Identification and quantification of disease-related gene clusters

Firneisz, Gábor; Zehavi, Idit; Vermes, Csaba; Hanyecz, Anita; Frieman, Joshua A.; Glant, Tibor T.

doi:10.1093/bioinformatics/btg252

Cited by 15 publications

(11 citation statements)

References 17 publications

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“…Genome-wide gene expression profiling using microarrays is a powerful emerging technology that has already been applied successfully to classification of tumors [24], infectious diseases [25,26], and autoimmune pathologic entities [27,28].…”

Section: Discussionmentioning

confidence: 99%

Reduced CD4+ T-cell-specific gene expression in human type 1 diabetes mellitus

Orban

Kis

Szereday

et al. 2007

Journal of Autoimmunity

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Section: Discussionmentioning

confidence: 99%

Reduced CD4+ T-cell-specific gene expression in human type 1 diabetes mellitus

Orban

Kis

Szereday

et al. 2007

Journal of Autoimmunity

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“…Despite these clinical differences, several autoimmune diseases appear to share common susceptibility loci, probably representing common factors in pathogenesis of the final disease. These colocalizing regions contain gene clusters which are differentially expressed during an autoimmune disease process (55) and are therefore of clinical interest as potential therapeutic targets. It is notable that genetic association studies for uveitis in patients suffering from ankylosing spondylitis (37) and Behcet's disease (40) also show overlapping genetic regions with those identified in patients with multiple sclerosis, Crohn's disease, rheumatoid arthritis, IDDM, and psoriasis.…”

Section: Discussionmentioning

confidence: 99%

Common Genetic Determinants of Uveitis Shared with Other Autoimmune Disorders

Mattapallil¹,

Şahin²,

Silver³

et al. 2008

The Journal of Immunology

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*Uveitis is a complex multifactorial autoimmune disease of the eye characterized by inflammation of the uvea and retina, degeneration of the retina, and blindness in genetically predisposed patients. Using the rat model of experimental autoimmune uveitis (EAU), we previously identified three quantitative trait loci (QTL) associated with EAU on rat chromosomes 4, 12, and 10 (Eau1, Eau2, and Eau3). The primary goal of the current study is to delineate additional non-MHC chromosomal regions that control susceptibility to EAU, and to identify any QTLs that overlap with the QTLs of other autoimmune diseases. Using a set of informative microsatellite markers and F 2 generations of resistant and susceptible MHC class II-matched rat strains (F344 and LEW), we have identified several new significant or suggestive QTLs on rat chromosomes 2, 3, 7, 10, and 19 that control susceptibility to EAU. A protective allele was identified in the susceptible LEW strain in the Eau5 locus at D7Wox18, and epistatic interactions between QTLs were found to influence the severity of disease. The newly identified regions (Eau4 through Eau9) colocalize with the genetic determinants of other autoimmune disease models, and to disease-regulating syntenic regions identified in autoimmune patients on human chromosomes 4q21-31, 5q31-33, 16q22-24, 17p11-q12, 20q11-13, and 22q12-13. Our results suggest that uveitis shares some of the pathogenic mechanisms associated with other autoimmune diseases, and lends support to the "common gene, common pathway" hypothesis for autoimmune disorders.

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“…These arrays contain a limited, manageable number of cDNAs [24] up to several thousands of genes, e.g. as provided by Affimetrix ® chips [14,18,25,26]. Using this high numbers of genes, however it is difficult if not impossible to analyze every single gene on the chip in a statistically valid manner.…”

Section: Microarraysmentioning

confidence: 99%

“…Using this high numbers of genes, however it is difficult if not impossible to analyze every single gene on the chip in a statistically valid manner. Therefore, cluster analysis using specific softwares has been developed to manage the high number of data derived from a single or few experiments [14,25,26].…”

Section: Microarraysmentioning

confidence: 99%

High Resolution Molecular Analysis as Tool for Evaluation of Arthritis Pathology

Neumann¹,

Ingo²,

Gay³

et al. 2006

CRR

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Evaluation of differentially regulated genes is essential for the development of novel therapeutic approaches in multifactorial diseases such as rheumatoid arthritis (RA). The analysis of the pathophysiology of RA requires also a functional understanding of the interactions between different cell types, the cell matrix, intracellular signaling pathways, often also called 'functional genomics', as well as between the different tissues in the joint such as cartilage, bone, adipose tissue, and the synovium.In addition, the identification of disease-or treatment-specific genes has become an important tool in arthritis research to determine novel molecular markers for diagnosis and monitoring of RA, and to elucidate the exact mode of operation and the potential target molecules for therapeutic intervention.Current approaches to analyze gene expression in arthritis are based on RNA isolated from cultured synovial cells or from synovial tissues and biopsies. Other approaches are directed to cultured cells such as RA synovial fibroblasts, one of the key players in inflammation and cartilage destruction, chondrocytes, macrophages or lymphocytes to characterize molecular changes and pathomechanisms in the RA synovium, especially at sites of adhesion and invasion of the synovium into the adjacent cartilage and bone.In this review, different methods to analyze gene expression of cells and tissues from patients with arthritides ranging from RNA fingerprinting to cDNA array are presented and discussed. In addition, a special focus is addressing the pitfalls resulting in over-or misinterpretation of the data obtained by these sensitive techniques.

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Identification and quantification of disease-related gene clusters

Cited by 15 publications

References 17 publications

Reduced CD4+ T-cell-specific gene expression in human type 1 diabetes mellitus

Reduced CD4+ T-cell-specific gene expression in human type 1 diabetes mellitus

Common Genetic Determinants of Uveitis Shared with Other Autoimmune Disorders

High Resolution Molecular Analysis as Tool for Evaluation of Arthritis Pathology

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