Publisher:
Oxford University Press (OUP)
Journal:
Nucleic Acids Research
KAUST Grant Number:
URF/1/1976-04; CCF URF 1976
Issue Date:
12-Oct-2016
DOI:
10.1093/nar/gkw973
Type:
Article
ISSN:
0305-1048; 1362-4962
Sponsors:
King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [URF/1/1976-04]; KAUST base research funds (to V.B.B.). Funding for open access charge: KAUST [CCF URF 1976].
Additional Links:
http://nar.oxfordjournals.org/content/early/2016/10/24/nar.gkw973
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorAlam, Tanviren
dc.contributor.authorUludag, Mahmuten
dc.contributor.authorEssack, Magbubahen
dc.contributor.authorSalhi, Adilen
dc.contributor.authorAshoor, Haithamen
dc.contributor.authorHanks, John B.en
dc.contributor.authorKapfer, Craig Ericen
dc.contributor.authorMineta, Katsuhikoen
dc.contributor.authorGojobori, Takashien
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2016-12-20T05:52:11Z-
dc.date.available2016-12-20T05:52:11Z-
dc.date.issued2016-10-12en
dc.identifier.citationAlam T, Uludag M, Essack M, Salhi A, Ashoor H, et al. (2016) FARNA: knowledgebase of inferred functions of non-coding RNA transcripts. Nucleic Acids Research: gkw973. Available: http://dx.doi.org/10.1093/nar/gkw973.en
dc.identifier.issn0305-1048en
dc.identifier.issn1362-4962en
dc.identifier.doi10.1093/nar/gkw973en
dc.identifier.urihttp://hdl.handle.net/10754/622041-
dc.description.abstractNon-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, we present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcripts (2,734 microRNA and 7,555 long ncRNA) in 119 tissues and 177 primary cells of human. Since transcription factors (TFs) and TF co-factors (TcoFs) are crucial components of regulatory machinery for activation of gene transcription, cellular processes and diseases in which TFs and TcoFs are involved suggest functions of the transcripts they regulate. In FARNA, functions of a transcript are inferred from TFs and TcoFs whose genes co-express with the transcript controlled by these TFs and TcoFs in a considered cell/tissue. Transcripts were annotated using statistically enriched GO terms, pathways and diseases across cells/tissues based on guilt-by-association principle. Expression profiles across cells/tissues based on Cap Analysis of Gene Expression (CAGE) are provided. FARNA, having the most comprehensive function annotation of considered ncRNAs across widest spectrum of human cells/tissues, has a potential to greatly contribute to our understanding of ncRNA roles and their regulatory mechanisms in human. FARNA can be accessed at: http://cbrc.kaust.edu.sa/farnaen
dc.description.sponsorshipKing Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [URF/1/1976-04]; KAUST base research funds (to V.B.B.). Funding for open access charge: KAUST [CCF URF 1976].en
dc.publisherOxford University Press (OUP)en
dc.relation.urlhttp://nar.oxfordjournals.org/content/early/2016/10/24/nar.gkw973en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.comen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/en
dc.titleFARNA: knowledgebase of inferred functions of non-coding RNA transcriptsen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalNucleic Acids Researchen
dc.eprint.versionPublisher's Version/PDFen
kaust.authorAlam, Tanviren
kaust.authorUludag, Mahmuten
kaust.authorEssack, Magbubahen
kaust.authorSalhi, Adilen
kaust.authorAshoor, Haithamen
kaust.authorHanks, John B.en
kaust.authorKapfer, Craig Ericen
kaust.authorMineta, Katsuhikoen
kaust.authorGojobori, Takashien
kaust.authorBajic, Vladimir B.en
kaust.grant.numberURF/1/1976-04en
kaust.grant.numberCCF URF 1976en
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