{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/110638"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/110638","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Integration of bioinformatics approaches to study transcriptome patterns associated with complex traits at the gene and isoform levels","abstract":"The student, Pan Zhang, accepted the attached license on 2021-03-21 at 20:12.","abstract_html":"The student, Pan Zhang, accepted the attached license on 2021-03-21 at 20:12.","abstract_has_math":false,"creators":["Zhang, Pan"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Informatics","degree_department":null,"school":null,"contributors":["Rodriguez-Zas, Sandra Luisa","Caetano-Anolles, Gustavo","Villamil, Maria Bonita","Yan, Huihuang"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2021,"date_issued":"2021-09-17T02:34:19Z","date_published":"2021-09-17T02:34:19Z","updated_at":"2026-07-22T22:24:52Z","subjects":["RNA-seq, differential expression, alternative splicing, co-expression network, Gaussian Markov random fields"],"languages":["en"],"rights":["Copyright 2021 Pan Zhang"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/110638","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Rodriguez-Zas, Sandra Luisa","Caetano-Anolles, Gustavo","Villamil, Maria Bonita","Yan, Huihuang"]},{"key":"dc:creator","label":"Author","values":["Zhang, Pan"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2021-09-17T02:34:19Z","2023-09-17T02:34:57Z","2021-03-23","2021-05"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Informatics"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["RNA-seq, differential expression, alternative splicing, co-expression network, Gaussian Markov random fields"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2021 Pan Zhang"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/110638"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["The student, Pan Zhang, accepted the attached license on 2021-03-21 at 20:12.","The student, Pan Zhang, submitted this Dissertation for approval on 2021-03-21 at 20:31.","This Dissertation was approved for publication on 2021-03-23 at 11:26.","DSpace SAF Submission Ingestion Package generated from Vireo submission #16200 on 2021-09-16 at 17:02:30","Made available in DSpace on 2021-09-17T02:34:19Z (GMT). No. of bitstreams: 2 ZHANG-DISSERTATION-2021.pdf: 6693076 bytes, checksum: 9c98525af8ce93483adc3be5fec2731c (MD5) LICENSE.txt: 4206 bytes, checksum: b8a73218696109c7b674ad405cfef95b (MD5) Previous issue date: 2021-03-23","Embargo set by: Seth Robbins for item 118481 Lift date: 2023-09-17T02:34:57Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","U of I Only","The study of the molecules associated with complex traits such as diseases can advance the understanding of traits and help identify biomarkers and potential remedies. In this study, high-throughput RNA-seq technology, statistical models and bioinformatics approaches were used to profile the transcriptome and uncover the underlying molecular mechanisms associated with activity addiction and opioid-induced hyperalgesia with brain region or central nervous system region dependencies considered. Functional category enrichment, reconstruction of molecular interactions, and regulatory networks added systematic insights into the dysregulation of the transcriptome. In addition, co-expression networks at various aggregate levels (e.g., gene family, gene, or transcript isoform) were estimated using Gaussian Markov random fields based on the abundance of mRNA. Multiple criteria were used to benchmark the inferred networks against the pathways in Kyoto Encyclopedia of Genes and Genomes reference. Our findings suggest that the inference of networks using granular information can enhance the network performance, especially when high splicing variation is involved.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2023-05-01"]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Integration of bioinformatics approaches to study transcriptome patterns associated with complex traits at the gene and isoform levels"]}]}],"canonical_facts":{"dc:contributor":["Rodriguez-Zas, Sandra Luisa","Caetano-Anolles, Gustavo","Villamil, Maria Bonita","Yan, Huihuang"],"dc:creator":["Zhang, Pan"],"dc:date":["2021-09-17T02:34:19Z","2023-09-17T02:34:57Z","2021-03-23","2021-05"],"dc:description":["The student, Pan Zhang, accepted the attached license on 2021-03-21 at 20:12.","The student, Pan Zhang, submitted this Dissertation for approval on 2021-03-21 at 20:31.","This Dissertation was approved for publication on 2021-03-23 at 11:26.","DSpace SAF Submission Ingestion Package generated from Vireo submission #16200 on 2021-09-16 at 17:02:30","Made available in DSpace on 2021-09-17T02:34:19Z (GMT). No. of bitstreams: 2 ZHANG-DISSERTATION-2021.pdf: 6693076 bytes, checksum: 9c98525af8ce93483adc3be5fec2731c (MD5) LICENSE.txt: 4206 bytes, checksum: b8a73218696109c7b674ad405cfef95b (MD5) Previous issue date: 2021-03-23","Embargo set by: Seth Robbins for item 118481 Lift date: 2023-09-17T02:34:57Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","U of I Only","The study of the molecules associated with complex traits such as diseases can advance the understanding of traits and help identify biomarkers and potential remedies. In this study, high-throughput RNA-seq technology, statistical models and bioinformatics approaches were used to profile the transcriptome and uncover the underlying molecular mechanisms associated with activity addiction and opioid-induced hyperalgesia with brain region or central nervous system region dependencies considered. Functional category enrichment, reconstruction of molecular interactions, and regulatory networks added systematic insights into the dysregulation of the transcriptome. In addition, co-expression networks at various aggregate levels (e.g., gene family, gene, or transcript isoform) were estimated using Gaussian Markov random fields based on the abundance of mRNA. Multiple criteria were used to benchmark the inferred networks against the pathways in Kyoto Encyclopedia of Genes and Genomes reference. Our findings suggest that the inference of networks using granular information can enhance the network performance, especially when high splicing variation is involved.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2023-05-01"],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/2142/110638"],"dc:language":["en"],"dc:rights":["Copyright 2021 Pan Zhang"],"dc:subject":["RNA-seq, differential expression, alternative splicing, co-expression network, Gaussian Markov random fields"],"dc:title":["Integration of bioinformatics approaches to study transcriptome patterns associated with complex traits at the gene and isoform levels"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Informatics"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:52Z"}