{"id":"https://openalex.org/W2932401127","doi":"https://doi.org/10.1142/s0219720019500136","title":"Deeper investigation into the utility of functional class scoring in missing protein prediction from proteomics data","display_name":"Deeper investigation into the utility of functional class scoring in missing protein prediction from proteomics data","publication_year":2019,"publication_date":"2019-04-01","ids":{"openalex":"https://openalex.org/W2932401127","doi":"https://doi.org/10.1142/s0219720019500136","mag":"2932401127","pmid":"https://pubmed.ncbi.nlm.nih.gov/31057071"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720019500136","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019500136","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5101058025","display_name":"Yaxing Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaxing Zhao","raw_affiliation_strings":["School of Pharmaceutical Science and Technology, Tianjin University, No. 92, Weijin Road, 30072 Tianjin, P.\u00a0R.\u00a0China"],"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Science and Technology, Tianjin University, No. 92, Weijin Road, 30072 Tianjin, P.\u00a0R.\u00a0China","institution_ids":["https://openalex.org/I162868743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006499990","display_name":"Andrew C.\u2010H. Sue","orcid":"https://orcid.org/0000-0001-9557-2658"},"institutions":[{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Andrew Chi-Hau Sue","raw_affiliation_strings":["School of Pharmaceutical Science and Technology, Tianjin University, No. 92, Weijin Road, 30072 Tianjin, P.\u00a0R.\u00a0China"],"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Science and Technology, Tianjin University, No. 92, Weijin Road, 30072 Tianjin, P.\u00a0R.\u00a0China","institution_ids":["https://openalex.org/I162868743"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054040512","display_name":"Wilson Wen Bin Goh","orcid":"https://orcid.org/0000-0003-3863-7501"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Wilson Wen Bin Goh","raw_affiliation_strings":["School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore"],"affiliations":[{"raw_affiliation_string":"School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5054040512"],"corresponding_institution_ids":["https://openalex.org/I172675005"],"apc_list":null,"apc_paid":null,"fwci":0.4262,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.60911893,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"17","issue":"02","first_page":"1950013","last_page":"1950013"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9984999895095825,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9984999895095825,"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":0.9973999857902527,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9966999888420105,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.5576742887496948},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5170555710792542},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.49700215458869934},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.47829729318618774},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39379632472991943},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3762900233268738},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3204459249973297},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29423895478248596},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2810942828655243},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2777918577194214}],"concepts":[{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.5576742887496948},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5170555710792542},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.49700215458869934},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.47829729318618774},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39379632472991943},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3762900233268738},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3204459249973297},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29423895478248596},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2810942828655243},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2777918577194214},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007668","descriptor_name":"Kidney","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007668","descriptor_name":"Kidney","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007668","descriptor_name":"Kidney","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007680","descriptor_name":"Kidney Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007680","descriptor_name":"Kidney Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007680","descriptor_name":"Kidney Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1142/s0219720019500136","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019500136","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:31057071","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31057071","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":"Journal of bioinformatics and computational biology","raw_type":null},{"id":"pmh:oai:dr.ntu.edu.sg:10356/144754","is_oa":false,"landing_page_url":"https://hdl.handle.net/10356/144754","pdf_url":null,"source":{"id":"https://openalex.org/S4306402609","display_name":"DR-NTU (Nanyang Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172675005","host_organization_name":"Nanyang Technological University","host_organization_lineage":["https://openalex.org/I172675005"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W80748578","https://openalex.org/W1967822181","https://openalex.org/W1968609398","https://openalex.org/W1986214964","https://openalex.org/W2004437908","https://openalex.org/W2014376224","https://openalex.org/W2018126724","https://openalex.org/W2027136463","https://openalex.org/W2033047611","https://openalex.org/W2068835382","https://openalex.org/W2075418882","https://openalex.org/W2076057012","https://openalex.org/W2079843936","https://openalex.org/W2092006323","https://openalex.org/W2096248890","https://openalex.org/W2098979213","https://openalex.org/W2100155101","https://openalex.org/W2107411032","https://openalex.org/W2109506073","https://openalex.org/W2140280811","https://openalex.org/W2148043260","https://openalex.org/W2160313295","https://openalex.org/W2166168546","https://openalex.org/W2240164355","https://openalex.org/W2423436432","https://openalex.org/W2501521581","https://openalex.org/W2503225714","https://openalex.org/W2562577192","https://openalex.org/W2727689452","https://openalex.org/W2761163030","https://openalex.org/W2769195606","https://openalex.org/W2789028618","https://openalex.org/W2805376159","https://openalex.org/W2886867051","https://openalex.org/W2886992141"],"related_works":["https://openalex.org/W1982829397","https://openalex.org/W2106414650","https://openalex.org/W2347437365","https://openalex.org/W1999412725","https://openalex.org/W4390205769","https://openalex.org/W2124137418","https://openalex.org/W2391458050","https://openalex.org/W2086860678","https://openalex.org/W3022402204","https://openalex.org/W2114732768"],"abstract_inverted_index":{"Functional":[0],"Class":[1],"Scoring":[2],"(FCS)":[3],"is":[4,149,161],"a":[5,150],"network-based":[6],"approach":[7],"previously":[8],"demonstrated":[9],"to":[10,109,119,132],"be":[11,101],"powerful":[12,151],"in":[13],"missing":[14],"protein":[15],"prediction":[16],"(MPP).":[17],"We":[18,44],"update":[19],"its":[20,156],"performance":[21,85],"evaluation":[22],"using":[23,36],"data":[24],"derived":[25],"from":[26,61],"new":[27],"proteomics":[28],"technology":[29],"(SWATH)":[30],"and":[31,53,75,112,122,124],"also":[32,45],"checked":[33],"for":[34,103],"reproducibility":[35],"two":[37],"independent":[38],"datasets":[39],"profiling":[40],"kidney":[41],"tissue":[42],"proteome.":[43],"evaluated":[46],"the":[47,50,57],"objectivity":[48],"of":[49,59,129],"FCS":[51,69,141,148],"<i>p</i>-value,":[52],"followed":[54],"up":[55],"on":[56,155],"value":[58],"MPP":[60],"predicted":[62,98],"complexes.":[63,146],"Our":[64],"results":[65],"suggest":[66],"that":[67,140],"(1)":[68],"<mml:math":[70,92,158],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"><mml:mi>p</mml:mi></mml:math>":[71,93,159],"-values":[72],"are":[73,76,107,113],"non-objective,":[74],"confounded":[77,115],"strongly":[78],"by":[79,116],"complex":[80],"size,":[81],"(2)":[82],"best":[83,143],"recovery":[84],"do":[86],"not":[87],"necessarily":[88],"lie":[89],"at":[90],"standard":[91],"-value":[94,160],"cutoffs,":[95],"(3)":[96],"while":[97],"complexes":[99,128],"may":[100],"used":[102],"augmenting":[104],"MPP,":[105],"they":[106],"inferior":[108],"real":[110],"complexes,":[111],"further":[114],"issues":[117],"relating":[118],"network":[120],"coverage":[121],"quality":[123],"(4)":[125],"moderate":[126],"sized":[127],"size":[130],"5":[131],"10":[133],"still":[134],"exhibit":[135],"considerable":[136],"instability,":[137],"we":[138],"find":[139],"works":[142],"with":[144],"big":[145],"While":[147],"approach,":[152],"blind":[153],"reliance":[154],"non-objective":[157],"ill-advised.":[162]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
