Compact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Park, Heejin | - |
dc.contributor.author | Bae, Junwoo | - |
dc.contributor.author | Kim, Hyunwoo | - |
dc.contributor.author | Kim, Sangok | - |
dc.contributor.author | Kim, Hokeun | - |
dc.contributor.author | Mun, Dong-Gi | - |
dc.contributor.author | Joh, Yoonsung | - |
dc.contributor.author | Lee, Wonyeop | - |
dc.contributor.author | Chae, Sehyun | - |
dc.contributor.author | Lee, Sanghyuk | - |
dc.contributor.author | Kim, Hark Kyun | - |
dc.contributor.author | Hwang, Daehee | - |
dc.contributor.author | Lee, Sang-Won | - |
dc.contributor.author | Paek, Eunok | - |
dc.date.accessioned | 2021-09-05T02:35:00Z | - |
dc.date.available | 2021-09-05T02:35:00Z | - |
dc.date.created | 2021-06-15 | - |
dc.date.issued | 2014-12 | - |
dc.identifier.issn | 1615-9853 | - |
dc.identifier.uri | https://scholar.korea.ac.kr/handle/2021.sw.korea/96662 | - |
dc.description.abstract | In proteogenomic analysis, construction of a compact, customized database from mRNA-seq data and a sensitive search of both reference and customized databases are essential to accurately determine protein abundances and structural variations at the protein level. However, these tasks have not been systematically explored, but rather performed in an ad-hoc fashion. Here, we present an effective method for constructing a compact database containing comprehensive sequences of sample-specific variantssingle nucleotide variants, insertions/deletions, and stop-codon mutations derived from Exome-seq and RNA-seq data. It, however, occupies less space by storing variant peptides, not variant proteins. We also present an efficient search method for both customized and reference databases. The separate searches of the two databases increase the search time, and a unified search is less sensitive to identify variant peptides due to the smaller size of the customized database, compared to the reference database, in the target-decoy setting. Our method searches the unified database once, but performs target-decoy validations separately. Experimental results show that our approach is as fast as the unified search and as sensitive as the separate searches. Our customized database includes mutation information in the headers of variant peptides, thereby facilitating the inspection of peptide-spectrum matches. | - |
dc.language | English | - |
dc.language.iso | en | - |
dc.publisher | WILEY-BLACKWELL | - |
dc.subject | RNA-SEQ DATA | - |
dc.subject | PEPTIDE IDENTIFICATION | - |
dc.subject | PROTEIN IDENTIFICATION | - |
dc.subject | CONSTRUCTION | - |
dc.subject | PROTEOMICS | - |
dc.subject | FRAMEWORK | - |
dc.subject | STRATEGY | - |
dc.subject | CANCER | - |
dc.subject | PAIRS | - |
dc.title | Compact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses | - |
dc.type | Article | - |
dc.contributor.affiliatedAuthor | Lee, Sang-Won | - |
dc.identifier.doi | 10.1002/pmic.201400225 | - |
dc.identifier.scopusid | 2-s2.0-84913526299 | - |
dc.identifier.wosid | 000345915200012 | - |
dc.identifier.bibliographicCitation | PROTEOMICS, v.14, no.23-24, pp.2742 - 2749 | - |
dc.relation.isPartOf | PROTEOMICS | - |
dc.citation.title | PROTEOMICS | - |
dc.citation.volume | 14 | - |
dc.citation.number | 23-24 | - |
dc.citation.startPage | 2742 | - |
dc.citation.endPage | 2749 | - |
dc.type.rims | ART | - |
dc.type.docType | Article | - |
dc.description.journalClass | 1 | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.relation.journalResearchArea | Biochemistry & Molecular Biology | - |
dc.relation.journalWebOfScienceCategory | Biochemical Research Methods | - |
dc.relation.journalWebOfScienceCategory | Biochemistry & Molecular Biology | - |
dc.subject.keywordPlus | RNA-SEQ DATA | - |
dc.subject.keywordPlus | PEPTIDE IDENTIFICATION | - |
dc.subject.keywordPlus | PROTEIN IDENTIFICATION | - |
dc.subject.keywordPlus | CONSTRUCTION | - |
dc.subject.keywordPlus | PROTEOMICS | - |
dc.subject.keywordPlus | FRAMEWORK | - |
dc.subject.keywordPlus | STRATEGY | - |
dc.subject.keywordPlus | CANCER | - |
dc.subject.keywordPlus | PAIRS | - |
dc.subject.keywordAuthor | Bioinformatics | - |
dc.subject.keywordAuthor | Early onset gastric cancer | - |
dc.subject.keywordAuthor | Peptide identification | - |
dc.subject.keywordAuthor | Proteogenomics | - |
dc.subject.keywordAuthor | Sequence database | - |
Items in ScholarWorks are protected by copyright, with all rights reserved, unless otherwise indicated.
(02841) 서울특별시 성북구 안암로 14502-3290-1114
COPYRIGHT © 2021 Korea University. All Rights Reserved.
Certain data included herein are derived from the © Web of Science of Clarivate Analytics. All rights reserved.
You may not copy or re-distribute this material in whole or in part without the prior written consent of Clarivate Analytics.