{"id":"https://openalex.org/W2119028181","doi":"https://doi.org/10.1093/bioinformatics/btm460","title":"TAPPA: topological analysis of pathway phenotype association","display_name":"TAPPA: topological analysis of pathway phenotype association","publication_year":2007,"publication_date":"2007-09-21","ids":{"openalex":"https://openalex.org/W2119028181","doi":"https://doi.org/10.1093/bioinformatics/btm460","mag":"2119028181","pmid":"https://pubmed.ncbi.nlm.nih.gov/17890270"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm460","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm460","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/22/3100/49857534/bioinformatics_23_22_3100.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/23/22/3100/49857534/bioinformatics_23_22_3100.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029264687","display_name":"Shouguo Gao","orcid":"https://orcid.org/0000-0002-8275-0598"},"institutions":[{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]},{"id":"https://openalex.org/I126218986","display_name":"Children's Hospital of Wisconsin","ror":"https://ror.org/049cbmb74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I126218986"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shouguo Gao","raw_affiliation_strings":["The Max McGee National Research Center for Juvenile Diabetes & The Human and Molecular Genetics Center, The Medical College of Wisconsin and Children's Hospital of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA"],"affiliations":[{"raw_affiliation_string":"The Max McGee National Research Center for Juvenile Diabetes & The Human and Molecular Genetics Center, The Medical College of Wisconsin and Children's Hospital of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA","institution_ids":["https://openalex.org/I126218986","https://openalex.org/I204308271"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102788743","display_name":"Xujing Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I126218986","display_name":"Children's Hospital of Wisconsin","ror":"https://ror.org/049cbmb74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I126218986"]},{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xujing Wang","raw_affiliation_strings":["The Max McGee National Research Center for Juvenile Diabetes & The Human and Molecular Genetics Center, The Medical College of Wisconsin and Children's Hospital of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA"],"affiliations":[{"raw_affiliation_string":"The Max McGee National Research Center for Juvenile Diabetes & The Human and Molecular Genetics Center, The Medical College of Wisconsin and Children's Hospital of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA","institution_ids":["https://openalex.org/I126218986","https://openalex.org/I204308271"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5029264687"],"corresponding_institution_ids":["https://openalex.org/I126218986","https://openalex.org/I204308271"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8067,"has_fulltext":true,"cited_by_count":66,"citation_normalized_percentile":{"value":0.71774381,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"23","issue":"22","first_page":"3100","last_page":"3102"},"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":0.9890000224113464,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.946399986743927,"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/phenotype","display_name":"Phenotype","score":0.7934876680374146},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6230702996253967},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5770834684371948},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5325279235839844},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.4995388984680176},{"id":"https://openalex.org/keywords/pathway-analysis","display_name":"Pathway analysis","score":0.49336114525794983},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4809103012084961},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.44012895226478577},{"id":"https://openalex.org/keywords/genetic-association","display_name":"Genetic association","score":0.4292076528072357},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.41196078062057495},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.26778703927993774},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.21659818291664124},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.11729410290718079},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.11182445287704468}],"concepts":[{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.7934876680374146},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6230702996253967},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5770834684371948},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5325279235839844},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.4995388984680176},{"id":"https://openalex.org/C2779230013","wikidata":"https://www.wikidata.org/wiki/Q25303877","display_name":"Pathway analysis","level":4,"score":0.49336114525794983},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4809103012084961},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.44012895226478577},{"id":"https://openalex.org/C186413461","wikidata":"https://www.wikidata.org/wiki/Q744727","display_name":"Genetic association","level":5,"score":0.4292076528072357},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41196078062057495},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.26778703927993774},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.21659818291664124},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.11729410290718079},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.11182445287704468},{"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/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btm460","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm460","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/22/3100/49857534/bioinformatics_23_22_3100.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:17890270","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17890270","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:2473868","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2473868","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":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/btm460","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm460","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/22/3100/49857534/bioinformatics_23_22_3100.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/G4180072099","display_name":null,"funder_award_id":"R01DK080100","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"}],"funders":[{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2119028181.pdf","grobid_xml":"https://content.openalex.org/works/W2119028181.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1864299022","https://openalex.org/W2056254608","https://openalex.org/W2103246308","https://openalex.org/W2119789108","https://openalex.org/W2130410032","https://openalex.org/W2133747068","https://openalex.org/W2142720308","https://openalex.org/W2146045333"],"related_works":["https://openalex.org/W2143066563","https://openalex.org/W2157166663","https://openalex.org/W1530402712","https://openalex.org/W3032357680","https://openalex.org/W2132993604","https://openalex.org/W2125731289","https://openalex.org/W2121760608","https://openalex.org/W2134976939","https://openalex.org/W2790180944","https://openalex.org/W2151866902"],"abstract_inverted_index":{"Extracting":[0],"biological":[1],"insight":[2],"from":[3,60],"microarray":[4],"data":[5],"is":[6,29],"important":[7],"but":[8,65,70],"challenging.":[9],"Here":[10],"we":[11],"describe":[12],"TAPPA,":[13],"a":[14,34,80,96],"java-based":[15],"tool,":[16],"for":[17,39],"identification":[18],"of":[19,83,93],"phenotype-associated":[20],"genetic":[21],"pathways":[22],"utilizing":[23],"the":[24,48,58,74,87],"pathway":[25,97],"topological":[26],"measures.":[27],"This":[28],"achieved":[30],"by":[31,43],"first":[32],"calculating":[33],"Pathway":[35],"Connectivity":[36],"Index":[37],"(PCI)":[38],"each":[40],"pathway,":[41],"followed":[42],"evaluating":[44],"its":[45],"correlation":[46],"to":[47,101],"phenotypic":[49],"variation.":[50],"Our":[51],"PCI":[52],"definition":[53],"not":[54],"only":[55],"efficiently":[56],"captures":[57],"contributions":[59],"genes":[61,76,85],"that":[62,77],"show":[63],"subtle":[64],"consistent":[66],"changes":[67],"in":[68,86],"expression,":[69],"also":[71,90],"naturally":[72],"overweighs":[73],"hub":[75],"interact":[78],"with":[79],"large":[81],"number":[82],"other":[84],"pathway.":[88],"TAPPA":[89],"allows":[91],"evaluation":[92],"sub-modules":[94],"within":[95],"and":[98],"their":[99],"association":[100],"phenotypes.":[102]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}