Show simple item record

dc.contributor.authorJha, Alokkumar
dc.contributor.authorKhan, Yasar
dc.contributor.authorIqbal, Aftab
dc.contributor.authorZappa, Achille
dc.contributor.authorMehdi, Muntazir
dc.contributor.authorSahay, Ratnesh
dc.contributor.authorRebholz-Schuhmann, Dietrich
dc.date.accessioned2018-08-08T08:04:26Z
dc.date.available2018-08-08T08:04:26Z
dc.date.issued2015-12-09
dc.identifier.citationJha, Alokkumar , Khan, Yasar , Mehdi, Muntazir , Iqbal, Aftab , Zappa, Achille , Sahay, Ratnesh , & Rebholz-Schuhmann, Dietrich. (2015). Linked Functional Annotation For Differentially Expressed Gene (DEG) Demonstrated using Illumina Body Map 2.0. Paper presented at the International Conference of Semantic Web Applications and Tools for the Life Sciences (SWAT4LS), Cambridge, United Kingdom, 09 December.en_IE
dc.identifier.urihttp://hdl.handle.net/10379/7472
dc.description.abstractSemantic Web technologies are core for the integration of disparate data resources. It can be used to exploit data from next generation sequencing (NGS) for therapeutic decisions regarding cancer. In this manuscript, we describe how different data resources, which inform on the expression of specific genes in a tissue and its variants, can be brought together to indicate a risk for tissue-specific cancer for NGS data. This approach can be used to judge patient genomic data against public reference data resources. The TCGA and COSMIC repositories are being processed to connect and query information concerning the expression of genes, copy number variants (CNV), and somatic mutations. We annotated sets of differential expression data provided from the Illumina Body map 2.0 (HBM) concerning 16 different tissue types and identify genes with an RPKM (Reads Per Kilobase of transcript per Million mapped reads) value greater than 0.5 as measure indicating an associated risk for cancer. Thus, the differential expressed genes from HBM can be associated with a tissue type and gene expressions in COSMIC and TCGA leading to a potential biomarker for that particular tissue specific cancer. In the case of ovarian cancer, we retrieved the genomic positions (loci) and the associated genes of potential biomarker candidates, and suggest that this approach and platform can serve future studies well. Altogether, the presented linked annotation platform is the first approach to represent the COSMIC data in an RDF format and to link the data with the TCGA datasets. The proposed approach enriches mutations by filling in missing links from COSMIC and TCGA datasets which in turn helped to map mutations with associated phenotypes.en_IE
dc.description.sponsorshipThis publication has emanated from research supported by the research grant from Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/2289.en_IE
dc.formatapplication/pdfen_IE
dc.language.isoenen_IE
dc.publisherCEUR-WS.orgen_IE
dc.relation.ispartofSWAT4LSen
dc.subjectDifferentially Expressed genes(DEG),en_IE
dc.subjectLinked dataen_IE
dc.subjectClinical genomicsen_IE
dc.subjectCopy Number Variation (CNV)en_IE
dc.titleLinked functional annotation for differentially expressed gene (DEG) demonstrated using Illumina Body Map 2.0en_IE
dc.typeConference Paperen_IE
dc.date.updated2018-07-10T17:49:02Z
dc.local.publishedsourcehttp://ceur-ws.org/Vol-1546/paper_12.pdfen_IE
dc.description.peer-reviewednon-peer-reviewed
dc.contributor.funderScience Foundation Irelanden_IE
dc.internal.rssid14543969
dc.local.contactRatnesh Nandan Sahay, Deri, Dangan Business Park, Nui Galway. 5253 Email: ratnesh.sahay@nuigalway.ie
dc.local.copyrightcheckedYes
dc.local.versionACCEPTED
nui.item.downloads1


Files in this item

Attribution-NonCommercial-NoDerivs 3.0 Ireland
This item is available under the Attribution-NonCommercial-NoDerivs 3.0 Ireland. No item may be reproduced for commercial purposes. Please refer to the publisher's URL where this is made available, or to notes contained in the item itself. Other terms may apply.

The following license files are associated with this item:

Thumbnail

This item appears in the following Collection(s)

Show simple item record