title: Unveiling transcription factor regulation and differential co-expression genes in Duchenne muscular dystrophy.
abstract: BACKGROUND
  Gene expression analysis is powerful for investigating the underlying mechanisms of Duchenne muscular dystrophy (DMD). Previous studies mainly neglected co-expression or transcription factor (TF) information. Here we integrated TF information into differential co-expression analysis (DCEA) to explore new understandings of DMD pathogenesis.
  
  
  METHODS
  Using two microarray datasets from Gene Expression Omnibus (GEO) database, we firstly detected differentially expressed genes (DEGs) and pathways enriched with DEGs. Secondly, we constructed differentially regulated networks to integrate the TF-to-target information and the differential co-expression genes.
  
  
  RESULTS
  A total of 454 DEGs were detected and both KEGG pathway and ingenuity pathway analysis revealed that pathways enriched with aberrantly regulated genes are mostly involved in the immune response processes. DCEA results generated 610 pairs of DEGs regulated by at least one common TF, including 78 pairs of co-expressed DEGs. A network was constructed to illustrate their relationships and a subnetwork for DMD related molecules was constructed to show genes and TFs that may play important roles in the secondary changes of DMD. Among the DEGs which shared TFs with DMD, six genes were co-expressed with DMD, including ATP1A2, C1QB, MYOF, SAT1, TRIP10, and IFI6.
  
  
  CONCLUSIONS
  Our results may provide a new understanding of DMD and contribute potential targets for future therapeutic tests.
  The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_210.
authors.affiliation: Clinical laboratory, Xuzhou Children's Hospital, No. 18 Sudibei Road, Xuzhou, Jiangsu Province, China. tlj1168@163.com.
authors.forename: Lijun
authors.initials: L
authors.lastname: Tian
authors.affiliation: Clinical laboratory, Xuzhou Children's Hospital, No. 18 Sudibei Road, Xuzhou, Jiangsu Province, China. junhuacaos@163.com.
authors.forename: Junhua
authors.initials: J
authors.lastname: Cao
authors.affiliation: Clinical laboratory, Xuzhou Children's Hospital, No. 18 Sudibei Road, Xuzhou, Jiangsu Province, China. xingqiangdengs@163.com.
authors.forename: Xingqiang
authors.initials: X
authors.lastname: Deng
authors.affiliation: Clinical laboratory, Xuzhou Children's Hospital, No. 18 Sudibei Road, Xuzhou, Jiangsu Province, China. chuanlingzhangs@126.com.
authors.forename: Chuanling
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Clinical laboratory, Xuzhou Children's Hospital, No. 18 Sudibei Road, Xuzhou, Jiangsu Province, China. tongqians@126.com.
authors.forename: Tong
authors.initials: T
authors.lastname: Qian
authors.affiliation: Clinical laboratory, Xuzhou Children's Hospital, No. 18 Sudibei Road, Xuzhou, Jiangsu Province, China. xianxiangsongs@126.com.
authors.forename: Xianxiang
authors.initials: X
authors.lastname: Song
authors.affiliation: Clinical laboratory, Xuzhou Children's Hospital, No. 18 Sudibei Road, Xuzhou, Jiangsu Province, China. baoshanhuangs@126.com.
authors.forename: Baoshan
authors.initials: B
authors.lastname: Huang
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D005819:Genetic Markers; D020022:Genetic Predisposition to Disease; D006801:Humans; D020388:Muscular Dystrophy, Duchenne / Q000175:diagnosis / Q000235:genetics* / Q000628:therapy; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D011379:Prognosis; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D005819:Genetic Markers; D014157:Transcription Factors