title: Novel approach for coexpression analysis of E2F1-3 and MYC target genes in chronic myelogenous leukemia.
abstract: BACKGROUND
  Chronic myelogenous leukemia (CML) is characterized by tremendous amount of immature myeloid cells in the blood circulation. E2F1-3 and MYC are important transcription factors that form positive feedback loops by reciprocal regulation in their own transcription processes. Since genes regulated by E2F1-3 or MYC are related to cell proliferation and apoptosis, we wonder if there exists difference in the coexpression patterns of genes regulated concurrently by E2F1-3 and MYC between the normal and the CML states.
  
  
  RESULTS
  We proposed a method to explore the difference in the coexpression patterns of those candidate target genes between the normal and the CML groups. A disease-specific cutoff point for coexpression levels that classified the coexpressed gene pairs into strong and weak coexpression classes was identified. Our developed method effectively identified the coexpression pattern differences from the overall structure. Moreover, we found that genes related to the cell adhesion and angiogenesis properties were more likely to be coexpressed in the normal group when compared to the CML group.
  
  
  CONCLUSIONS
  Our findings may be helpful in exploring the underlying mechanisms of CML and provide useful information in cancer treatment.
authors.affiliation: Department of Health Technology and Informatics, Hong Kong Polytechnic University, Lee Shau Kee Building, Hung Hom, Kowloon, Hong Kong.
authors.forename: Fengfeng
authors.identifier: 0000-0003-4959-4527
authors.initials: F
authors.lastname: Wang
authors.affiliation: Department of Health Technology and Informatics, Hong Kong Polytechnic University, Lee Shau Kee Building, Hung Hom, Kowloon, Hong Kong.
authors.forename: Lawrence W C
authors.identifier: 0000-0001-6451-2273
authors.initials: LW
authors.lastname: Chan
authors.affiliation: Department of Clinical Oncology, Queen Elizabeth Hospital, 30 Gascoigne Road, Kowloon, Hong Kong.
authors.forename: William C S
authors.initials: WC
authors.lastname: Cho
authors.affiliation: Bioinformatics Center, Chang Gung University, Taoyuan 333, Taiwan.
authors.forename: Petrus
authors.initials: P
authors.lastname: Tang
authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang District, Beijing 100029, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.affiliation: Department of Computer Science, Informatics Institute, University of Missouri, Columbia, MO 65211, USA.
authors.forename: Chi-Ren
authors.initials: CR
authors.lastname: Shyu
authors.affiliation: Department of Health Technology and Informatics, Hong Kong Polytechnic University, Lee Shau Kee Building, Hung Hom, Kowloon, Hong Kong.
authors.forename: Nancy B Y
authors.initials: NB
authors.lastname: Tsui
authors.affiliation: Department of Health Technology and Informatics, Hong Kong Polytechnic University, Lee Shau Kee Building, Hung Hom, Kowloon, Hong Kong.
authors.forename: S C Cesar
authors.initials: SC
authors.lastname: Wong
authors.affiliation: Department of Health Technology and Informatics, Hong Kong Polytechnic University, Lee Shau Kee Building, Hung Hom, Kowloon, Hong Kong.
authors.forename: Parco M
authors.initials: PM
authors.lastname: Siu
authors.affiliation: Department of Health Technology and Informatics, Hong Kong Polytechnic University, Lee Shau Kee Building, Hung Hom, Kowloon, Hong Kong.
authors.forename: S P
authors.initials: SP
authors.lastname: Yip
authors.affiliation: Department of Health Technology and Informatics, Hong Kong Polytechnic University, Lee Shau Kee Building, Hung Hom, Kowloon, Hong Kong.
authors.forename: Benjamin Y M
authors.initials: BY
authors.lastname: Yung
mesh_terms: D002478:Cells, Cultured; D050687:E2F1 Transcription Factor / Q000378:metabolism*; D050699:E2F3 Transcription Factor / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D018390:Gene Targeting; D006801:Humans; D015464:Leukemia, Myelogenous, Chronic, BCR-ABL Positive / Q000378:metabolism*; D009363:Neoplasm Proteins / Q000378:metabolism*; D016271:Proto-Oncogene Proteins c-myc / Q000378:metabolism*
chemical_list: D050687:E2F1 Transcription Factor; C493753:E2F1 protein, human; D050699:E2F3 Transcription Factor; C098319:E2F3 protein, human; D009363:Neoplasm Proteins; D016271:Proto-Oncogene Proteins c-myc