{"id":"https://openalex.org/W2160699408","doi":"https://doi.org/10.1093/bioinformatics/btp498","title":"Next generation software for functional trend analysis","display_name":"Next generation software for functional trend analysis","publication_year":2009,"publication_date":"2009-08-28","ids":{"openalex":"https://openalex.org/W2160699408","doi":"https://doi.org/10.1093/bioinformatics/btp498","mag":"2160699408","pmid":"https://pubmed.ncbi.nlm.nih.gov/19717575"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp498","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp498","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/22/3043/48998001/bioinformatics_25_22_3043.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/22/3043/48998001/bioinformatics_25_22_3043.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004263988","display_name":"Gabriel F. Berriz","orcid":null},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gabriel F. Berriz","raw_affiliation_strings":["1 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue and 2Center for Cancer Systems Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue and 2Center for Cancer Systems Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041273898","display_name":"John Beaver","orcid":null},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John E. Beaver","raw_affiliation_strings":["1 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue and 2Center for Cancer Systems Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue and 2Center for Cancer Systems Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047557155","display_name":"Can Cenik","orcid":"https://orcid.org/0000-0001-6370-0889"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Can Cenik","raw_affiliation_strings":["1 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue and 2Center for Cancer Systems Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue and 2Center for Cancer Systems Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026802459","display_name":"Murat Ta\u015fan","orcid":"https://orcid.org/0000-0003-1490-7626"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Murat Tasan","raw_affiliation_strings":["1 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue and 2Center for Cancer Systems Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue and 2Center for Cancer Systems Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090936599","display_name":"Frederick P. Roth","orcid":"https://orcid.org/0000-0002-6628-649X"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Frederick P. Roth","raw_affiliation_strings":["1 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue and 2Center for Cancer Systems Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue and 2Center for Cancer Systems Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5090936599"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210117453"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":10.681,"has_fulltext":false,"cited_by_count":302,"citation_normalized_percentile":{"value":0.98940012,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"25","issue":"22","first_page":"3043","last_page":"3044"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10887","display_name":"Bioinformatics and Genomic Networks","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":0.9983999729156494,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9944000244140625,"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/computer-science","display_name":"Computer science","score":0.7575953006744385},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5784644484519958},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5030679106712341},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.48201480507850647},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3739260733127594},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16664761304855347},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.07801595330238342}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7575953006744385},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5784644484519958},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5030679106712341},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.48201480507850647},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3739260733127594},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16664761304855347},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.07801595330238342},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"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/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp498","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp498","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/22/3043/48998001/bioinformatics_25_22_3043.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19717575","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19717575","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2800365","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2800365","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp498","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp498","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/22/3043/48998001/bioinformatics_25_22_3043.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1290029838","display_name":null,"funder_award_id":"HL081341","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G1783734454","display_name":null,"funder_award_id":"R01 HG003224","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G2470583414","display_name":null,"funder_award_id":"HG004233","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4118909504","display_name":null,"funder_award_id":"P50 HG004233","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4666976601","display_name":null,"funder_award_id":"HG0017115","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G5676844610","display_name":null,"funder_award_id":"NS035611","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G5868643487","display_name":null,"funder_award_id":"R01 NS054052","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G6544923010","display_name":null,"funder_award_id":"U01 HL081341","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G7851930865","display_name":null,"funder_award_id":"HG003224","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G7991278360","display_name":null,"funder_award_id":"P01 NS035611","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G8683578291","display_name":null,"funder_award_id":"NS054052","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"}],"funders":[{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W2061291780","https://openalex.org/W2096525273","https://openalex.org/W2097057598","https://openalex.org/W2103017472","https://openalex.org/W2118572979","https://openalex.org/W2122261141","https://openalex.org/W2126664691","https://openalex.org/W2133465414","https://openalex.org/W2148071771","https://openalex.org/W2151763757","https://openalex.org/W4210430020","https://openalex.org/W4242161096","https://openalex.org/W4250297812"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2130043461","https://openalex.org/W2381929017","https://openalex.org/W2369108811"],"abstract_inverted_index":{"UNLABELLED:":[0],"FuncAssociate":[1,66],"is":[2,69],"a":[3,28],"web":[4,67],"application":[5,26,68],"that":[6,16],"discovers":[7],"properties":[8],"enriched":[9],"in":[10],"lists":[11],"of":[12],"genes":[13],"or":[14],"proteins":[15],"emerge":[17],"from":[18],"large-scale":[19],"experimentation.":[20],"Here":[21],"we":[22],"describe":[23],"an":[24],"updated":[25],"with":[27],"new":[29,33],"interface":[30],"and":[31,46],"several":[32],"features.":[34],"For":[35],"example,":[36],"enrichment":[37,59],"analysis":[38,60],"can":[39],"now":[40],"be":[41],"performed":[42],"within":[43],"multiple":[44],"gene-":[45],"protein-naming":[47],"systems.":[48],"This":[49],"feature":[50],"avoids":[51],"potentially":[52],"serious":[53],"translation":[54],"artifacts":[55],"to":[56,72],"which":[57],"other":[58],"strategies":[61],"are":[62],"subject.":[63],"AVAILABILITY:":[64],"The":[65],"freely":[70],"available":[71],"all":[73],"users":[74],"at":[75],"http://llama.med.harvard.edu/funcassociate.":[76]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":32},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":14},{"year":2017,"cited_by_count":16},{"year":2016,"cited_by_count":16},{"year":2015,"cited_by_count":21},{"year":2014,"cited_by_count":31},{"year":2013,"cited_by_count":36},{"year":2012,"cited_by_count":36}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
