Supplemental Data

1. Longitudinal, global transcriptomic profiling of preclinical systemic sclerosis provides insights into molecular changes associated with disease progression
   • Supplemental data
2. Large-scale analysis of longitudinal skin gene expression in systemic sclerosis reveals relationships of immune cell and fibroblast activity with skin thickness and a trend towards normalization over time. Ann Rheum Dis. 2022 Apr;81(4):516-523.
   • List of differentially expressed genes
3. Large-scale characterization of systemic sclerosis serum protein profile: Comparison to peripheral blood cell transcriptome and correlations with skin/lung fibrosis. Arthritis Rheumatol. 2021 Apr;73(4):660-670.
   • Supplementary database SCOT baseline proteomic data
4.  Global skin gene expression profile of early diffuse cutaneous systemic sclerosis shows a prominent innate and adaptive inflammatory profile. Ann Rheum Dis. 2019 Nov 25. pii: annrheumdis-2019-215894. Ann Rheum Dis. 2020 Mar;79(3):379-386.
   • List of differentially expressed and correlating transcripts PRESS skin study
5. Treatment with myeloablation followed by autologous stem cell transplantation normalizes the systemic sclerosis molecular signatures. Ann Rheum Dis. 2019 Oct;78(10):1371-1378
   • List of differentially expressed genes and investigated proteins
6. Downregulation of CFIm25 amplifies dermal fibrosis through alternative polyadenylation. J Exp Med. 2020 Feb 3;217(2).
   • List of genes with significant 3″ UTR shortening
7. CCL2 in the Circulation Predicts Long-Term Progression of Interstitial Lung Disease in Patients with Early Systemic Sclerosis Data from Two Independent Cohorts. Arthritis Rheumatol. 2017 Sep;69(9):1871-1878.
   • Comparison of plasma cytokine/chemokine levels in SSc patients not treated with immunosuppressive agents vs. control subjects
8. Dissecting the Heterogeneity of Skin Gene Expression Patterns in Systemic Sclerosis. Arthritis Rheumatol. 2015 Nov;67(11):3016-26
   • Additional Table 1
   • Additional Table 2
9. Skin Gene Expression Correlates of Severity of Interstitial Lung Disease in Systemic Sclerosis. Arthritis Rheum. 2013 Nov;65(11):2917-27
   • Methods
   • Table 2
   • Table 3
   • Table 4
   • Table 5
10. Secondary use of existing public microarray data to predict outcome for hepatocellular carcinoma. J Surg Res. 2014 May 1;188(1):137-42
    • Supplemental data
11. 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 comparison 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 Pathway 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
12. Major histocompatibility complex (MHC) class II alleles and epitopes which confer susceptibility or protection in systemic sclerosis: analyses in 1300 Caucasian, African-American and Hispanic cases and 1000 controls. Ann Rheum Dis 2010 69: 822-827
    • Supplemental Table
13. 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
14. 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 of scleroderma and normal fibroblasts
    • Comparative gene ontology (GO) analysis of MZ twins
    • Cluster analysis of twin and control sample
15. 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