Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Genome-wide analysis of immune system genes by EST profiling

doi: 10.4049/jimmunol.1203471

Figure Lengend Snippet: (A) Graphical representation of known or predicted locations and functions of transmembrane proteins and/or genes related to metabolism or nutrient/ion transport in the Immunogene dataset. Green circles indicate transmembrane proteins or transporters associated with complex or Mendelian diseases; red circles indicate transporters with known function; black circles indicate transmembrane proteins with predicted localization and no known function. (B) A divergently transcribed lncRNA is co-regulated with LRRK2. Top: Schematic of exon structure of LRRK2 and the divergent antisense (AS)-LRRK2 transcript(s), with location of SNP rs11175593 associated with Crohn’s disease (37). Bottom: The THP-1 monocytic cell line was stimulated with γ-interferon for the indicated time. RT-qPCR of LRRK2 and AS-LRRK2 transcript levels are shown normalized to S18 transcript and relative to expression levels of LRRK2 in resting THP-1 cells. Data shown are representative of one of two biological replicates with errors bars representing standard deviation of triplicate technical replicates. (C) The distance (2-kb bins) between SNPs associated by GWAS with immune diseases/traits (red) and the nearest Immunogene is shown in comparison to the distance between SNPs not associated with immune diseases/traits (blue) and the nearest Immunogene.

Article Snippet: Hierarchical clustering and heat map representation of the 1,927 EST Immunogene profiles separated by immune versus non-immune tissue is shown in , revealing enrichment of EST-derived Immunogenes in the BioGPS compendia and providing further cross-validation of our methodology. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 3 caption a7 caption a8 Cross-validation of EST profiling methodology with microarray profiling, GO pathway analysis, and epigenetic signatures (A) Of the 1,927 genes found to be significantly enriched by EST profiling, 1,522 genes (79%) exhibited significantly higher expression by Wilcoxon rank sum test and FDR ( P < 0.05) in the immune system based on analysis of the GNF BioGPS microarray data tissue compendium. (B) Microarray profile clustering in GNF tissue/cell compendium of 1,927 immune-enriched genes defined by EST profiling segregating immune versus non-immune tissue types. (C) Examples of GO biological process terms statistically enriched ( P < 0.05, Bonferroni corrected) for all EST Immunogenes. (D) The Wilcoxon signed rank (Y axis) for 1,336 Immunogenes compared to their WIP score (X axis) showing that most Immunogenes show a positively signed rank.

Techniques: Quantitative RT-PCR, Expressing, Standard Deviation, Comparison