Gene Set Enrichment Analysis Identifies Key Innate Immune Pathways in Primary Graft Dysfunction After Lung Transplantation
Version of Record online: 24 MAY 2013
© Copyright 2013 The American Society of Transplantation and the American Society of Transplant Surgeons
American Journal of Transplantation
Volume 13, Issue 7, pages 1898–1904, July 2013
How to Cite
Cantu, E., Lederer, D. J., Meyer, K., Milewski, K., Suzuki, Y., Shah, R. J., Diamond, J. M., Meyer, N. J., Tobias, J. W., Baldwin, D. A., Van Deerlin, V. M., Olthoff, K. M., Shaked, A., Christie, J. D. and for the CTOT Investigators (2013), Gene Set Enrichment Analysis Identifies Key Innate Immune Pathways in Primary Graft Dysfunction After Lung Transplantation. American Journal of Transplantation, 13: 1898–1904. doi: 10.1111/ajt.12283
- Issue online: 26 JUN 2013
- Version of Record online: 24 MAY 2013
- Manuscript Accepted: 7 APR 2013
- Manuscript Revised: 19 MAR 2013
- Manuscript Received: 5 FEB 2013
- NIH. Grant Numbers: AI063589, HL087115, HL081619, HL096845, HL116656, HL090021, RWJ AMFDP11642
Additional Supporting Information may be found in the online version of this article at the publisher's web-site.
Table S1: Expanded gene set enrichment analysis. NES, normalized enrichment score (accounts for differences in gene set size and in correlations between gene sets and the expression dataset to allow for comparisons across gene sets); NOM p-val, nominal p value (estimates the statistical significance of the enrichment score for a single gene set); FDR, false discovery rate (estimated probability that a gene set with a given NES represents a false positive finding); FWER, familywise-error rate (conservative correction that seeks to ensure that the list of reported results does not include even a single false-positive gene set).
Table S2: Ranked gene list of PGD positively correlated transcripts.
Figure S1: All significantly enriched gene sets meeting FWER corrected cutoff. The top portion of the plot shows the running enrichment score (ES) for the gene set from decreasing values of the rank list. The score at the peak of the plot (the score furthest from 0.0) is the ES for the overall gene set. The middle portion of the plot shows where the members of the gene set appear in the ranked list of genes. The bottom portion of the plot shows the value of the ranking metric as the list of ranked genes decreases in value. The ranking metric measures an individual transcript's correlation with the PGD phenotype.
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