{"id":"https://openalex.org/W2589680347","doi":null,"title":"Characterizing the Evolutionary Dynamics of Protein Phosphorylation Sites for Functional Phospho-proteomics","display_name":"Characterizing the Evolutionary Dynamics of Protein Phosphorylation Sites for Functional Phospho-proteomics","publication_year":2012,"publication_date":"2012-08-31","ids":{"openalex":"https://openalex.org/W2589680347","mag":"2589680347"},"language":"en","primary_location":{"id":"pmh:oai:utoronto.scholaris.ca:1807/32822","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1807/32822","pdf_url":"https://utoronto.scholaris.ca/bitstreams/59c7c3af-2fd9-4a25-915d-c1355ea34319/download","source":{"id":"https://openalex.org/S4306400261","display_name":"TSpace (University of Toronto)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I185261750","host_organization_name":"University of Toronto","host_organization_lineage":["https://openalex.org/I185261750"],"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":null,"raw_type":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://utoronto.scholaris.ca/bitstreams/59c7c3af-2fd9-4a25-915d-c1355ea34319/download","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055189639","display_name":"Soon Heng Tan","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Soon Heng Tan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5055189639"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.8827999830245972,"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"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.8827999830245972,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.06679999828338623,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.01140000019222498,"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/protein-phosphorylation","display_name":"protein phosphorylation","score":0.9900000095367432},{"id":"https://openalex.org/keywords/phosphorylation-sites","display_name":"phosphorylation sites","score":0.7680000066757202},{"id":"https://openalex.org/keywords/evolutionary-conservation","display_name":"evolutionary conservation","score":0.722000002861023},{"id":"https://openalex.org/keywords/kinase-substrate-interactions","display_name":"kinase-substrate interactions","score":0.8019999861717224},{"id":"https://openalex.org/keywords/network-alignment","display_name":"network alignment","score":0.7570000290870667},{"id":"https://openalex.org/keywords/sequence-conservation","display_name":"sequence conservation","score":0.7250000238418579},{"id":"https://openalex.org/keywords/protein-levels","display_name":"protein abundance","score":0.6380000114440918},{"id":"https://openalex.org/keywords/disordered-protein-regions","display_name":"disordered protein regions","score":0.6790000200271606},{"id":"https://openalex.org/keywords/phosphotyrosine-signaling","display_name":"phosphotyrosine signaling","score":0.9369999766349792},{"id":"https://openalex.org/keywords/cancer-genes","display_name":"cancer genes","score":0.5720000267028809},{"id":"https://openalex.org/keywords/orthologous-proteins","display_name":"orthologous proteins","score":0.6579999923706055}],"concepts":[{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.6606582999229431},{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.5941858887672424},{"id":"https://openalex.org/C87325107","wikidata":"https://www.wikidata.org/wiki/Q7251493","display_name":"Protein phosphorylation","level":4,"score":0.4880315363407135},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4455205798149109},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.4287257194519043},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39086949825286865},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3549993336200714},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.24943652749061584},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.20365139842033386},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15457656979560852},{"id":"https://openalex.org/C97029542","wikidata":"https://www.wikidata.org/wiki/Q281417","display_name":"Protein kinase A","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C19417346","wikidata":"https://www.wikidata.org/wiki/Q7922","display_name":"Pedagogy","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:utoronto.scholaris.ca:1807/32822","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1807/32822","pdf_url":"https://utoronto.scholaris.ca/bitstreams/59c7c3af-2fd9-4a25-915d-c1355ea34319/download","source":{"id":"https://openalex.org/S4306400261","display_name":"TSpace (University of Toronto)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I185261750","host_organization_name":"University of Toronto","host_organization_lineage":["https://openalex.org/I185261750"],"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":null,"raw_type":"Thesis"},{"id":"pmh:oai:collectionscanada.gc.ca:OTU.1807/32822","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/1807/32822","pdf_url":null,"source":{"id":"https://openalex.org/S4306402307","display_name":"Library and Archives Canada (Government of Canada)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2802286613","host_organization_name":"Government of Canada","host_organization_lineage":["https://openalex.org/I2802286613"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Thesis"},{"id":"mag:2589680347","doi":null,"is_oa":false,"landing_page_url":"https://tspace.library.utoronto.ca/bitstream/1807/32822/6/Tan_SoonHeng_20126_PhD_thesis.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:utoronto.scholaris.ca:1807/32822","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1807/32822","pdf_url":"https://utoronto.scholaris.ca/bitstreams/59c7c3af-2fd9-4a25-915d-c1355ea34319/download","source":{"id":"https://openalex.org/S4306400261","display_name":"TSpace (University of Toronto)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I185261750","host_organization_name":"University of Toronto","host_organization_lineage":["https://openalex.org/I185261750"],"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":null,"raw_type":"Thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2589680347.pdf","grobid_xml":"https://content.openalex.org/works/W2589680347.grobid-xml"},"referenced_works_count":177,"referenced_works":["https://openalex.org/W1493799579","https://openalex.org/W1503880077","https://openalex.org/W1521353297","https://openalex.org/W1538925875","https://openalex.org/W1570204439","https://openalex.org/W1575415973","https://openalex.org/W1592870802","https://openalex.org/W1884509322","https://openalex.org/W1965694122","https://openalex.org/W1965807926","https://openalex.org/W1970871693","https://openalex.org/W1973695911","https://openalex.org/W1975938671","https://openalex.org/W1976662277","https://openalex.org/W1977414640","https://openalex.org/W1978177843","https://openalex.org/W1978254752","https://openalex.org/W1980843814","https://openalex.org/W1981836992","https://openalex.org/W1984164188","https://openalex.org/W1984871500","https://openalex.org/W1986557818","https://openalex.org/W1987030497","https://openalex.org/W1989053944","https://openalex.org/W1994803330","https://openalex.org/W1995404781","https://openalex.org/W1996693787","https://openalex.org/W1997813173","https://openalex.org/W1998300401","https://openalex.org/W1999123701","https://openalex.org/W1999237781","https://openalex.org/W1999450178","https://openalex.org/W1999811798","https://openalex.org/W2000042427","https://openalex.org/W2001097406","https://openalex.org/W2001291651","https://openalex.org/W2002204923","https://openalex.org/W2004704197","https://openalex.org/W2006172444","https://openalex.org/W2006331214","https://openalex.org/W2007530728","https://openalex.org/W2007733980","https://openalex.org/W2007942027","https://openalex.org/W2009152568","https://openalex.org/W2010161321","https://openalex.org/W2010413075","https://openalex.org/W2011147958","https://openalex.org/W2011912935","https://openalex.org/W2011953977","https://openalex.org/W2012223636","https://openalex.org/W2013947447","https://openalex.org/W2018732798","https://openalex.org/W2020459598","https://openalex.org/W2023389323","https://openalex.org/W2024962796","https://openalex.org/W2027469236","https://openalex.org/W2028903194","https://openalex.org/W2029487801","https://openalex.org/W2030205108","https://openalex.org/W2030397967","https://openalex.org/W2030776726","https://openalex.org/W2030779556","https://openalex.org/W2030828466","https://openalex.org/W2031028006","https://openalex.org/W2032225851","https://openalex.org/W2036837630","https://openalex.org/W2040709819","https://openalex.org/W2042412160","https://openalex.org/W2046515690","https://openalex.org/W2047630272","https://openalex.org/W2047746661","https://openalex.org/W2048666997","https://openalex.org/W2050721857","https://openalex.org/W2051170583","https://openalex.org/W2052033556","https://openalex.org/W2052663694","https://openalex.org/W2053411009","https://openalex.org/W2055043387","https://openalex.org/W2055193239","https://openalex.org/W2059337817","https://openalex.org/W2059345773","https://openalex.org/W2062574001","https://openalex.org/W2066099419","https://openalex.org/W2073234837","https://openalex.org/W2075420324","https://openalex.org/W2077797834","https://openalex.org/W2078964925","https://openalex.org/W2081933515","https://openalex.org/W2081954164","https://openalex.org/W2085289028","https://openalex.org/W2088381634","https://openalex.org/W2089367187","https://openalex.org/W2090806203","https://openalex.org/W2091375086","https://openalex.org/W2092089306","https://openalex.org/W2096699854","https://openalex.org/W2101181377","https://openalex.org/W2104244040","https://openalex.org/W2104303958","https://openalex.org/W2106446195","https://openalex.org/W2107591926","https://openalex.org/W2109248504","https://openalex.org/W2110663167","https://openalex.org/W2110817748","https://openalex.org/W2111330902","https://openalex.org/W2111502892","https://openalex.org/W2111756560","https://openalex.org/W2113613985","https://openalex.org/W2113654464","https://openalex.org/W2114099497","https://openalex.org/W2114508508","https://openalex.org/W2118025286","https://openalex.org/W2118127847","https://openalex.org/W2119362018","https://openalex.org/W2120016245","https://openalex.org/W2123527017","https://openalex.org/W2123672359","https://openalex.org/W2123929534","https://openalex.org/W2124285343","https://openalex.org/W2126910411","https://openalex.org/W2127816425","https://openalex.org/W2128387395","https://openalex.org/W2128987420","https://openalex.org/W2129777487","https://openalex.org/W2129913176","https://openalex.org/W2130277691","https://openalex.org/W2130589938","https://openalex.org/W2134604442","https://openalex.org/W2135805255","https://openalex.org/W2136133297","https://openalex.org/W2137104501","https://openalex.org/W2137198216","https://openalex.org/W2137581426","https://openalex.org/W2138229005","https://openalex.org/W2140638448","https://openalex.org/W2140946052","https://openalex.org/W2141376777","https://openalex.org/W2141708714","https://openalex.org/W2143210482","https://openalex.org/W2145173401","https://openalex.org/W2145487893","https://openalex.org/W2145658930","https://openalex.org/W2146228871","https://openalex.org/W2147013899","https://openalex.org/W2147054306","https://openalex.org/W2149049196","https://openalex.org/W2150271494","https://openalex.org/W2151527633","https://openalex.org/W2153458172","https://openalex.org/W2154392018","https://openalex.org/W2154846744","https://openalex.org/W2155239883","https://openalex.org/W2155814768","https://openalex.org/W2156842451","https://openalex.org/W2157058776","https://openalex.org/W2159675211","https://openalex.org/W2160406438","https://openalex.org/W2161651587","https://openalex.org/W2164220403","https://openalex.org/W2165002727","https://openalex.org/W2165266462","https://openalex.org/W2167188257","https://openalex.org/W2167350014","https://openalex.org/W2167827705","https://openalex.org/W2167899780","https://openalex.org/W2167932805","https://openalex.org/W2168264491","https://openalex.org/W2168514491","https://openalex.org/W2168691181","https://openalex.org/W2169424993","https://openalex.org/W2169703913","https://openalex.org/W2171030481","https://openalex.org/W2171463101","https://openalex.org/W2409913804","https://openalex.org/W2442857327","https://openalex.org/W2916483810","https://openalex.org/W3036846224"],"related_works":["https://openalex.org/W2123527017","https://openalex.org/W4412709048","https://openalex.org/W2131947487","https://openalex.org/W2154846744","https://openalex.org/W2737086165","https://openalex.org/W2010824534","https://openalex.org/W2332954283","https://openalex.org/W2001922182","https://openalex.org/W2078964925","https://openalex.org/W1574203041"],"abstract_inverted_index":{"Protein":[0],"phosphorylation":[1,37,62,82,99,111,245,262],"is":[2],"a":[3,122,154],"prevalent":[4],"reversible":[5],"post-translational":[6],"modification":[7],"that":[8,172,234,271,291],"influences":[9],"protein":[10,180,203,217],"functions.":[11,70],"The":[12,29],"advent":[13],"of":[14,22,32,35,162,179,208,227,266,293],"phospho-proteomic":[15,93],"technologies":[16],"now":[17],"enables":[18],"proteome-wide":[19],"quantitative":[20],"detection":[21],"residues":[23,165,240,268],"phosphorylated":[24,164,228,239],"under":[25],"different":[26,216],"physiological":[27],"conditions.":[28],"functional":[30],"consequences":[31],"the":[33,159,175,222,259],"majority":[34],"these":[36,86],"events":[38,83,100,112],"are":[39,139,241,249],"unknown.":[40],"This":[41,53,288],"calls":[42],"for":[43,142],"endeavors":[44],"to":[45,60,84,95,109,128,157,189,220],"characterize":[46],"their":[47,65,69,197],"molecular":[48],"functions":[49],"and":[50,67,76,121,148,169,181,211,237,247,269,277,283],"cellular":[51],"effects.":[52],"can":[54],"be":[55],"facilitated":[56],"by":[57,145],"systematic":[58],"approaches":[59],"categorize":[61],"events,":[63],"interpret":[64],"importance":[66],"infer":[68],"I":[71,89,152,257],"carried":[72],"out":[73],"comparative,":[74],"evolutionary":[75],"integrative":[77],"analyses":[78],"on":[79,166,252],"in":[80,101,174,199,205,212,243,264,286],"vivo":[81],"address":[85],"challenges.":[87],"First,":[88],"performed":[90],"cross-species":[91],"comparative":[92],"analysis":[94,232],"identify":[96,110,129,221],"evolutionarily":[97,131],"conserved":[98,113,132],"human.":[102],"A":[103],"sequence":[104,116,160,225],"alignment":[105,124],"approach":[106,125,156],"was":[107,126],"used":[108],"at":[114],"similar":[115],"positions":[117],"across":[118],"orthologous":[119],"proteins":[120,143,171,207,214],"network":[123],"applied":[127],"potential":[130],"kinase-substrate":[133],"interactions.":[134],"Conserved":[135],"human":[136],"phosphoproteins":[137],"identified":[138],"found":[140],"enriched":[141],"encoded":[144],"known":[146,163],"cancer-":[147],"disease-associated":[149],"genes.":[150],"Next,":[151],"developed":[153],"new":[155],"analyze":[158],"conservation":[161,226],"human,":[167],"mouse":[168],"yeast":[170],"factored":[173],"background":[176],"mutational":[177],"rates":[178],"phosphorylatable":[182,267],"residue.":[183],"Furthermore,":[184],"sites":[185],"were":[186],"analyzed":[187],"according":[188],"(i)":[190],"characterized":[191,258],"functions,":[192],"(ii)":[193],"prevalence,":[194],"(iii)":[195],"stoichiometry,":[196],"occurrence":[198],"(iv)":[200],"structurally":[201],"disordered/ordered":[202],"regions,":[204],"(v)":[206],"various":[209],"abundance":[210,254],"(vi)":[213],"with":[215,279],"interaction":[218],"propensity":[219],"factors":[223],"influencing":[224],"residues.":[229],"Importantly,":[230],"my":[231],"suggests":[233,290],"false":[235],"positives":[236],"randomly":[238],"present":[242],"existing":[244],"datasets":[246],"they":[248],"more":[250],"common":[251],"high":[253],"proteins.":[255],"Lastly,":[256],"theoretical":[260],"maximum":[261],"capacity":[263],"terms":[265],"discovered":[270],"genomic":[272],"tyrosine":[273,280,300],"frequency":[274,282],"correlates":[275],"negatively":[276],"significantly":[278],"kinase":[281],"cell":[284],"type":[285],"metazoan.":[287],"observation":[289],"fidelity":[292],"phosphotyrosine":[294],"signaling":[295],"occurred":[296],"partially":[297],"through":[298],"global":[299],"depletion.":[301]},"counts_by_year":[],"updated_date":"2026-09-26T08:19:03.415552","created_date":"2017-03-03T00:00:00"}