title: Meta-analysis of genetic programs between idiopathic pulmonary fibrosis and sarcoidosis.
abstract: BACKGROUND
  Idiopathic pulmonary fibrosis (IPF) and pulmonary sarcoidosis are typical interstitial lung diseases with unknown etiology that cause lethal lung damages. There are notable differences between these two pulmonary disorders, although they do share some similarities. Gene expression profiles have been reported independently, but differences on the transcriptional level between these two entities have not been investigated.
  
  
  RESULTS
  All expression data of lung tissue samples for IPF and sarcoidosis were from published datasets in the Gene Expression Omnibus (GEO) repository. After cross platform normalization, the merged sample data were grouped together and were subjected to statistical analysis for finding discriminate genes. Gene enrichments with their corresponding functions were analyzed by the online analysis engine "Database for Annotation, Visualization and Integrated Discovery" (DAVID) 6.7, and genes interactions and functional networks were further analyzed by STRING 9.0 and Cytoscape 3.0.0 Beta1. One hundred and thirty signature genes could potentially differentiate one disease state from another. Compared with normal lung tissue, tissue affected by IPF and sarcoidosis displayed similar signatures that concentrated on proliferation and differentiation. Distinctly expressed genes that could distinguish IPF from sarcoidosis are more enriched in processes of cilium biogenesis or degradation and regulating T cell activations. Key discriminative network modules involve aspects of bone morphogenetic protein receptor two (BMPR2) related and v-myb myeloblastosis viral oncogene (MYB) related proliferation.
  
  
  CONCLUSIONS
  This study is the first attempt to examine the transcriptional regulation of IPF and sarcoidosis across different studies based on different working platforms. Groups of significant genes were found to clearly distinguish one condition from the other. While IPF and sarcoidosis share notable similarities in cell proliferation, differentiation and migration, remarkable differences between the diseases were found at the transcription level, suggesting that the two diseases are regulated by overlapping yet distinctive transcriptional networks.
authors: Clinical Laboratory, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
authors: Dong
authors: D
authors: Leng
authors: Caijuan
authors: C
authors: Huan
authors: Ting
authors: T
authors: Xie
authors: Jiurong
authors: J
authors: Liang
authors: Jun
authors: J
authors: Wang
authors: Huaping
authors: H
authors: Dai
authors: Chen
authors: C
authors: Wang
authors: Dianhua
authors: D
authors: Jiang
mesh_terms: D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D054990:Idiopathic Pulmonary Fibrosis / Q000235:genetics*; D017565:Sarcoidosis, Pulmonary / Q000235:genetics*
references: J Clin Invest. 2007 Nov;117(11):3576-82
references: 17975675
references: Cancer Res. 2002 Aug 1;62(15):4427-33
references: 12154050
references: Pulm Med. 2012;2012:808260
references: 22448328
references: Am J Respir Crit Care Med. 2010 Jun 15;181(12):1367-75
references: 20194811
references: Proc Am Thorac Soc. 2007 Aug 15;4(5):461-4
references: 17684290
references: Endocr Rev. 2004 Aug;25(4):581-611
references: 15294883
references: Am J Respir Crit Care Med. 2009 May 15;179(10):929-38
references: 19218196
references: BMC Bioinformatics. 2005 Nov 04;6:265
references: 16271137
references: Orphanet J Rare Dis. 2007 Nov 19;2:46
references: 18021432
references: Genomics. 2010 Sep;96(3):134-45
references: 20451601
references: BMC Med Genomics. 2011 Oct 05;4:70
references: 21974901
references: Bioinformatics. 2011 Feb 1;27(3):431-2
references: 21149340
references: Lancet. 2003 Mar 29;361(9363):1111-8
references: 12672326
references: J Clin Invest. 2012 Aug;122(8):2756-62
references: 22850886
references: Nucleic Acids Res. 2000 Sep 15;28(18):3442-4
references: 10982861
references: FEBS Lett. 2012 Jul 4;586(14):1885-96
references: 22293501
references: Tissue Antigens. 2011 Feb;77(2):112-7
references: 21214523
references: Nat Protoc. 2009;4(1):44-57
references: 19131956
references: Hum Immunol. 2011 Jul;72(7):571-5
references: 21513758
references: PLoS One. 2009;4(4):e5134
references: 19347046
references: Am J Respir Crit Care Med. 2002 Jul 15;166(2):236-46
references: 12119236
references: Am J Respir Crit Care Med. 1999 Aug;160(2):736-55
references: 10430755
references: Clin Dermatol. 2007 May-Jun;25(3):267-75
references: 17560304
references: Respir Res. 2010 Nov 08;11:156
references: 21059230
references: Genes Cells. 2007 Nov;12(11):1235-44
references: 17986007
references: Annu Rev Cell Dev Biol. 2011;27:493-512
references: 21639799
references: J Clin Invest. 2004 Jul;114(2):165-8
references: 15254582
references: Methods Enzymol. 2006;411:352-69
references: 16939800
references: Mol Med. 2007 Sep-Oct;13(9-10):527-41
references: 17660860
references: Clin Cancer Res. 2008 Sep 1;14(17):5357-67
references: 18765527
references: J Pathol. 1999 Mar;187(4):475-80
references: 10398109
references: BMC Bioinformatics. 2011 Dec 07;12:467
references: 22151536
references: Curr Opin Pulm Med. 2011 Sep;17(5):303-7
references: 21681100
references: Proc Am Thorac Soc. 2007 Aug 15;4(5):465-8
references: 17684291
references: Cell Biochem Funct. 2011 Dec;29(8):686-93
references: 21953443
references: Respir Res. 2004 Dec 07;5:26
references: 15585067
references: Lancet. 2011 Dec 3;378(9807):1949-61
references: 21719092
references: Curr Med Chem. 2008;15(7):724-8
references: 18336287
references: Nucleic Acids Res. 2009 Jan;37(1):1-13
references: 19033363
references: Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21
references: 11309499
references: JAMA. 2003 Jun 25;289(24):3300-3
references: 12824213
references: Bioinformatics. 2008 May 1;24(9):1154-60
references: 18325927
references: Am J Respir Crit Care Med. 2011 Mar 1;183(5):573-81
references: 21037016
references: Am J Respir Crit Care Med. 2009 Jul 15;180(2):167-75
references: 19363140
references: Chest. 2006 Oct;130(4):982-8
references: 17035428
references: Int J Biochem Cell Biol. 2002 Dec;34(12):1534-8
references: 12379275
references: Prog Neurobiol. 2007 Apr;81(5-6):294-330
references: 17379385
references: J Biol Chem. 2011 Sep 23;286(38):33134-40
references: 21808054
references: Nat Biotechnol. 2006 Sep;24(9):1151-61
references: 16964229