Publication:
Topological, functional, and structural analyses of protein-protein interaction networks of breast cancer lung and brain metastases

dc.contributor.coauthorN/A
dc.contributor.departmentDepartment of Computer Engineering
dc.contributor.departmentDepartment of Chemical and Biological Engineering
dc.contributor.departmentGraduate School of Sciences and Engineering
dc.contributor.kuauthorGürsoy, Attila
dc.contributor.kuauthorHalakou, Farideh
dc.contributor.kuauthorKeskin, Özlem
dc.contributor.kuauthorKılıç, Emel Şen
dc.contributor.schoolcollegeinstituteCollege of Engineering
dc.contributor.schoolcollegeinstituteGRADUATE SCHOOL OF SCIENCES AND ENGINEERING
dc.date.accessioned2024-11-09T23:42:59Z
dc.date.issued2017
dc.description.abstractBreast cancer is the second most common cause of death among women. However, it is not deadly if the cancerous cells remain in the breast. The life threat starts when cancerous cells travel to other parts of body like lung, liver, bone and brain. So, most breast cancer deaths derive from metastasis to other organs. In this study, we introduce novel proteins and cellular pathways that play important roles in brain and lung metastases of breast cancer using Protein-Protein Interaction (PPI) networks. Our topological analysis identified genes such as RPL5, MMP2 and DPP4 which are already known to be associated with lung or brain metastasis. Additionally, we found four and nine novel candidate genes that are specific to lung and brain metastases, respectively. The functional enrichment analysis showed that KEGG pathways associated with the immune system and infectious diseases, particularly the chemokine signaling pathway, are important for lung metastasis. On the other hand, pathways related to genetic information processing were more involved in brain metastasis. By enriching the traditional PPI network with protein structural data, we show the effects of mutations on specific protein-protein interactions. By using the different conformations of protein CXCL12, we show the effect of H25R mutation on CXCL12 dimerization.
dc.description.indexedbyWOS
dc.description.indexedbyScopus
dc.description.openaccessYES
dc.description.publisherscopeInternational
dc.description.sponsoredbyTubitakEuTÜBİTAK
dc.identifier.doi10.1109/CIBCB.2017.8058539
dc.identifier.isbn9781-4673-8988-4
dc.identifier.scopus2-s2.0-85034649001
dc.identifier.urihttps://doi.org/10.1109/CIBCB.2017.8058539
dc.identifier.urihttps://hdl.handle.net/20.500.14288/13417
dc.identifier.wos463852500020
dc.keywordsBreast cancer
dc.keywordsMetastasis
dc.keywordsPPI network
dc.keywordsProtein-protein interactions
dc.keywordsStructural PPI network
dc.language.isoeng
dc.publisherInstitute of Electrical and Electronics Engineers (IEEE)
dc.relation.ispartof2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2017
dc.subjectComputer science
dc.subjectMathematical and computational biology
dc.titleTopological, functional, and structural analyses of protein-protein interaction networks of breast cancer lung and brain metastases
dc.typeConference Proceeding
dspace.entity.typePublication
local.contributor.kuauthorHalakou, Farideh
local.contributor.kuauthorGürsoy, Attila
local.contributor.kuauthorKılıç, Emel Şen
local.contributor.kuauthorKeskin, Özlem
local.publication.orgunit1GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
local.publication.orgunit1College of Engineering
local.publication.orgunit2Department of Computer Engineering
local.publication.orgunit2Department of Chemical and Biological Engineering
local.publication.orgunit2Graduate School of Sciences and Engineering
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