{"id":"https://openalex.org/W2017831408","doi":"https://doi.org/10.1186/1471-2105-14-s13-s10","title":"Fuzzy clustering of CPP family in plants with evolution and interaction analyses","display_name":"Fuzzy clustering of CPP family in plants with evolution and interaction analyses","publication_year":2013,"publication_date":"2013-10-01","ids":{"openalex":"https://openalex.org/W2017831408","doi":"https://doi.org/10.1186/1471-2105-14-s13-s10","mag":"2017831408"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-s13-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s13-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S13-S10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S13-S10","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021334306","display_name":"Tao Lu","orcid":"https://orcid.org/0000-0002-8247-8387"},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tao Lu","raw_affiliation_strings":["School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, Nebraska, USA","School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, USA"],"affiliations":[{"raw_affiliation_string":"School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, Nebraska, USA","institution_ids":["https://openalex.org/I114395901"]},{"raw_affiliation_string":"School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, USA","institution_ids":["https://openalex.org/I114395901"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065035890","display_name":"Yongchao Dou","orcid":"https://orcid.org/0000-0001-9315-1155"},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yongchao Dou","raw_affiliation_strings":["School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, Nebraska, USA","School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, USA"],"affiliations":[{"raw_affiliation_string":"School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, Nebraska, USA","institution_ids":["https://openalex.org/I114395901"]},{"raw_affiliation_string":"School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, USA","institution_ids":["https://openalex.org/I114395901"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100458161","display_name":"Chi Zhang","orcid":"https://orcid.org/0000-0002-1827-8137"},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chi Zhang","raw_affiliation_strings":["School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, Nebraska, USA","School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, USA"],"affiliations":[{"raw_affiliation_string":"School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, Nebraska, USA","institution_ids":["https://openalex.org/I114395901"]},{"raw_affiliation_string":"School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, USA","institution_ids":["https://openalex.org/I114395901"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5021334306"],"corresponding_institution_ids":["https://openalex.org/I114395901"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.8502,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.86879503,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"14","issue":"S13","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12991","display_name":"Phytase and its Applications","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12991","display_name":"Phytase and its Applications","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9965999722480774,"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/T12566","display_name":"Nitrogen and Sulfur Effects on Brassica","score":0.9948999881744385,"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/transcription-factor","display_name":"Transcription factor","score":0.7473655939102173},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6200793981552124},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6069187521934509},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6031744480133057},{"id":"https://openalex.org/keywords/arabidopsis","display_name":"Arabidopsis","score":0.5399110317230225},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4917019009590149},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.4777050018310547},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4668954610824585},{"id":"https://openalex.org/keywords/taf2","display_name":"TAF2","score":0.4383803606033325},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.40301814675331116},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.26338064670562744},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1805737018585205}],"concepts":[{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.7473655939102173},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6200793981552124},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6069187521934509},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6031744480133057},{"id":"https://openalex.org/C2779491563","wikidata":"https://www.wikidata.org/wiki/Q157892","display_name":"Arabidopsis","level":4,"score":0.5399110317230225},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4917019009590149},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4777050018310547},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4668954610824585},{"id":"https://openalex.org/C146027311","wikidata":"https://www.wikidata.org/wiki/Q18031820","display_name":"TAF2","level":5,"score":0.4383803606033325},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.40301814675331116},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.26338064670562744},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1805737018585205},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-14-s13-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s13-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S13-S10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:digitalcommons.unl.edu:plantscifacpub-1081","is_oa":true,"landing_page_url":"http://digitalcommons.unl.edu/plantscifacpub/82","pdf_url":null,"source":{"id":"https://openalex.org/S4306513441","display_name":"Insecta mundi","issn_l":"0749-6737","issn":["0749-6737","1942-1354","1942-1362"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310316217","host_organization_name":"Center for Systematic Entomology","host_organization_lineage":["https://openalex.org/P4310316217"],"host_organization_lineage_names":["Center for Systematic Entomology"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications from the Center for Plant Science Innovation","raw_type":"text"},{"id":"pmh:oai:digitalcommons.unl.edu:plantscifacpub-1089","is_oa":false,"landing_page_url":"http://digitalcommons.unl.edu/plantscifacpub/90","pdf_url":null,"source":{"id":"https://openalex.org/S4306513441","display_name":"Insecta mundi","issn_l":"0749-6737","issn":["0749-6737","1942-1354","1942-1362"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310316217","host_organization_name":"Center for Systematic Entomology","host_organization_lineage":["https://openalex.org/P4310316217"],"host_organization_lineage_names":["Center for Systematic Entomology"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications from the Center for Plant Science Innovation","raw_type":"text"},{"id":"pmh:oai:europepmc.org:2839725","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3849782","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3849782","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3849782","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-14-s13-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s13-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S13-S10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.6499999761581421}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2017831408.pdf","grobid_xml":"https://content.openalex.org/works/W2017831408.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1493454437","https://openalex.org/W1499421302","https://openalex.org/W1981099684","https://openalex.org/W1981194976","https://openalex.org/W1987971958","https://openalex.org/W1996835973","https://openalex.org/W2003243455","https://openalex.org/W2012128982","https://openalex.org/W2069244164","https://openalex.org/W2094448442","https://openalex.org/W2097382368","https://openalex.org/W2098448352","https://openalex.org/W2101416849","https://openalex.org/W2102513034","https://openalex.org/W2103017472","https://openalex.org/W2103546861","https://openalex.org/W2111211467","https://openalex.org/W2119398371","https://openalex.org/W2123765724","https://openalex.org/W2124073224","https://openalex.org/W2141885858","https://openalex.org/W2143210482","https://openalex.org/W2147434872","https://openalex.org/W2152379610","https://openalex.org/W2155941894","https://openalex.org/W2158427522","https://openalex.org/W2158714788","https://openalex.org/W2158887534","https://openalex.org/W2160964063","https://openalex.org/W2161511344","https://openalex.org/W2999729612","https://openalex.org/W4210400672"],"related_works":["https://openalex.org/W2108865053","https://openalex.org/W2125854412","https://openalex.org/W2151951608","https://openalex.org/W3033095439","https://openalex.org/W3177876754","https://openalex.org/W4235022749","https://openalex.org/W2063649295","https://openalex.org/W2418889562","https://openalex.org/W2038605451","https://openalex.org/W2740037612"],"abstract_inverted_index":{"Transcription":[0],"factors":[1,19,59,141,180],"have":[2,33,72],"been":[3,73],"studied":[4,74],"intensively":[5],"because":[6],"they":[7],"play":[8],"an":[9],"important":[10],"role":[11],"in":[12,20,42,60,81],"gene":[13],"expression":[14],"regulation.":[15],"However,":[16],"the":[17,21,96,114,121,126,133,168,171,178],"transcription":[18,30,58,104,140,179],"CPP":[22,57,103,139],"family":[23],"(cystein-rich":[24],"polycomb-like":[25],"protein),":[26],"compared":[27],"with":[28],"other":[29],"factor":[31],"families,":[32],"not":[34],"received":[35],"sufficient":[36],"attention,":[37],"despite":[38],"their":[39,92],"wide":[40],"prevalence":[41],"a":[43],"broad":[44],"spectrum":[45],"of":[46,55,70,109,128,173],"species,":[47],"from":[48,64,181],"plants":[49,61],"to":[50,90,100,166],"animals.":[51],"The":[52,106],"total":[53],"number":[54],"known":[56],"is":[62,118,164],"111":[63],"16":[65],"plants,":[66],"but":[67],"only":[68],"2":[69],"them":[71],"so":[75],"far,":[76],"namely":[77],"TSO1":[78],"and":[79,84,125,161],"CPP1":[80],"Arabidopsis":[82],"thaliana":[83],"soybean,":[85],"respectively.":[86],"In":[87],"this":[88],"work,":[89],"study":[91],"functions,":[93],"we":[94],"applied":[95],"fuzzy":[97,115,134],"clustering":[98,116,135,169],"method":[99,117],"all":[101,137],"plant":[102,138],"factors.":[105],"feature":[107],"vector":[108],"each":[110],"protein":[111],"sequence":[112],"for":[113],"encoded":[119],"by":[120],"short":[122],"length":[123],"peptides":[124],"combination":[127],"functional":[129],"domain":[130],"models.":[131],"With":[132],"method,":[136],"are":[142],"grouped":[143],"into":[144],"two":[145],"subfamilies.":[146],"A":[147],"systems":[148],"approach,":[149],"including":[150],"Expressed":[151],"Sequence":[152],"Tag":[153],"analysis,":[154,156,163],"evolutionary":[155],"protein-protein":[157],"interaction":[158],"network":[159],"analysis":[160],"co-expression":[162],"employed":[165],"validate":[167],"results,":[170],"results":[172],"which":[174],"also":[175],"indicates":[176],"that":[177],"different":[182],"subfamilies":[183],"show":[184],"uncorrelated":[185],"responses.":[186]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":2}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}