{"id":"https://openalex.org/W4394296889","doi":"https://doi.org/10.6084/m9.figshare.9616355","title":"ICeD-T Provides Accurate Estimates of Immune Cell Abundance in Tumor Samples by Allowing for Aberrant Gene Expression Patterns","display_name":"ICeD-T Provides Accurate Estimates of Immune Cell Abundance in Tumor Samples by Allowing for Aberrant Gene Expression Patterns","publication_year":2019,"publication_date":"2019-01-01","ids":{"openalex":"https://openalex.org/W4394296889","doi":"https://doi.org/10.6084/m9.figshare.9616355"},"language":"en","primary_location":{"id":"pmh:oai:figshare.com:article/9616355","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/ICeD-T_Provides_Accurate_Estimates_of_Immune_Cell_Abundance_in_Tumor_Samples_by_Allowing_for_Aberrant_Gene_Expression_Patterns/9616355","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},"volume":null,"type":"dataset","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://figshare.com/articles/dataset/ICeD-T_Provides_Accurate_Estimates_of_Immune_Cell_Abundance_in_Tumor_Samples_by_Allowing_for_Aberrant_Gene_Expression_Patterns/9616355","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Wilson, Douglas R.","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wilson, Douglas R.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101950203","display_name":"Chong Jin","orcid":"https://orcid.org/0000-0003-4863-3328","observed_orcids":["https://orcid.org/0000-0003-4863-3328"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jin, Chong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078399867","display_name":"Joseph G. Ibrahim","orcid":"https://orcid.org/0000-0003-2428-6552","observed_orcids":["https://orcid.org/0000-0003-2428-6552"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ibrahim, Joseph G.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5086153438","display_name":"Wei Sun","orcid":"https://orcid.org/0000-0002-6350-1107","observed_orcids":["https://orcid.org/0000-0002-6350-1107"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sun, Wei","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"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":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9214000105857849,"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":0.9214000105857849,"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":0.07410000264644623,"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/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.0017999999690800905,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/immune-cell-deconvolution","display_name":"immune cell deconvolution","score":0.9309999942779541},{"id":"https://openalex.org/keywords/tumor-immune-cell-composition","display_name":"tumor immune cell composition","score":0.8289999961853027},{"id":"https://openalex.org/keywords/abnormal-gene-expression","display_name":"aberrant gene expression","score":0.9020000100135803},{"id":"https://openalex.org/keywords/tumor-microenvironment","display_name":"tumor microenvironment","score":0.9169999957084656},{"id":"https://openalex.org/keywords/immunotherapy-response","display_name":"immunotherapy response","score":0.8569999933242798},{"id":"https://openalex.org/keywords/precision-immunotherapy","display_name":"precision immunotherapy","score":0.7229999899864197}],"concepts":[{"id":"https://openalex.org/C77077793","wikidata":"https://www.wikidata.org/wiki/Q336019","display_name":"Abundance (ecology)","level":2,"score":0.787559986114502},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.545973002910614},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.5224879384040833},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5195122957229614},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4788253605365753},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4783977270126343},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.46395343542099},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2965937852859497},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2550933063030243},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.15098842978477478},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"pmh:oai:figshare.com:article/9616355","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/ICeD-T_Provides_Accurate_Estimates_of_Immune_Cell_Abundance_in_Tumor_Samples_by_Allowing_for_Aberrant_Gene_Expression_Patterns/9616355","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"doi:10.6084/m9.figshare.9616355","doi":"https://doi.org/10.6084/m9.figshare.9616355","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.9616355","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},{"id":"doi:10.6084/m9.figshare.9616355.v1","doi":"https://doi.org/10.6084/m9.figshare.9616355.v1","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.9616355.v1","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Other"},{"id":"doi:10.6084/m9.figshare.9616355.v2","doi":"https://doi.org/10.6084/m9.figshare.9616355.v2","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.9616355.v2","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"}],"best_oa_location":{"id":"pmh:oai:figshare.com:article/9616355","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/ICeD-T_Provides_Accurate_Estimates_of_Immune_Cell_Abundance_in_Tumor_Samples_by_Allowing_for_Aberrant_Gene_Expression_Patterns/9616355","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.8048999905586243,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3009162653","https://openalex.org/W4401914352","https://openalex.org/W2803058913","https://openalex.org/W2953365463","https://openalex.org/W2887241857","https://openalex.org/W2995696691","https://openalex.org/W3005889306","https://openalex.org/W2739685638","https://openalex.org/W2478472433","https://openalex.org/W3112357451"],"abstract_inverted_index":{"Immunotherapies":[0],"have":[1,38],"attracted":[2],"lots":[3],"of":[4,15,65,125],"research":[5],"interests":[6],"recently.":[7],"The":[8],"need":[9],"to":[10,18,41,61,116,144,151,165],"understand":[11],"the":[12,33,109,123,153],"underlying":[13],"mechanisms":[14],"immunotherapies":[16],"and":[17,79,112,133,158],"develop":[19],"precision":[20],"immunotherapy":[21,156],"regimens":[22],"has":[23],"spurred":[24],"great":[25],"interest":[26],"in":[27,96,130],"characterizing":[28],"immune":[29,43,159],"cell":[30,44,71,117,160],"composition":[31,45],"within":[32],"tumor":[34,52,80],"microenvironment.":[35],"Several":[36],"methods":[37,56,129,150],"been":[39],"developed":[40],"estimate":[42],"using":[46],"gene":[47,66,73],"expression":[48,67,74,89,105],"data":[49,136],"from":[50],"bulk":[51],"samples.":[53,81],"However,":[54],"these":[55,145,149],"are":[57,106,170],"not":[58],"flexible":[59],"enough":[60],"handle":[62],"aberrant":[63,102],"patterns":[64],"data,":[68],"e.g.,":[69],"inconsistent":[70,107],"type-specific":[72],"between":[75,155],"purified":[76],"reference":[77],"samples":[78],"We":[82,121],"propose":[83],"a":[84],"novel":[85],"statistical":[86],"method":[87],"for":[88],"deconvolution":[90,110],"called":[91],"ICeD-T":[92,99,126,138,162],"(Immune":[93],"Cell":[94],"Deconvolution":[95],"Tumor":[97],"tissues).":[98],"automatically":[100],"identifies":[101],"genes":[103],"whose":[104],"with":[108],"model":[111],"down-weights":[113],"their":[114],"contributions":[115],"type":[118],"abundance":[119],"estimates.":[120],"evaluated":[122],"performance":[124,143],"versus":[127],"existing":[128],"simulation":[131],"studies":[132],"several":[134],"real":[135],"analyses.":[137],"displayed":[139],"comparable":[140],"or":[141],"superior":[142],"competing":[146],"methods.":[147],"Applying":[148],"assess":[152],"relationship":[154],"response":[157],"composition,":[161],"is":[163],"able":[164],"identify":[166],"significant":[167],"associations":[168],"that":[169],"missed":[171],"by":[172],"its":[173],"competitors.":[174]},"counts_by_year":[],"updated_date":"2026-10-09T09:14:12.587421","created_date":"2024-04-08T00:00:00"}
