{"id":"https://openalex.org/W4388865848","doi":"https://doi.org/10.1158/2767-9764.24599544.v1","title":"FIGURE 2 from Exogenous Sequences in Tumors and Immune Cells (Exotic): A Tool for Estimating the Microbe Abundances in Tumor RNA-seq Data","display_name":"FIGURE 2 from Exogenous Sequences in Tumors and Immune Cells (Exotic): A Tool for Estimating the Microbe Abundances in Tumor RNA-seq Data","publication_year":2023,"publication_date":"2023-11-21","ids":{"openalex":"https://openalex.org/W4388865848","doi":"https://doi.org/10.1158/2767-9764.24599544.v1"},"language":"en","primary_location":{"id":"doi:10.1158/2767-9764.24599544.v1","doi":"https://doi.org/10.1158/2767-9764.24599544.v1","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1158/2767-9764.24599544.v1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"American Association for Cancer Research","raw_type":"posted-content"},"volume":null,"type":"other","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"http://dx.doi.org/10.1158/2767-9764.24599544.v1","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022597516","display_name":"Rebecca Hoyd","orcid":"https://orcid.org/0000-0003-1210-4491","observed_orcids":["https://orcid.org/0000-0003-1210-4491"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rebecca Hoyd","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-1210-4491","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079846181","display_name":"Caroline E. Wheeler","orcid":"https://orcid.org/0000-0002-3374-4909","observed_orcids":["https://orcid.org/0000-0002-3374-4909"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Caroline E. Wheeler","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-3374-4909","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028643512","display_name":"YunZhou Liu","orcid":"https://orcid.org/0000-0002-9892-2438","observed_orcids":["https://orcid.org/0000-0002-9892-2438"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"YunZhou Liu","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-9892-2438","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002837933","display_name":"Malvenderjit S. Jagjit Singh","orcid":"https://orcid.org/0000-0001-8198-9153","observed_orcids":["https://orcid.org/0000-0001-8198-9153"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Malvenderjit S. Jagjit Singh","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-8198-9153","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080186286","display_name":"Mitchell Muniak","orcid":"https://orcid.org/0000-0001-9919-1457","observed_orcids":["https://orcid.org/0000-0001-9919-1457"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mitchell Muniak","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-9919-1457","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054686355","display_name":"Ning Yi Jin","orcid":"https://orcid.org/0000-0002-6689-4671","observed_orcids":["https://orcid.org/0000-0002-6689-4671"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ning Jin","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-6689-4671","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056692526","display_name":"Nicholas C. Denko","orcid":"https://orcid.org/0000-0001-6875-734X","observed_orcids":["https://orcid.org/0000-0001-6875-734X"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nicholas C. Denko","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-6875-734X","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059652753","display_name":"David Paul Carbone","orcid":"https://orcid.org/0000-0003-3002-1921","observed_orcids":["https://orcid.org/0000-0003-3002-1921"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"David P. Carbone","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-3002-1921","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015153331","display_name":"Xiaokui Molly Mo","orcid":"https://orcid.org/0000-0002-9797-2687","observed_orcids":["https://orcid.org/0000-0002-9797-2687"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiaokui Mo","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-9797-2687","affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5031691358","display_name":"Daniel J. Spakowicz","orcid":"https://orcid.org/0000-0003-2314-6435","observed_orcids":["https://orcid.org/0000-0003-2314-6435"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Daniel J. Spakowicz","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-2314-6435","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/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.4359999895095825,"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"}},"topics":[{"id":"https://openalex.org/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.4359999895095825,"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"}},{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.16189999878406525,"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":0.07739999890327454,"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/tumor-microbiota","display_name":"tumor microbiome","score":0.824999988079071},{"id":"https://openalex.org/keywords/survival-analysis","display_name":"survival analysis","score":0.7379999756813049},{"id":"https://openalex.org/keywords/the-cancer-genome-atlas","display_name":"TCGA","score":0.9919999837875366},{"id":"https://openalex.org/keywords/tumor-microenvironment","display_name":"tumor microenvironment","score":0.6349999904632568},{"id":"https://openalex.org/keywords/immune-cell-deconvolution","display_name":"immune cell deconvolution","score":0.9639999866485596},{"id":"https://openalex.org/keywords/clinical-factors","display_name":"clinical factors","score":0.4560000002384186}],"concepts":[{"id":"https://openalex.org/C160798450","wikidata":"https://www.wikidata.org/wiki/Q4230870","display_name":"Concordance","level":2,"score":0.7400549650192261},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6371850967407227},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.5597549676895142},{"id":"https://openalex.org/C2776107976","wikidata":"https://www.wikidata.org/wiki/Q1786433","display_name":"Tumor microenvironment","level":3,"score":0.4855453670024872},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.45246008038520813},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.43059858679771423},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4224255383014679},{"id":"https://openalex.org/C143998085","wikidata":"https://www.wikidata.org/wiki/Q162555","display_name":"Oncology","level":1,"score":0.3519937992095947},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32650649547576904},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.17762523889541626},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12475991249084473},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1158/2767-9764.24599544.v1","doi":"https://doi.org/10.1158/2767-9764.24599544.v1","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1158/2767-9764.24599544.v1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"American Association for Cancer Research","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1158/2767-9764.24599544.v1","doi":"https://doi.org/10.1158/2767-9764.24599544.v1","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1158/2767-9764.24599544.v1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"American Association for Cancer Research","raw_type":"posted-content"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.8048999905586243,"display_name":"Good health and well-being"}],"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/W4388865606","https://openalex.org/W4387729581","https://openalex.org/W4282030196","https://openalex.org/W4388865684","https://openalex.org/W4379983343","https://openalex.org/W7149043216","https://openalex.org/W3082997745","https://openalex.org/W4398555516","https://openalex.org/W4416132523","https://openalex.org/W4391531287"],"abstract_inverted_index":{"Estimating":[0],"the":[1,9,54,70,85],"clinical":[2,78],"relevance":[3],"of":[4,62,84,113],"observed":[5],"tumor":[6,86],"microbes":[7,114],"through":[8],"concordance":[10],"between":[11,69],"two":[12,63,71],"independent":[13],"datasets.":[14,59,72],"A,":[15],"Survival":[16],"analyses":[17,39],"by":[18,21],"cancer":[19],"stratified":[20],"microbe":[22],"presence/absence":[23],"at":[24],"every":[25],"taxonomic":[26],"level.":[27],"Colors":[28],"indicate":[29],"a":[30],"significant":[31,43],"association":[32],"with":[33,76,115],"survival.":[34],"The":[35],"ORIEN":[36,96],"and":[37,50,80,97],"TCGA":[38,98,107],"separately":[40],"show":[41,66],"many":[42,109],"associations,":[44],"whereas":[45],"few":[46],"are":[47,92],"consistent":[48],"(significant":[49],"affecting":[51],"survival":[52],"in":[53,106],"same":[55],"direction)":[56],"across":[57],"both":[58],"B,":[60],"Examples":[61],"taxa":[64],"that":[65],"concordant":[67,93],"associations":[68],"C,":[73],"Microbes":[74],"correlate":[75],"representative":[77],"variables":[79],"an":[81],"expression":[82],"signature":[83],"microenvironment":[87],"(Buffa":[88],"hypoxia":[89],"score).":[90],"Shown":[91],"correlations":[94],"for":[95,101,108],"data,":[99],"except":[100],"BMI,":[102],"which":[103],"is":[104],"missing":[105],"cancers.":[110],"D,":[111],"Correlation":[112],"deconvolved":[116],"immune":[117],"cell":[118],"abundances":[119],"within":[120],"each":[121],"cancer.":[122]},"counts_by_year":[],"updated_date":"2026-09-22T06:50:58.402377","created_date":"2023-11-22T00:00:00"}