{"id":"https://openalex.org/W1978206260","doi":"https://doi.org/10.1145/2506583.2506690","title":"Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between Arabidopsis and Poplar","display_name":"Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between Arabidopsis and Poplar","publication_year":2013,"publication_date":"2013-09-22","ids":{"openalex":"https://openalex.org/W1978206260","doi":"https://doi.org/10.1145/2506583.2506690","mag":"1978206260"},"language":"en","primary_location":{"id":"doi:10.1145/2506583.2506690","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506690","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","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/A5053240500","display_name":"Daifeng Wang","orcid":"https://orcid.org/0000-0001-9190-3704"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daifeng Wang","raw_affiliation_strings":["Yale University","Yale University ;"],"affiliations":[{"raw_affiliation_string":"Yale University","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Yale University ;","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111605595","display_name":"Eric Pan","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Pan","raw_affiliation_strings":["Yale University","Yale University ;"],"affiliations":[{"raw_affiliation_string":"Yale University","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Yale University ;","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071245512","display_name":"Gang Fang","orcid":"https://orcid.org/0000-0002-2462-9124"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gang Fang","raw_affiliation_strings":["Yale University","Yale University ;"],"affiliations":[{"raw_affiliation_string":"Yale University","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Yale University ;","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101597727","display_name":"Sunita Kumari","orcid":"https://orcid.org/0000-0001-9166-1450"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sunita Kumari","raw_affiliation_strings":["Cold Spring Harbor Laboratory","#N##TAB##TAB##TAB##TAB# Cold Spring Harbor Laboratory#N##TAB##TAB##TAB#"],"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory","institution_ids":["https://openalex.org/I2750212522"]},{"raw_affiliation_string":"#N##TAB##TAB##TAB##TAB# Cold Spring Harbor Laboratory#N##TAB##TAB##TAB#","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014834476","display_name":"Fei He","orcid":"https://orcid.org/0000-0002-1165-3248"},"institutions":[{"id":"https://openalex.org/I200870766","display_name":"Brookhaven National Laboratory","ror":"https://ror.org/02ex6cf31","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I200870766","https://openalex.org/I39565521","https://openalex.org/I4210142672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fei He","raw_affiliation_strings":["Brookhaven National Laboratory","[Brookhaven National Laboratory]"],"affiliations":[{"raw_affiliation_string":"Brookhaven National Laboratory","institution_ids":["https://openalex.org/I200870766"]},{"raw_affiliation_string":"[Brookhaven National Laboratory]","institution_ids":["https://openalex.org/I200870766"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077105419","display_name":"Doreen Ware","orcid":"https://orcid.org/0000-0002-8125-3821"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Doreen Ware","raw_affiliation_strings":["Cold Spring Harbor Laboratory, USDA-ARS"],"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, USDA-ARS","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017591427","display_name":"Sergei Maslov","orcid":"https://orcid.org/0000-0002-3701-492X"},"institutions":[{"id":"https://openalex.org/I200870766","display_name":"Brookhaven National Laboratory","ror":"https://ror.org/02ex6cf31","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I200870766","https://openalex.org/I39565521","https://openalex.org/I4210142672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergei Maslov","raw_affiliation_strings":["Brookhaven National Laboratory","[Brookhaven National Laboratory]"],"affiliations":[{"raw_affiliation_string":"Brookhaven National Laboratory","institution_ids":["https://openalex.org/I200870766"]},{"raw_affiliation_string":"[Brookhaven National Laboratory]","institution_ids":["https://openalex.org/I200870766"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042321575","display_name":"Mark Gerstein","orcid":"https://orcid.org/0000-0002-9746-3719"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Gerstein","raw_affiliation_strings":["Yale University","Yale University ;"],"affiliations":[{"raw_affiliation_string":"Yale University","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Yale University ;","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5053240500"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":null,"apc_paid":null,"fwci":0.14178895,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.57273009,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"689","last_page":"690"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11237","display_name":"Plant Gene Expression Analysis","score":0.9941999912261963,"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/T11237","display_name":"Plant Gene Expression Analysis","score":0.9941999912261963,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9940000176429749,"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/T10171","display_name":"Biofuel production and bioconversion","score":0.9857000112533569,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/arabidopsis","display_name":"Arabidopsis","score":0.9029134511947632},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.860774040222168},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7417460083961487},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.550875186920166},{"id":"https://openalex.org/keywords/gene-family","display_name":"Gene family","score":0.5430412292480469},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.5253695249557495},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5172439217567444},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.47303980588912964},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.44996708631515503},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.06084024906158447}],"concepts":[{"id":"https://openalex.org/C2779491563","wikidata":"https://www.wikidata.org/wiki/Q157892","display_name":"Arabidopsis","level":4,"score":0.9029134511947632},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.860774040222168},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7417460083961487},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.550875186920166},{"id":"https://openalex.org/C5911399","wikidata":"https://www.wikidata.org/wiki/Q2278983","display_name":"Gene family","level":4,"score":0.5430412292480469},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.5253695249557495},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5172439217567444},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.47303980588912964},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.44996708631515503},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.06084024906158447},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2506583.2506690","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506690","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"},{"id":"pmh:oai:repository.cshl.edu:28879","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.6600000262260437,"display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W2024467994","https://openalex.org/W2082521963","https://openalex.org/W2098830771","https://openalex.org/W2156737316","https://openalex.org/W2163296727","https://openalex.org/W2165442817","https://openalex.org/W2171780673"],"related_works":["https://openalex.org/W2155421142","https://openalex.org/W2107185252","https://openalex.org/W2065442504","https://openalex.org/W2360211276","https://openalex.org/W3157566535","https://openalex.org/W2088917547","https://openalex.org/W3016406257","https://openalex.org/W1923070859","https://openalex.org/W2085717580","https://openalex.org/W2059099171"],"abstract_inverted_index":{"In":[0,412],"this":[1],"study,":[2],"we":[3,96,140,245,274,311,381],"established":[4],"a":[5,62,73,172,232,262],"computational":[6],"framework":[7,418,447],"of":[8,19,89,103,149,208,231,266,271,338,397],"comparative":[9,63,415],"network":[10,101,229,248,264,269,416],"analysis":[11,64,417],"to":[12,31,48,76,85,215,240,257,333,340,387,452],"identify":[13,388],"the":[14,87,100,125,142,147,150,183,187,225,247,251,295,314,362,383,389,394,398,424,468],"conserved":[15,79,184,315,440],"and":[16,41,98,115,119,205,285,307,318,405,435,437,441,444],"species-specific":[17,81,199,390,410,442],"functions":[18,58,82,88,243,260,443,460],"cell-wall":[20],"(CW)":[21],"related":[22,30,357,427],"genes":[23,45,91,105,132,152,169,194,212,226,253,301,317,321,330,345,402,428],"[1,":[24],"2],":[25],"an":[26],"important":[27],"gene":[28,68,126,202,420,455],"family":[29],"plant":[32,364],"bio-fuel":[33],"productions":[34],"across":[35,65,106,308,403,429,461],"multiple":[36,462],"tissue":[37,94,110,138,143,304,431],"types":[38,111,144,432],"between":[39,133,254],"Arabidopsis":[40,118,434],"Poplar.":[42],"The":[43,201,268,328],"co-expressed":[44,210,400],"are":[46,238,276,346],"believed":[47,239],"coordinate":[49,170,374],"in":[50,92,171,182,198,261,322,349,365,393,433],"transcription":[51],"so":[52,234],"that":[53,167,273,331,354],"they":[54,372],"may":[55,179,195,359,373],"have":[56,180,241],"similar":[57,173],"[3,":[59],"4].":[60],"Also,":[61],"species":[66],"for":[67,117,136,175,219,250,280,289,302,423,470],"co-expression":[69],"networks":[70,422],"(GCNs)":[71],"provides":[72],"systematic":[74],"way":[75,174],"understand":[77,86,258],"genomic":[78,384],"or":[80,325],"[5].":[83],"Therefore,":[84],"CW":[90,104,131,151,168,193,252,329,344,399],"different":[93,109,430],"types,":[95],"integrated":[97],"compared":[99],"characteristics":[102],"GCNs":[107],"from":[108],"including":[112],"leaf,":[113],"flower":[114],"shoot":[116],"Poplar":[120],"[6].":[121],"First,":[122],"by":[123,467],"aligning":[124],"coexpression":[127,421],"sub-networks":[128],"associated":[129],"with":[130,154,162,189,227,361,375,408,458],"two":[134,255,309],"plants":[135,256],"each":[137,303],"type,":[139],"grouped":[141],"based":[145],"on":[146],"alignment":[148],"along":[153,457],"their":[155,209,259,439,459],"neighboring":[156,211,401],"orthologous":[157],"genes.":[158],"For":[159,186],"those":[160,366],"tissues":[161,188],"good":[163],"alignments,":[164,191],"it":[165,352],"suggests":[166],"both":[176],"plants,":[177,310],"which":[178],"involved":[181],"functions.":[185,200,411],"poor":[190],"however,":[192],"take":[196],"part":[197],"ontology":[203],"enrichment":[204],"signaling":[206],"pathways":[207],"were":[213,336],"identified":[214,313,438],"provide":[216],"new":[217],"insight":[218],"cell":[220,355,425],"wall":[221,356,426],"biology.":[222],"Second,":[223],"since":[224],"high":[228],"centralities":[230,249,270],"GCN,":[233],"called":[235],"\"hub\"":[236],"genes,":[237],"key":[242],"[7],":[244],"investigated":[246],"global":[263,292,326,347],"point":[265],"view.":[267],"GCN":[272],"used":[275,382,451],"clustering":[277],"coefficient":[278],"(CC)":[279],"measuring":[281,290],"gene's":[282,291],"local":[283,324,370,377],"cliqueness,":[284],"eigenvector":[286],"centrality":[287],"(EC)":[288],"influence":[293],"over":[294],"entire":[296],"network.":[297],"Besides":[298],"finding":[299],"hub":[300,316,320,335],"type":[305],"within":[306],"also":[312,449],"tissue-specific":[319],"either":[323],"fashion.":[327],"happen":[332],"become":[334],"particularly":[337],"interest":[339],"study.":[341],"If":[342],"many":[343],"hubs":[348],"certain":[350,376],"tissues,":[351,367,404],"implies":[353],"activities":[358,378],"interact":[360],"whole":[363],"but":[368],"if":[369],"hubs,":[371],"only.":[379],"Finally,":[380],"variation":[385],"data":[386],"SNPs,":[391],"especially":[392],"promoter":[395],"regions":[396],"associate":[406],"them":[407],"corresponding":[409],"summary,":[413],"our":[414],"studied":[419],"Poplar,":[436],"variations.":[445],"This":[446],"can":[448],"be":[450],"study":[453],"other":[454],"families":[456],"species.":[463],"Copyright":[464],"\u00a9":[465],"2007":[466],"Association":[469],"Computing":[471],"Machinery.":[472]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
