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Integrating proteomic and phosphoproteomic data for pathway analysis in breast cancer

Abstract Background As protein is the basic unit of cell function and biological pathway, shotgun proteomics, the large-scale analysis of proteins, is contributing greatly to our understanding of disease mechanisms. Proteomics study could detect the changes of both protein expression and modificatio... Full description

Journal Title: BMC Systems Biology 01 December 2018, Vol.12(S8), pp.97-105
Main Author: Jie Ren
Other Authors: Bo Wang , Jing Li
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 1752-0509 ; DOI: 10.1186/s12918-018-0646-y
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recordid: doaj_soai_doaj_org_article_94356407b84244e0bbb59f3161393a56
title: Integrating proteomic and phosphoproteomic data for pathway analysis in breast cancer
format: Article
creator:
  • Jie Ren
  • Bo Wang
  • Jing Li
subjects:
  • Proteomics
  • Phosphoproteomics
  • Integration
  • Pathway Analysis
  • Breast Cancer
  • Biology
ispartof: BMC Systems Biology, 01 December 2018, Vol.12(S8), pp.97-105
description: Abstract Background As protein is the basic unit of cell function and biological pathway, shotgun proteomics, the large-scale analysis of proteins, is contributing greatly to our understanding of disease mechanisms. Proteomics study could detect the changes of both protein expression and modification. With the releases of large-scale cancer proteome studies, how to integrate acquired proteomic and phosphoproteomic data in more comprehensive pathway analysis becomes implemented, but remains challenging. Integrative pathway analysis at proteome level provides a systematic insight into the signaling network adaptations in the development of cancer. Results Here we integrated proteomic and phosphoproteomic data to perform pathway prioritization in breast cancer. We manually collected and curated breast cancer well-known related pathways from the literature as target pathways (TPs) or positive control in method evaluation. Three different strategies including Hypergeometric test based...
language: eng
source:
identifier: E-ISSN: 1752-0509 ; DOI: 10.1186/s12918-018-0646-y
fulltext: fulltext_linktorsrc
issn:
  • 1752-0509
  • 17520509
url: Link


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titleIntegrating proteomic and phosphoproteomic data for pathway analysis in breast cancer
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identifierE-ISSN: 1752-0509 ; DOI: 10.1186/s12918-018-0646-y
subjectProteomics ; Phosphoproteomics ; Integration ; Pathway Analysis ; Breast Cancer ; Biology
descriptionAbstract Background As protein is the basic unit of cell function and biological pathway, shotgun proteomics, the large-scale analysis of proteins, is contributing greatly to our understanding of disease mechanisms. Proteomics study could detect the changes of both protein expression and modification. With the releases of large-scale cancer proteome studies, how to integrate acquired proteomic and phosphoproteomic data in more comprehensive pathway analysis becomes implemented, but remains challenging. Integrative pathway analysis at proteome level provides a systematic insight into the signaling network adaptations in the development of cancer. Results Here we integrated proteomic and phosphoproteomic data to perform pathway prioritization in breast cancer. We manually collected and curated breast cancer well-known related pathways from the literature as target pathways (TPs) or positive control in method evaluation. Three different strategies including Hypergeometric test based...
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Abstract Background As protein is the basic unit of cell function and biological pathway, shotgun proteomics, the large-scale analysis of proteins, is contributing greatly to our understanding of disease mechanisms. Proteomics study could detect the changes of both protein expression and modification. With the releases of large-scale cancer proteome studies, how to integrate acquired proteomic and phosphoproteomic data in more comprehensive pathway analysis becomes implemented, but remains challenging. Integrative pathway analysis at proteome level provides a systematic insight into the signaling network adaptations in the development of cancer. Results Here we integrated proteomic and phosphoproteomic data to perform pathway prioritization in breast cancer. We manually collected and curated breast cancer well-known related pathways from the literature as target pathways (TPs) or positive control in method evaluation. Three different strategies including Hypergeometric test based...

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Abstract Background As protein is the basic unit of cell function and biological pathway, shotgun proteomics, the large-scale analysis of proteins, is contributing greatly to our understanding of disease mechanisms. Proteomics study could detect the changes of both protein expression and modification. With the releases of large-scale cancer proteome studies, how to integrate acquired proteomic and phosphoproteomic data in more comprehensive pathway analysis becomes implemented, but remains challenging. Integrative pathway analysis at proteome level provides a systematic insight into the signaling network adaptations in the development of cancer. Results Here we integrated proteomic and phosphoproteomic data to perform pathway prioritization in breast cancer. We manually collected and curated breast cancer well-known related pathways from the literature as target pathways (TPs) or positive control in method evaluation. Three different strategies including Hypergeometric test based...

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