{"id":"https://openalex.org/W2057922644","doi":"https://doi.org/10.1145/2695664.2695773","title":"Discovering weighted motifs in gene co-expression networks","display_name":"Discovering weighted motifs in gene co-expression networks","publication_year":2015,"publication_date":"2015-04-13","ids":{"openalex":"https://openalex.org/W2057922644","doi":"https://doi.org/10.1145/2695664.2695773","mag":"2057922644"},"language":"en","primary_location":{"id":"doi:10.1145/2695664.2695773","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2695664.2695773","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 30th Annual ACM Symposium on Applied Computing","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://repositorio.inesctec.pt/handle/123456789/6967","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014999744","display_name":"Sarvenaz Choobdar","orcid":null},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Sarvenaz Choobdar","raw_affiliation_strings":["Universidade do Porto, Portugal","Universidade do Porto - Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universidade do Porto, Portugal","institution_ids":["https://openalex.org/I182534213"]},{"raw_affiliation_string":"Universidade do Porto - Portugal","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114374332","display_name":"Pedro Ribeiro","orcid":"https://orcid.org/0000-0002-5768-1383"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Pedro Ribeiro","raw_affiliation_strings":["Universidade do Porto, Portugal","Universidade do Porto - Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universidade do Porto, Portugal","institution_ids":["https://openalex.org/I182534213"]},{"raw_affiliation_string":"Universidade do Porto - Portugal","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100363368","display_name":"Fernando Silva","orcid":"https://orcid.org/0000-0001-8411-7094"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Fernando Silva","raw_affiliation_strings":["Universidade do Porto, Portugal","Universidade do Porto - Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universidade do Porto, Portugal","institution_ids":["https://openalex.org/I182534213"]},{"raw_affiliation_string":"Universidade do Porto - Portugal","institution_ids":["https://openalex.org/I182534213"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I182534213"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"10","last_page":"17"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9970999956130981,"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":0.9965000152587891,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/network-motif","display_name":"Network motif","score":0.666993260383606},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.6204385757446289},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5975262522697449},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.5014896392822266},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49082955718040466},{"id":"https://openalex.org/keywords/statistic","display_name":"Statistic","score":0.48136240243911743},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.47113436460494995},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4630117416381836},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4607679843902588},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.456278920173645},{"id":"https://openalex.org/keywords/thresholding","display_name":"Thresholding","score":0.42940810322761536},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.42408937215805054},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41627007722854614},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.38579243421554565},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3172975778579712},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2901880145072937},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28600582480430603},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20956996083259583},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.12042924761772156}],"concepts":[{"id":"https://openalex.org/C60723933","wikidata":"https://www.wikidata.org/wiki/Q7001080","display_name":"Network motif","level":3,"score":0.666993260383606},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.6204385757446289},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5975262522697449},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.5014896392822266},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49082955718040466},{"id":"https://openalex.org/C89128539","wikidata":"https://www.wikidata.org/wiki/Q1949963","display_name":"Statistic","level":2,"score":0.48136240243911743},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.47113436460494995},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4630117416381836},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4607679843902588},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.456278920173645},{"id":"https://openalex.org/C191178318","wikidata":"https://www.wikidata.org/wiki/Q2256906","display_name":"Thresholding","level":3,"score":0.42940810322761536},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.42408937215805054},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41627007722854614},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.38579243421554565},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3172975778579712},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2901880145072937},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28600582480430603},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20956996083259583},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.12042924761772156},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2695664.2695773","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2695664.2695773","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 30th Annual ACM Symposium on Applied Computing","raw_type":"proceedings-article"},{"id":"pmh:oai:repositorio.inesctec.pt:123456789/6967","is_oa":true,"landing_page_url":"http://repositorio.inesctec.pt/handle/123456789/6967","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"conference object"}],"best_oa_location":{"id":"pmh:oai:repositorio.inesctec.pt:123456789/6967","is_oa":true,"landing_page_url":"http://repositorio.inesctec.pt/handle/123456789/6967","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"conference object"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1167214205","display_name":null,"funder_award_id":"COMPETE","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1578237752","display_name":null,"funder_award_id":"COMPETE","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G2416185022","display_name":null,"funder_award_id":"NORTE-07-0124-FEDER-000059","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G282610808","display_name":null,"funder_award_id":"SFRH/BD/72697/2010","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G287731076","display_name":null,"funder_award_id":"-01-0124-FEDER-037281","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G436679445","display_name":null,"funder_award_id":"SFRH/BPD/81695/2011","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G5128072183","display_name":null,"funder_award_id":"NORTE-07-0124-FEDER-000059","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W96200431","https://openalex.org/W1553420678","https://openalex.org/W1561416896","https://openalex.org/W1671250342","https://openalex.org/W1932560099","https://openalex.org/W1981124118","https://openalex.org/W1989119979","https://openalex.org/W1991613592","https://openalex.org/W1995907191","https://openalex.org/W2000367221","https://openalex.org/W2023832559","https://openalex.org/W2052938577","https://openalex.org/W2057498577","https://openalex.org/W2057626690","https://openalex.org/W2060705109","https://openalex.org/W2067273299","https://openalex.org/W2068229930","https://openalex.org/W2070491228","https://openalex.org/W2074041690","https://openalex.org/W2082565035","https://openalex.org/W2103017472","https://openalex.org/W2110065044","https://openalex.org/W2118349699","https://openalex.org/W2123838014","https://openalex.org/W2124025352","https://openalex.org/W2138582694","https://openalex.org/W2149640531","https://openalex.org/W2150881673","https://openalex.org/W2151820055","https://openalex.org/W2153624566","https://openalex.org/W2160556205","https://openalex.org/W2161917555","https://openalex.org/W2162142896","https://openalex.org/W2166481425","https://openalex.org/W2170726034","https://openalex.org/W2262408051","https://openalex.org/W3016005719","https://openalex.org/W4213245422","https://openalex.org/W6603982109","https://openalex.org/W6678511256","https://openalex.org/W6684661360"],"related_works":["https://openalex.org/W3079957389","https://openalex.org/W2796517744","https://openalex.org/W15348386","https://openalex.org/W2807926763","https://openalex.org/W2951915565","https://openalex.org/W4205962317","https://openalex.org/W2090574217","https://openalex.org/W2143557297","https://openalex.org/W3119507950","https://openalex.org/W2129949791"],"abstract_inverted_index":{"A":[0],"important":[1],"dimension":[2],"of":[3,11,17,22,30,46,64,82,93,113,142,150,170,180,213,244],"complex":[4],"networks":[5,56,152,164,182,201],"is":[6,33,183],"embedded":[7],"in":[8,68,128],"the":[9,20,34,44,65,69,111,116,134,139,143,146,181,200,210,257],"weights":[10,112],"its":[12],"edges.":[13],"Incorporating":[14],"this":[15,74],"source":[16],"information":[18,42,66,84],"on":[19,234],"analysis":[21,247],"a":[23,78,105,108,119,129,218],"network":[24,101],"can":[25],"greatly":[26],"enhance":[27],"our":[28,159,190,214],"understanding":[29],"it.":[31],"This":[32],"case":[35],"for":[36,59],"gene":[37,49,54,87,162,245],"co-expression":[38,55,88,163],"networks,":[39],"which":[40],"encapsulate":[41],"about":[43],"strength":[45],"correlation":[47],"between":[48],"expression":[50],"profiles.":[51],"Classical":[52],"unweighted":[53],"use":[57,133,229],"thresholding":[58],"defining":[60],"connectivity,":[61],"losing":[62],"some":[63],"contained":[67],"different":[70,121,168],"connection":[71],"strengths.":[72],"In":[73],"paper,":[75],"we":[76,194],"propose":[77],"mining":[79],"method":[80],"capable":[81],"extracting":[83],"from":[85],"weighted":[86,186,215,250],"networks.":[89],"We":[90,103,132,157,207,228],"study":[91],"groups":[92],"differently":[94],"connected":[95],"nodes":[96],"and":[97,172,189,202,239],"their":[98],"importance":[99],"as":[100,107],"motifs.":[102,259],"define":[104],"subgraph":[106,117],"motif":[109,187,222],"if":[110],"edges":[114,225],"inside":[115],"hold":[118],"significantly":[120],"distribution":[122],"than":[123,256],"what":[124],"would":[125],"be":[126],"found":[127],"random":[130,151],"distribution.":[131],"Kolmogorov-Smirnov":[135],"test":[136],"to":[137,153,161,166,174,197,217],"calculate":[138],"significance":[140],"score":[141],"subgraph,":[144],"avoiding":[145],"time":[147],"consuming":[148],"generation":[149],"determine":[154],"statistic":[155],"significance.":[156],"apply":[158],"approach":[160,216],"related":[165],"three":[167],"types":[169],"cancer":[171],"also":[173,208],"two":[175],"healthy":[176],"datasets.":[177],"The":[178,242],"structure":[179],"compared":[184],"using":[185],"profiles,":[188],"results":[191,243],"show":[192,248],"that":[193,249],"are":[195,226,252],"able":[196],"clearly":[198],"distinguish":[199],"separate":[203],"them":[204],"by":[205],"type.":[206],"compare":[209],"biological":[211,235],"relevance":[212],"more":[219,254],"classical":[220],"binary":[221,258],"profile,":[223],"where":[224],"unweighted.":[227],"shared":[230],"Gene":[231],"Ontology":[232],"annotations":[233],"processes,":[236],"cellular":[237],"components":[238],"molecular":[240],"functions.":[241],"enrichment":[246],"motifs":[251],"biologically":[253],"significant":[255]},"counts_by_year":[{"year":2017,"cited_by_count":5}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
