SUPPLEMENTAL DATA

1. Skin gene expression correlates of severity of interstitial lung disease in systemic sclerosis (in press)

•  Methods
• Table 2
• Table 3
• Table 4
• Table 5
  

2. Secondary use of existing public microarray data to predict outcome for hepatocellular carcinoma (submitted)

• Supplemental data

3. Systemic sclerosis and Lupus: Points in an interferon-mediated continuum. Arthritis Rheum, 2010, 62:589-598

• Supplement 1 - Methods
• Supplement 2 - Functional grouping of transcripts differentially expressed in SLE and SSc compared to controls
  
• Class comparsion of SLE vs controls
• Class comparison of SSc vs controls
• Class comparison of SLE vs SSc
• Supplement 3 - Modeling of IFN signaling pathways in Ingenuity Pathyway Analysis
  • SLE vs control peripheral blood cells
    
  • SSc vs control peripheral blood cells
    
  • SSc vs control skin biopsies
    
  • Comparison of SLE vs SSc peripheral blood cells
    

• Supplement 4 - Quantitative RT-PCR results
• Supplement 5 - Genotypic correlation with IFN score  

4. Major histocompatibility complex (MHC) class II alleles and epitopes which confer susceptibility or protection in systemic sclerosis: analyses in 1300 Caucasina, African-American and Hispanic cases and 1000 controls. Ann Rheum Dis 2010 69: 822-827

• Supplemental Table
  

5. Signatures of differentially regulated interferon gene expression and vasculotropism in the peripheral blood cells of systemic sclerosis patients. Rheumatology (Oxford), 2006, 45: 694-702

• Genes differentially expressed in SSc PBCs by SAM
• Class comparison with the random variance T-test and conditional false discovery rate with SPLOSH (Large!)
  
• Cluster analysis of SSc and control peripheral blood samples
  
• Biological pathways differentially regulated in SSc PBC samples
  
• Comparative gene ontology (GO) analysis

6. Clinically discordant scleroderma monozygotic twins show concordance for fibroblast gene expression profiles. Arthritis Rheum, 2005, 52: 3305-3314

• Genes differentially expressed by SAM
• Comparative gene ontology analysis
• Comparative gene ontology (GO) analysis of MZ twins
• Genes used for cluster analysis of twin samples
• Cluster analysis of twin and control sample

7. Classification analysis of the transcriptosome of non-lesional cultured dermal fibroblasts from scleroderma patients with early disease. Arthritis Rheum 2005, 52:865-876

• Genes differentially expressed by Significance Analysis of Microarrays (SAM)
• Genes differentially expressed by the random variance t-test
• Class Prediction (nominal gene set)
• Comparative gene ontology analysis
• Cluster analysis of SSc samples
• Biological pathway comparison
• Pathway analysis(Pathway Assist)
  • Common targets
  • Common regulators