{"id":"https://openalex.org/W2577837183","doi":"https://doi.org/10.1109/bibm.2016.7822538","title":"Network-based analysis of reverse phase protein array data","display_name":"Network-based analysis of reverse phase protein array data","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2577837183","doi":"https://doi.org/10.1109/bibm.2016.7822538","mag":"2577837183"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2016.7822538","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822538","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027269811","display_name":"Rency S. Varghese","orcid":"https://orcid.org/0000-0002-4236-7316"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rency S Varghese","raw_affiliation_strings":["Department of Oncology, Georgetown University, Washington, DC, USA"],"affiliations":[{"raw_affiliation_string":"Department of Oncology, Georgetown University, Washington, DC, USA","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102508019","display_name":"Yiming Zuo","orcid":null},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yiming Zuo","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA","Department of Oncology, Georgetown University, Washington, DC, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Oncology, Georgetown University, Washington, DC, USA","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000991048","display_name":"Yi Zhao","orcid":"https://orcid.org/0000-0001-6046-8420"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]},{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yi Zhao","raw_affiliation_strings":["Department of Biostatistics, Brown University, Rhode Island, Providence, USA","Department of Oncology, Georgetown University, Washington, DC, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Brown University, Rhode Island, Providence, USA","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Department of Oncology, Georgetown University, Washington, DC, USA","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100675815","display_name":"Yongwei Zhang","orcid":"https://orcid.org/0000-0003-2900-1149"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yong-Wei Zhang","raw_affiliation_strings":["Department of Oncology, Georgetown University, Washington, DC, USA"],"affiliations":[{"raw_affiliation_string":"Department of Oncology, Georgetown University, Washington, DC, USA","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066733981","display_name":"Sandra A. Jablonski","orcid":"https://orcid.org/0000-0001-7220-8159"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sandra A Jablonski","raw_affiliation_strings":["Department of Oncology, Georgetown University, Washington, DC, USA"],"affiliations":[{"raw_affiliation_string":"Department of Oncology, Georgetown University, Washington, DC, USA","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073337554","display_name":"Mariaelena Pierobon","orcid":"https://orcid.org/0000-0003-2084-1029"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mariaelena Pierobon","raw_affiliation_strings":["Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA"],"affiliations":[{"raw_affiliation_string":"Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023762376","display_name":"Emanuel F. Petricoin","orcid":"https://orcid.org/0000-0001-9146-5572"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emanuel F Petricoin","raw_affiliation_strings":["Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA"],"affiliations":[{"raw_affiliation_string":"Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025125310","display_name":"Habtom W. Ressom","orcid":"https://orcid.org/0000-0001-9296-2132"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Habtom W Ressom","raw_affiliation_strings":["Department of Oncology, Georgetown University, Washington, DC, USA"],"affiliations":[{"raw_affiliation_string":"Department of Oncology, Georgetown University, Washington, DC, USA","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045107557","display_name":"Louis M. Weiner","orcid":"https://orcid.org/0000-0001-5192-0710"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Louis M Weiner","raw_affiliation_strings":["Department of Oncology, Georgetown University, Washington, DC, USA"],"affiliations":[{"raw_affiliation_string":"Department of Oncology, Georgetown University, Washington, DC, USA","institution_ids":["https://openalex.org/I184565670"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5027269811"],"corresponding_institution_ids":["https://openalex.org/I184565670"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1103964,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"57","issue":null,"first_page":"312","last_page":"317"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9937999844551086,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6504822373390198},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5108284950256348},{"id":"https://openalex.org/keywords/protein-microarray","display_name":"Protein microarray","score":0.4758707880973816},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44283390045166016},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.4112699627876282},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3372807204723358},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25323742628097534},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.22666412591934204},{"id":"https://openalex.org/keywords/microarray","display_name":"Microarray","score":0.1480879783630371}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6504822373390198},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5108284950256348},{"id":"https://openalex.org/C195814341","wikidata":"https://www.wikidata.org/wiki/Q494918","display_name":"Protein microarray","level":5,"score":0.4758707880973816},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44283390045166016},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.4112699627876282},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3372807204723358},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25323742628097534},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.22666412591934204},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.1480879783630371}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2016.7822538","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822538","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6899999976158142,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1502739652","https://openalex.org/W1519967920","https://openalex.org/W1959107924","https://openalex.org/W1966663727","https://openalex.org/W1983340023","https://openalex.org/W2032346433","https://openalex.org/W2059686851","https://openalex.org/W2066636486","https://openalex.org/W2096283457","https://openalex.org/W2110065044","https://openalex.org/W2120018526","https://openalex.org/W2124681904","https://openalex.org/W2140593657","https://openalex.org/W2144370915","https://openalex.org/W2159675211","https://openalex.org/W2162475911","https://openalex.org/W2162632817","https://openalex.org/W2163430198","https://openalex.org/W2469147100","https://openalex.org/W2469796139","https://openalex.org/W2490926353"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"In":[0],"this":[1],"paper,":[2],"we":[3,151],"introduce":[4],"a":[5,76,105,147],"computational":[6],"method":[7,27],"for":[8,82,153],"constructing":[9],"networks":[10,87,132],"based":[11,135,149],"on":[12,136],"reverse":[13],"phase":[14],"protein":[15,24,102,139,166],"array":[16],"(RPPA)":[17],"data":[18,55],"to":[19,30,117,156],"identify":[20,158],"complex":[21],"patterns":[22,155],"in":[23,43,68,169],"signaling.":[25],"The":[26],"is":[28,115],"applied":[29],"phosphoproteomic":[31],"profiles":[32],"of":[33,38,101,108,126],"basal":[34],"expression":[35,99,167],"and":[36,51,61,91],"activation/phosphorylation":[37],"76":[39],"key":[40,159],"signaling":[41],"proteins":[42,90,93,120],"three":[44,128],"breast":[45,83],"cancer":[46,84],"cell":[47],"lines":[48],"(MCF7,":[49],"LCC1,":[50],"LCC9).":[52],"Temporal":[53],"RPPA":[54,144],"are":[56,73,94,133,163],"acquired":[57],"at":[58,124],"48h,":[59],"96h,":[60],"144h":[62],"after":[63],"knocking":[64],"down":[65],"four":[66],"genes":[67,72],"separate":[69],"experiments.":[70],"These":[71],"selected":[74,141],"from":[75,142],"previous":[77],"study":[78],"as":[79],"important":[80],"determinants":[81],"survival.":[85],"Interaction":[86],"between":[88],"the":[89,98,119,127,143],"phosphorylated":[92],"constructed":[95,134],"by":[96],"analyzing":[97],"levels":[100],"pairs":[103,140],"using":[104],"multivariate":[106],"analysis":[107],"variance":[109],"model.":[110],"A":[111],"new":[112],"scoring":[113],"criterion":[114],"introduced":[116],"determine":[118],"that":[121,162],"changed":[122],"significantly":[123],"each":[125],"time":[129],"points.":[130],"Signaling":[131],"statistically":[137],"significant":[138],"data.":[145],"Through":[146],"topology":[148],"analysis,":[150],"search":[152],"wiring":[154],"help":[157],"network":[160],"nodes":[161],"associated":[164],"with":[165],"changes":[168],"various":[170],"experimental":[171],"conditions.":[172]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}