GO-Elite: a flexible solution for pathway and ontology over-representation

Zambon, Alexander C.; Gaj, Stan; Ho, Isaac; Hanspers, Kristina; Vranizan, Karen; Evelo, Chris T.; Conklin, Bruce R.; Pico, Alexander R.; Salomonis, Nathan

doi:10.1093/bioinformatics/bts366

Cited by 250 publications

(238 citation statements)

References 7 publications

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“…To gain functional insight into the pattern of regulated genes, we applied an automated unbiased functional clustering using GOElite software (33) and gene ontology annotations to determine which functional clusters among regulated genes were statistically overrepresented (Supplemental Table III). In addition to the GO nomenclature, we identified functional clusters among regulated genes by detailed research of published literature, analyzing the occurrence of subject headings related to the functional cluster in the National Center for Biotechnology Information's gene-centric "Gene" database using an algorithm described previously (8).…”

Section: Genome-wide Expression Screening and Phenotypic Characterizamentioning

confidence: 99%

Immune Suppression via Glucocorticoid-Stimulated Monocytes: A Novel Mechanism To Cope with Inflammation

Varga

Ehrchen

Brockhausen

et al. 2014

The Journal of Immunology

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Glucocorticoids (GCs) are used as first-line therapies for generalized suppression of inflammation (e.g., allergies or autoimmune diseases), but their long-term use is limited by severe side effects. Our previous work revealed that GCs induced a stable anti-inflammatory phenotype in monocytes, the GC-stimulated monocytes (GCsMs) that we exploited for targeted GC-mediated therapeutic effects. We demonstrate that GCsMs interact with T cells in suppressing proliferation, as well as cytokine release of CD8+ and, especially, CD4+ T cells in vitro, and that they support generation of Foxp3+ cells. Therefore, we tested their immunosuppressive potential in CD4+ T cell–induced colitis in vivo. We found that injection of GCsMs into mice with severe colitis abolished the inflammation and resulted in significant clinical improvement within a few days. T cells recovered from GCsM-treated mice exhibited reduced secretion of proinflammatory cytokines IFN-γ and IL-17. Furthermore, clusters of Foxp3+ CD4+ T cells were detectable at local sites of inflammation in the colon. Thus, GCsMs are able to modify T cell responses in vitro and in vivo, as well as to downregulate and clinically cure severe T cell–mediated colitis.

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Section: Genome-wide Expression Screening and Phenotypic Characterizamentioning

confidence: 99%

Immune Suppression via Glucocorticoid-Stimulated Monocytes: A Novel Mechanism To Cope with Inflammation

Varga

Ehrchen

Brockhausen

et al. 2014

The Journal of Immunology

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show abstract

“…Functional enrichment analysis was assessed using GOElite Pathway Analysis [44]. Two enrichment analyses were performed on the genes of interest by assessing: (1) enriched Gene Ontology (GO) categories, and (2) enriched KEGG pathways.…”

Section: Functional Enrichment Analysismentioning

confidence: 99%

Alteration in basal and depolarization induced transcriptional network in iPSC derived neurons from Timothy syndrome

et al. 2014

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Background: Common genetic variation and rare mutations in genes encoding calcium channel subunits have pleiotropic effects on risk for multiple neuropsychiatric disorders, including autism spectrum disorder (ASD) and schizophrenia. To gain further mechanistic insights by extending previous gene expression data, we constructed co-expression networks in Timothy syndrome (TS), a monogenic condition with high penetrance for ASD, caused by mutations in the L-type calcium channel, Ca v 1.2. Methods: To identify patient-specific alterations in transcriptome organization, we conducted a genome-wide weighted co-expression network analysis (WGCNA) on neural progenitors and neurons from multiple lines of induced pluripotent stem cells (iPSC) derived from normal and TS (G406R in CACNA1C) individuals. We employed transcription factor binding site enrichment analysis to assess whether TS associated co-expression changes reflect calcium-dependent co-regulation.

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“…Probability values were adjusted for multiple testing using the Benjamini Hochberg method for false discovery rate control. Apparent functional relationships between genes identified through these analyses were investigated further using DAVID Bioinformatic Resources 6.7 (da Huang et al 2009a, b), GO-Elite (Zambon et al 2012) to test for enrichment of pathways included in Wikipathways (www. wikipathways.org) using Cytoscape (www.cytoscape.org) for visualisation and BiblioSphere literature mining software (Genomatix Software GmbH, Munich, Germany).…”

Section: Array Data Analysismentioning

confidence: 99%

Transcriptome analysis of peripheral blood mononuclear cells in human subjects following a 36 h fast provides evidence of effects on genes regulating inflammation, apoptosis and energy metabolism

et al. 2014

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GO-Elite: a flexible solution for pathway and ontology over-representation

Cited by 250 publications

References 7 publications

Immune Suppression via Glucocorticoid-Stimulated Monocytes: A Novel Mechanism To Cope with Inflammation

Immune Suppression via Glucocorticoid-Stimulated Monocytes: A Novel Mechanism To Cope with Inflammation

Alteration in basal and depolarization induced transcriptional network in iPSC derived neurons from Timothy syndrome

Transcriptome analysis of peripheral blood mononuclear cells in human subjects following a 36 h fast provides evidence of effects on genes regulating inflammation, apoptosis and energy metabolism

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