{"id":"https://openalex.org/W3083300701","doi":"https://doi.org/10.1158/1538-7445.am2020-4411","title":"Abstract 4411: A gene set enrichment analysis approach in single-cells along pseudotime trajectories reveals the dynamic activity of oncogenic pathways","display_name":"Abstract 4411: A gene set enrichment analysis approach in single-cells along pseudotime trajectories reveals the dynamic activity of oncogenic pathways","publication_year":2020,"publication_date":"2020-08-15","ids":{"openalex":"https://openalex.org/W3083300701","doi":"https://doi.org/10.1158/1538-7445.am2020-4411","mag":"3083300701"},"language":"en","primary_location":{"id":"doi:10.1158/1538-7445.am2020-4411","doi":"https://doi.org/10.1158/1538-7445.am2020-4411","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.am2020-4411","pdf_url":null,"source":{"id":"https://openalex.org/S168522863","display_name":"Cancer Research","issn_l":"0008-5472","issn":["0008-5472","1538-7445"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","doyens","jufo-3","ki-jl-3","medline","norway-2"],"host_organization":"https://openalex.org/P4310320273","host_organization_name":"American Association for Cancer Research","host_organization_lineage":["https://openalex.org/P4310320273"],"host_organization_lineage_names":["American Association for Cancer Research"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cancer Research","raw_type":"journal-article"},"volume":null,"type":"conference-abstract","indexed_in":["crossref"],"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/A5068544289","display_name":"Alexander T. Wenzel","orcid":"https://orcid.org/0000-0002-2056-2938","observed_orcids":["https://orcid.org/0000-0002-2056-2938"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander T. Wenzel","raw_affiliation_strings":["UC San Diego, San Diego, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UC San Diego, San Diego, CA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058353322","display_name":"Devora Champa","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Devora Champa","raw_affiliation_strings":["UC San Diego, San Diego, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UC San Diego, San Diego, CA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024148760","display_name":"Stephen B. Howell","orcid":"https://orcid.org/0000-0002-0877-8226","observed_orcids":["https://orcid.org/0000-0002-0877-8226"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen B. Howell","raw_affiliation_strings":["UC San Diego, San Diego, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UC San Diego, San Diego, CA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077622597","display_name":"Jill P. Mesirov","orcid":"https://orcid.org/0000-0002-9755-2818","observed_orcids":["https://orcid.org/0000-0002-9755-2818"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jill P. Mesirov","raw_affiliation_strings":["UC San Diego, San Diego, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UC San Diego, San Diego, CA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036536597","display_name":"Olivier Harismendy","orcid":"https://orcid.org/0000-0002-8098-9888","observed_orcids":["https://orcid.org/0000-0002-8098-9888"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Olivier Harismendy","raw_affiliation_strings":["UC San Diego, San Diego, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UC San Diego, San Diego, CA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"80","issue":"16_Supplement","first_page":"4411","last_page":"4411"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9369999766349792,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9369999766349792,"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":0.05790000036358833,"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":0.0006000000284984708,"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/gene-set-enrichment-analysis","display_name":"gene set enrichment analysis","score":0.9449999928474426},{"id":"https://openalex.org/keywords/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.7749999761581421},{"id":"https://openalex.org/keywords/pseudotime-trajectory","display_name":"pseudotime trajectory","score":0.9290000200271606},{"id":"https://openalex.org/keywords/cell-cycle-progression","display_name":"cell cycle progression","score":0.7239999771118164},{"id":"https://openalex.org/keywords/ovarian-cancer-cell-lines","display_name":"ovarian cancer cell lines","score":0.7609999775886536},{"id":"https://openalex.org/keywords/carboplatin-resistance","display_name":"carboplatin resistance","score":0.9860000014305115},{"id":"https://openalex.org/keywords/interferon-alpha-signaling","display_name":"interferon-alpha signaling","score":0.9430000185966492}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6384617686271667},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6222921013832092},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.572035551071167},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5343173146247864},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5338019132614136},{"id":"https://openalex.org/C29537977","wikidata":"https://www.wikidata.org/wiki/Q188941","display_name":"Cell cycle","level":3,"score":0.5139946341514587},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4917302429676056},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.48408806324005127},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4314131736755371},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3554706871509552},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1158/1538-7445.am2020-4411","doi":"https://doi.org/10.1158/1538-7445.am2020-4411","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.am2020-4411","pdf_url":null,"source":{"id":"https://openalex.org/S168522863","display_name":"Cancer Research","issn_l":"0008-5472","issn":["0008-5472","1538-7445"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","doyens","jufo-3","ki-jl-3","medline","norway-2"],"host_organization":"https://openalex.org/P4310320273","host_organization_name":"American Association for Cancer Research","host_organization_lineage":["https://openalex.org/P4310320273"],"host_organization_lineage_names":["American Association for Cancer Research"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cancer Research","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.5683000087738037}],"sustainable_development_goals_aurora":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.75}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1976510917","https://openalex.org/W2073305407","https://openalex.org/W2052655934","https://openalex.org/W4206493863","https://openalex.org/W104645380","https://openalex.org/W2027213253","https://openalex.org/W2017047508","https://openalex.org/W2165201120","https://openalex.org/W2023641020","https://openalex.org/W2794352724"],"abstract_inverted_index":{"Abstract":[0],"Single":[1],"cell":[2,12,51,116,137,152,185,203],"RNA-sequencing":[3],"(scRNA-seq)":[4],"has":[5,110],"advanced":[6],"studies":[7],"of":[8,94,106,148,171,200,217,229,268,274,278],"heterogeneous":[9],"tissues":[10],"and":[11,17,58,67,77,209,236,289],"populations":[13],"in":[14,97,138,176,196,202,214,233,259],"both":[15],"healthy":[16],"disease":[18],"states.":[19],"Dimensionality":[20],"reduction":[21],"methods":[22],"leverage":[23],"this":[24,143],"highly":[25],"granular":[26],"data":[27],"to":[28,39,46,80,90,103,114,122,145,157,163,181],"identify":[29],"cellular":[30,54],"states":[31,57],"not":[32,68,111],"captured":[33],"by":[34,207],"\u201cbulk\u201d":[35],"gene":[36,69,95,124,254],"expression":[37,108,178],"or":[38,53,71],"organize":[40],"cells":[41,162],"along":[42,261],"\u2018pseudotime'":[43],"trajectories":[44,59,263],"related":[45],"biological":[47,81,230],"processes":[48,231],"such":[49],"as":[50],"cycle":[52,186,204],"differentiation.":[55],"Cellular":[56],"are":[60],"often":[61],"annotated":[62],"using":[63],"individual":[64],"marker":[65],"genes":[66],"sets":[70,96],"pathways,":[72],"despite":[73],"their":[74],"more":[75,226],"reliable":[76],"interpretable":[78,227],"association":[79],"processes.":[82],"Gene":[83],"Set":[84],"Enrichment":[85],"Analysis":[86],"(GSEA)":[87],"was":[88],"designed":[89],"test":[91],"the":[92,104,107,139,161,169,184,215,222,265,275,279],"enrichment":[93,126,133,256],"bulk":[98,177],"transcriptomic":[99],"data,":[100,109,129],"but":[101],"due":[102],"sparsity":[105],"been":[112],"adapted":[113],"single":[115],"analysis.":[117],"We":[118,141],"propose":[119],"a":[120,146,164,218],"method":[121,144,224],"compute":[123],"set":[125,147,255],"for":[127,135,282],"scRNA-seq":[128],"which":[130,173],"calculates":[131],"an":[132],"score":[134],"each":[136],"dataset.":[140],"apply":[142],"matched":[149],"ovarian":[150],"cancer":[151,234],"lines":[153],"with":[154,183],"acquired":[155],"resistance":[156],"carboplatin.":[158],"After":[159],"aligning":[160],"cell-cycle":[165],"derived":[166],"pseudotime":[167,220,262],"trajectory,":[168,221],"activity":[170,213,267],"pathways":[172,270],"were":[174],"dysregulated":[175],"profiles":[179],"appeared":[180],"change":[182],"progression.":[187,205],"The":[188],"analysis":[189,257],"further":[190],"identified":[191],"interferon":[192],"alpha":[193],"signaling":[194],"induction":[195],"resistant":[197],"cells,":[198],"independent":[199],"differences":[201],"Hence,":[206],"quantifying":[208],"analyzing":[210],"pathway-level":[211],"transcriptional":[212],"context":[216],"single-cell":[219],"proposed":[223],"provides":[225],"annotation":[228],"altered":[232],"progression":[235],"treatment.":[237],"Citation":[238],"Format:":[239],"Alexander":[240],"T.":[241],"Wenzel,":[242],"Devora":[243],"Champa,":[244],"Stephen":[245],"B.":[246],"Howell,":[247],"Jill":[248],"P.":[249],"Mesirov,":[250],"Olivier":[251],"Harismendy.":[252],"A":[253],"approach":[258],"single-cells":[260],"reveals":[264],"dynamic":[266],"oncogenic":[269],"[abstract].":[271],"In:":[272],"Proceedings":[273],"Annual":[276],"Meeting":[277],"American":[280],"Association":[281],"Cancer":[283,295],"Research":[284],"2020;":[285],"2020":[286],"Apr":[287],"27-28":[288],"Jun":[290],"22-24.":[291],"Philadelphia":[292],"(PA):":[293],"AACR;":[294],"Res":[296],"2020;80(16":[297],"Suppl):Abstract":[298],"nr":[299],"4411.":[300]},"counts_by_year":[],"updated_date":"2026-09-25T08:18:29.962427","created_date":"2025-10-10T00:00:00"}