Immunome: A reference set of genes and proteins for systems biology of the human immune system

Ortutay, Csaba; Vihinen, Mauno

doi:10.1016/j.cellimm.2007.01.012

Cited by 55 publications

(52 citation statements)

References 10 publications

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“…17 As the original GSEA only identifies the gene set showing either uniformly up-or downregulation, for the gene sets showing both up-and downregulated genes, absolute GSEA was additionally performed. 18 A total of 4395 gene sets were analyzed (Supplementary Table S2) and they included (1) NF-kB target genes, collated from online database, published works and careful bioinformatic search (Supplementary Table S3); (2) biological pathways involved in inflammatory and immune responses from human immunome database, 19 gene ontology (GO) and ingenuity and (3) gene sets from Molecular Signature database. The GSEA results were ranked according to the nominal P-value (o0.05) and false discovery rate (p0.25) as described previously.…”

Section: Gene Set Enrichment Analysis (Gsea)mentioning

confidence: 99%

Differential expression of NF-κB target genes in MALT lymphoma with and without chromosome translocation: insights into molecular mechanism

Hamoudi

Appert

et al. 2010

Leukemia

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Mucosa-associated lymphoid tissue (MALT) lymphoma is characterized by t(11;18)(q21;q21)/API2-MALT1, t(1;14)(p22;q32)/ BCL10-IGH and t(14;18)(q32;q21)/IGH-MALT1, which commonly activate the nuclear factor (NF)-jB pathway. Gastric MALT lymphomas harboring such translocations usually do not respond to Helicobacter pylori eradication, while most of those without translocation can be cured by antibiotics. To understand the molecular mechanism of these different MALT lymphoma subgroups, we performed gene expression profiling analysis of 21 MALT lymphomas (13 translocation-positive, 8 translocation-negative). Gene set enrichment analysis (GSEA) of the NF-jB target genes and 4394 additional gene sets covering various cellular pathways, biological processes and molecular functions have shown that translocation-positive MALT lymphomas are characterized by an enhanced expression of NF-jB target genes, particularly toll like receptor (TLR)6, chemokine, CC motif, receptor (CCR)2, cluster of differentiation (CD)69 and B-cell CLL/lymphoma (BCL)2, while translocationnegative cases were featured by active inflammatory and immune responses, such as interleukin-8, CD86, CD28 and inducible T-cell costimulator (ICOS). Separate analyses of the genes differentially expressed between translocation-positive and -negative cases and measurement of gene ontology term in these differentially expressed genes by hypergeometric test reinforced the above findings by GSEA. Finally, expression of TLR6, in the presence of TLR2, enhanced both API2-MALT1 and BCL10-mediated NF-jB activation in vitro. Our findings provide novel insights into the molecular mechanism of MALT lymphomas with and without translocation, potentially explaining their different clinical behaviors.

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Section: Gene Set Enrichment Analysis (Gsea)mentioning

confidence: 99%

Differential expression of NF-κB target genes in MALT lymphoma with and without chromosome translocation: insights into molecular mechanism

Hamoudi

Appert

et al. 2010

Leukemia

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“…Some species-specific databases have also been developed for the investigation of immune systems in specific model organisms. The Immunome database (Ortutay and Vihinen, 2006) is an example of such species-specific resources which gathers human genes and proteins relevant to immunity. This resource was extended to provide phylogenetic tree visualisation with ImmTree (Ortutay et al, 2007) to facilitate the study of the evolution of the human immune system with ortholog gene groups of over 1800 metazoan immunity genes stored within ImmunomeBase, a multi-species database of immunity.…”

Section: Introductionmentioning

confidence: 99%

Macrophages.com: An on-line community resource for innate immunity research

Robert

Law

et al. 2011

Immunobiology

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“…The cellular functions have been determined for all the genes and proteins required in the immunome (entirety of immune system) (49). There are functional groups for, e.g., the surface receptors in clusters of differentiation classification, chemokines, and their receptors, humoral immunity proteins, and those involved in cellular immunity, Ag processing, and transcription factors.…”

Section: Disease Clustersmentioning

confidence: 99%

Systematic Classification of Primary Immunodeficiencies Based on Clinical, Pathological, and Laboratory Parameters

Samarghitean

Ortutay²,

Vihinen

2009

The Journal of Immunology

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The classification of diseases has several important applications ranging from diagnosis and choice of treatment to demographics. To date, classifications have been successfully created manually, often within international consortia. Some groups of diseases, such as primary immunodeficiencies (PIDs), are especially hard to nosologically cluster due, on one hand, to the presence of a wide variety of disorders and, in contrast, because of overlapping characteristics. More than 200 PIDs affecting components of the innate and adaptive immune systems have been described. Clinical, pathological, and laboratory characteristics were collected and used to group PIDs. A consensus of at least five independent methods provided a novel classification of 11 groups, which revealed previously unknown features and relationships of PIDs. Comparison of the classification to independent features, including the severity and therapy of the diseases, functional classification of proteins, and network vulnerability, indicated a strong statistical support. The method can be applied to any group of diseases.

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Immunome: A reference set of genes and proteins for systems biology of the human immune system

Cited by 55 publications

References 10 publications

Differential expression of NF-κB target genes in MALT lymphoma with and without chromosome translocation: insights into molecular mechanism

Differential expression of NF-κB target genes in MALT lymphoma with and without chromosome translocation: insights into molecular mechanism

Macrophages.com: An on-line community resource for innate immunity research

Systematic Classification of Primary Immunodeficiencies Based on Clinical, Pathological, and Laboratory Parameters

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