{"id":"https://openalex.org/W6924931570","doi":"https://doi.org/10.17169/refubium-34273","title":"Computational analysis of cancer transcriptomes: drug response prediction in colorectal cancer and gene regulatory networks and long non-coding genes in medulloblastoma","display_name":"Computational analysis of cancer transcriptomes: drug response prediction in colorectal cancer and gene regulatory networks and long non-coding genes in medulloblastoma","publication_year":2022,"publication_date":"2022-01-01","ids":{"openalex":"https://openalex.org/W6924931570","doi":"https://doi.org/10.17169/refubium-34273"},"language":"en","primary_location":{"id":"pmh:oai:aleph.bib-bvb.de:BVB01-033627579","is_oa":false,"landing_page_url":"https://refubium.fu-berlin.de/handle/fub188/34555","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"software, multimedia"},"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hdl.handle.net/21.11116/0000-0011-98A2-A","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Risch, Thomas","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Risch, Thomas","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.23890836,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":{"id":"https://openalex.org/T12968","display_name":"Research on scale insects","score":0.9891999959945679,"subfield":{"id":"https://openalex.org/subfields/1109","display_name":"Insect Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12968","display_name":"Research on scale insects","score":0.9891999959945679,"subfield":{"id":"https://openalex.org/subfields/1109","display_name":"Insect Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T14310","display_name":"Botany and Geology in Latin America and Caribbean","score":0.0032999999821186066,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13971","display_name":"Synthesis and Biological Activity","score":0.0005000000237487257,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/transcriptome","display_name":"Transcriptome","score":0.775600016117096},{"id":"https://openalex.org/keywords/cetuximab","display_name":"Cetuximab","score":0.616599977016449},{"id":"https://openalex.org/keywords/colorectal-cancer","display_name":"Colorectal cancer","score":0.5562000274658203},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.542900025844574},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.49970000982284546},{"id":"https://openalex.org/keywords/wnt-signaling-pathway","display_name":"Wnt signaling pathway","score":0.4699000120162964},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.4269999861717224},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4092999994754791},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.38580000400543213}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.775600016117096},{"id":"https://openalex.org/C2779998722","wikidata":"https://www.wikidata.org/wiki/Q420296","display_name":"Cetuximab","level":4,"score":0.616599977016449},{"id":"https://openalex.org/C526805850","wikidata":"https://www.wikidata.org/wiki/Q188874","display_name":"Colorectal cancer","level":3,"score":0.5562000274658203},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5435000061988831},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.542900025844574},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.49970000982284546},{"id":"https://openalex.org/C137620995","wikidata":"https://www.wikidata.org/wiki/Q155769","display_name":"Wnt signaling pathway","level":3,"score":0.4699000120162964},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.4269999861717224},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42170000076293945},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4092999994754791},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.4066999852657318},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.4000999927520752},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.38580000400543213},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.3828999996185303},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.37880000472068787},{"id":"https://openalex.org/C2778264664","wikidata":"https://www.wikidata.org/wiki/Q422445","display_name":"Tumor suppressor gene","level":4,"score":0.3361999988555908},{"id":"https://openalex.org/C2781187634","wikidata":"https://www.wikidata.org/wiki/Q20969980","display_name":"KRAS","level":4,"score":0.31470000743865967},{"id":"https://openalex.org/C31695470","wikidata":"https://www.wikidata.org/wiki/Q11293125","display_name":"Organoid","level":2,"score":0.30090001225471497},{"id":"https://openalex.org/C179185449","wikidata":"https://www.wikidata.org/wiki/Q219699","display_name":"Suppressor","level":3,"score":0.28769999742507935},{"id":"https://openalex.org/C64903051","wikidata":"https://www.wikidata.org/wiki/Q2198549","display_name":"Drug development","level":3,"score":0.28450000286102295},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.2827000021934509},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.27720001339912415},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.27619999647140503},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.27619999647140503},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2703999876976013},{"id":"https://openalex.org/C55427017","wikidata":"https://www.wikidata.org/wiki/Q1638475","display_name":"Cancer stem cell","level":3,"score":0.2655999958515167},{"id":"https://openalex.org/C32220436","wikidata":"https://www.wikidata.org/wiki/Q2072214","display_name":"Personalized medicine","level":2,"score":0.2538999915122986},{"id":"https://openalex.org/C114851261","wikidata":"https://www.wikidata.org/wiki/Q12147416","display_name":"Drug resistance","level":2,"score":0.2531000077724457}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:aleph.bib-bvb.de:BVB01-033627579","is_oa":false,"landing_page_url":"https://refubium.fu-berlin.de/handle/fub188/34555","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"software, multimedia"},{"id":"pmh:oai:pure.mpg.de:item_3663983","is_oa":true,"landing_page_url":"https://hdl.handle.net/21.11116/0000-0011-98A2-A","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/doctoralThesis"},{"id":"doi:10.17169/refubium-34273","is_oa":true,"landing_page_url":"https://doi.org/10.17169/refubium-34273","pdf_url":null,"source":{"id":"https://openalex.org/S7407052913","display_name":"Universit\u00e4tsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"thesis"}],"best_oa_location":{"id":"pmh:oai:pure.mpg.de:item_3663983","is_oa":true,"landing_page_url":"https://hdl.handle.net/21.11116/0000-0011-98A2-A","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/doctoralThesis"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"During":[0],"cancer":[1,50,68,87],"development,":[2],"malignant":[3,33,371],"tumours":[4,34,123,433],"accumulate":[5],"genetic":[6,399],"and":[7,16,78,101,107,128,166,232,249,286,335,392,403,414,422,432,479,520,534,544,554,568,575,600,655,676,691],"epigenetic":[8],"alterations":[9,428],"that":[10,182,341,467,613,627,649,686],"cause":[11,409],"dysregulation":[12],"of":[13,22,32,40,48,57,75,94,122,133,172,186,191,207,225,246,268,284,306,332,345,359,364,378,482,501,530,581,588,604,635,642],"gene":[14,23,247,442,464,546,555,561,571,590,668],"expression":[15,24,248,282,547,562,591,631],"cellular":[17,27],"processes.":[18],"Since":[19],"the":[20,30,38,45,91,134,143,156,163,175,200,212,223,236,243,281,356,365,368,463,470,480,498,503,509,528,539,579,597,639,666],"regulation":[21,572],"controls":[25],"many":[26],"processes,":[28],"understanding":[29,206],"transcriptome":[31,88],"provides":[35],"insights":[36,496],"into":[37,460,497],"biology":[39,500],"cancer.":[41],"Key":[42],"technology":[43],"for":[44,202,229,596],"molecular":[46,205,357,401,445,471,499,536],"analysis":[47,93,245,358],"whole":[49],"transcriptomes":[51,69],"is":[52,113,194,367,634],"next-":[53],"generation":[54],"sequencing":[55],"(NGS)":[56],"RNA":[58],"(RNA-seq)":[59],"from":[60,70,97,254,560],"bulk":[61],"tumours.":[62],"However,":[63,462],"to":[64,125,141,174,196,274,279,300,308,397,469,515,638],"derive":[65],"information":[66],"about":[67],"RNA-seq":[71,95,525],"data,":[72],"a":[73,114,120,189,203,219,226,266,291,296,302,330,362,435,440,513,593,646,671,683],"variety":[74],"computational":[76,92],"tools":[77],"analyses":[79,664],"are":[80,179,429,475],"needed.":[81],"The":[82,323,352],"following":[83],"work":[84],"presents":[85],"two":[86],"studies":[89],"addressing":[90],"data":[96,252],"colorectal":[98],"carcinomas":[99],"(CRC)":[100],"medulloblastomas":[102],"(MB)":[103],"by":[104,551],"applying":[105],"statistical":[106,262],"machine":[108,294],"learning":[109],"(ML)":[110],"methods.":[111],"CRC":[112,208,230,340],"clinically":[115],"challenging":[116],"disease":[117],"because":[118],"only":[119,476],"fraction":[121,190],"responds":[124],"available":[126],"chemo-":[127],"targeted":[129],"therapies.":[130],"Functional":[131],"loss":[132],"tumour":[135,363,373,385,684],"suppressor":[136,685],"APC":[137],"has":[138,447],"been":[139,448],"suggested":[140],"represent":[142],"initial":[144],"mutation,":[145],"activating":[146],"Wnt":[147],"signalling.":[148],"Additional":[149,444],"events":[150],"include":[151],"mutually":[152],"exclusive":[153],"mutations":[154,181,328,407],"in":[155,162,209,338,349,374,412,419,473,490,570,592,617,674],"RAS/RAF":[157,180,327],"proto-oncogenes":[158],"as":[159,161,329,670,682],"well":[160,337],"TGF\u03b2,":[164],"PI3K,":[165],"TP53":[167],"pathways.":[168],"Routinely":[169],"used":[170,290],"biomarkers":[171,344],"resistance":[173],"EGFR":[176],"inhibitor":[177],"cetuximab":[178,197,333,346],"activate":[183],"signalling":[184],"downstream":[185],"EGFR.":[187],"Still,":[188],"wild-type":[192],"CRCs":[193],"resistant":[195],"treatment.":[198],"Addressing":[199,527],"need":[201],"better":[204],"precision":[210],"oncology,":[211],"OncoTrack":[213],"consortium":[214],"(Innovative":[215],"Medicine":[216],"Initiative)":[217],"designed":[218],"multi-omics":[220],"strategy":[221],"integrating":[222],"establishment":[224],"pre-clinical":[227],"platform":[228],"organoid":[231],"animal":[233],"models.":[234],"In":[235],"study":[237,354],"presented":[238],"below,":[239],"we":[240,264,311,518,532,583,609,622],"focused":[241],"on":[242],"integrative":[244],"drug":[250],"response":[251,273,307,334],"obtained":[253],"patient-derived":[255],"xenografts":[256],"(PDXs)":[257],"treated":[258],"with":[259,272,659],"cetuximab.":[260,309],"Applying":[261],"methods,":[263],"identified":[265,449,533,623,645],"signature":[267],"241":[269],"genes":[270,316,486,612,626,654,658],"associated":[271],"cetuximab,":[275],"which":[276,455,633],"allowed":[277],"us":[278],"dissect":[280],"profiles":[283,548],"responding":[285],"non-responding":[287],"CRC.":[288],"We":[289,644],"support":[292],"vector":[293],"(SVM),":[295],"supervised":[297],"ML":[298],"algorithm,":[299],"obtain":[301],"gene-expression-based":[303],"classifier":[304,325],"predictive":[305,315],"Here,":[310],"selected":[312],"16":[313],"highly":[314],"using":[317,380],"multiple":[318],"SVM":[319],"recursive":[320],"feature":[321],"elimination.":[322],"built":[324],"outperformed":[326],"predictor":[331],"performed":[336],"RAS/RAF-wild-type":[339],"currently":[342],"lacks":[343],"treatment":[347],"outcome":[348],"clinical":[350,404],"practice.":[351],"second":[353],"addressed":[355,489],"MB.":[360,607,618,643],"MB,":[361,416,425,502,531],"cerebellum,":[366],"most":[369],"common":[370],"brain":[372],"children.":[375],"Transcriptome":[376],"profiling":[377],"MB":[379,474,524],"microarrays":[381],"had":[382],"revealed":[383,566,665],"four":[384,452,540],"subgroups,":[386,454],"namely":[387],"WNT,":[388],"SHH,":[389],"Group":[390,393,420,423,605,677],"3":[391,421],"4,":[394],"each":[395],"related":[396],"distinct":[398],"alterations,":[400],"profiles,":[402],"features.":[405],"Recurrent":[406],"mainly":[408],"pathway":[410],"activation":[411],"WNT":[413],"SHH":[415,675],"respectively,":[417],"whereas":[418],"4":[424,606,678],"gross":[426],"chromosomal":[427],"more":[430],"prevalent":[431],"express":[434],"specific":[436],"cell-type-":[437],"rather":[438],"than":[439],"pathway-related":[441],"signature.":[443],"complexity":[446],"within":[450,508,538],"these":[451,620,657],"main":[453,541],"could":[456,584],"be":[457],"dissected":[458],"further":[459,495],"subtypes.":[461],"regulatory":[465,556],"networks":[466,557],"contribute":[468],"heterogeneity":[472,529],"partially":[477],"known,":[478],"role":[481],"long":[483],"non-coding":[484],"(lnc)":[485],"remains":[487],"poorly":[488],"this":[491,516],"disease.":[492],"To":[493],"gain":[494],"PedBrain":[504],"project":[505],"was":[506],"founded":[507],"ICGC":[510],"framework.":[511],"As":[512],"contribution":[514],"project,":[517],"sequenced":[519],"computationally":[521],"analysed":[522,550],"164":[523],"samples.":[526],"validated":[535],"subclusters":[537,574],"subgroups.":[542,576],"Subgroup-":[543],"subcluster-specific":[545,589],"were":[549,614],"functional":[552],"enrichments":[553],"(GRNs)":[558],"inferred":[559],"data.":[563],"These":[564],"GRNs":[565],"communalities":[567],"differences":[569],"among":[573],"By":[577],"estimating":[578],"impact":[580],"TFs,":[582],"unravel":[585],"master":[586],"regulators":[587,603],"systematic":[594],"fashion":[595],"first":[598],"time":[599],"highlight":[601],"unknown":[602],"Furthermore,":[608],"characterised":[610],"lnc":[611,625,653,667],"differentially":[615],"expressed":[616],"Among":[619],"genes,":[621],"20":[624],"show":[628],"brain-":[629],"development-associated":[630],"patterns,":[632],"interest":[636],"due":[637],"embryonic":[640],"origin":[641],"co-expression":[647],"cluster":[648],"accumulates":[650],"known":[651],"cancer-related":[652],"associates":[656],"cancer-promoting":[660],"protein":[661],"biogenesis.":[662],"Survival":[663],"MEG3":[669],"prognostic":[672],"marker":[673],"subcluster,":[679],"potentially":[680],"acting":[681],"negatively":[687],"regulates":[688],"cell":[689],"cycle":[690],"TGF\u03b2":[692],"receptor":[693],"expression.":[694]},"counts_by_year":[],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
