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BRCA-Pathway: a structural integration and visualization system of TCGA breast cancer data on KEGG pathways

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dc.contributor.authorKim, Inyoung-
dc.contributor.authorChoi, Saemi-
dc.contributor.authorKim, Sun-
dc.date.accessioned2018-03-19T00:17:01Z-
dc.date.available2018-03-19T09:18:22Z-
dc.date.issued2018-02-19-
dc.identifier.citationBMC Bioinformatics, 19(Suppl 1):42ko_KR
dc.identifier.issn1471-2105-
dc.identifier.urihttps://hdl.handle.net/10371/139616-
dc.description.abstractBackground
Bioinformatics research for finding biological mechanisms can be done by analysis of transcriptome data with pathway based interpretation. Therefore, researchers have tried to develop tools to analyze transcriptome data with pathway based interpretation. Over the years, the amount of omics data has become huge, e.g., TCGA, and the data types to be analyzed have come in many varieties, including mutations, copy number variations, and transcriptome. We also need to consider a complex relationship with regulators of genes, particularly Transcription Factors(TF). However, there has not been a system for pathway based exploration and analysis of TCGA multi-omics data. In this reason, We have developed a web based system BRCA-Pathway to fulfill the need for pathway based analysis of TCGA multi-omics data.

Results
BRCA-Pathway is a structured integration and visual exploration system of TCGA breast cancer data on KEGG pathways. For data integration, a relational database is designed and used to integrate multi-omics data of TCGA-BRCA, KEGG pathway data, Hallmark gene sets, transcription factors, driver genes, and PAM50 subtypes. For data exploration, multi-omics data such as SNV, CNV and gene expression can be visualized simultaneously in KEGG pathway maps, together with transcription factors-target genes (TF-TG) correlation and relationships among cancer driver genes. In addition, Pathways summary and Oncoprint with mutual exclusivity sort can be generated dynamically with a request by the user. Data in BRCA-Pathway can be downloaded by REST API for further analysis.

Conclusions
BRCA-Pathway helps researchers navigate omics data towards potentially important genes, regulators, and discover complex patterns involving mutations, CNV, and gene expression data of various patient groups in the biological pathway context. In addition, mutually exclusive genomic alteration patterns in a specific pathway can be generated. BRCA-Pathway can provide an integrative perspective on the breast cancer omics data, which can help researchers discover new insights on the biological mechanisms of breast cancer.
ko_KR
dc.description.sponsorshipThis work was supported by a grant of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number : HI15C3224), and Collaborative Genome Program for Fostering New Post-Genome industry through the National Research Foundation of Korea (NRF) funded by the Ministry of Science ICT and Future Planning (No.NRF2014M3C9A3063541), and Institute for Information & communications Technology Promotion (IITP) grant funded by the Korea government (MSIP) (No.B0717-16-0098, Development of homomorphic encryption for DNA analysis and biometry authentication). The publication cost was funded by Institute for Information & communications Technology Promotion (IITP) grant funded by the Korea government (MSIP) (No.B0717-16-0098, Development of homomorphic encryption for DNA analysis and biometry authentication).ko_KR
dc.language.isoenko_KR
dc.publisherBioMed Centralko_KR
dc.subjectTCGA breast cancerko_KR
dc.subjectKEGG-Pathwayko_KR
dc.subjectGene expressionko_KR
dc.subjectMutationko_KR
dc.subjectCopy number variationko_KR
dc.titleBRCA-Pathway: a structural integration and visualization system of TCGA breast cancer data on KEGG pathwaysko_KR
dc.typeArticleko_KR
dc.contributor.AlternativeAuthor김인영-
dc.contributor.AlternativeAuthor최새미-
dc.contributor.AlternativeAuthor김순-
dc.identifier.doi10.1186/s12859-018-2016-6-
dc.language.rfc3066en-
dc.rights.holderThe Author(s)-
dc.date.updated2018-02-25T04:17:59Z-
Appears in Collections:
College of Engineering/Engineering Practice School (공과대학/대학원)Dept. of Computer Science and Engineering (컴퓨터공학부)Journal Papers (저널논문_컴퓨터공학부)
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