GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support.

Rebhan, Michael; Chalifa‐Caspi, Vered; Prilusky, Jaime; Lancet, Doron

doi:10.1093/bioinformatics/14.8.656

Cited by 427 publications

(320 citation statements)

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“…The LIMMA analysis was performed on samples according to transplant TID status (both TID and normal [no TID] were investigated). Differentially expressed gene lists were interrogated using DAVID, 41 SOURCE, 42 GeneCards, 43 Entrez PubMed (http://www.ncbi.nlm.nih.gov) and Significance Analysis of Microarrays, 44 specifically focusing on EMT genes, and data were subgrouped according to TID and EMT status and compared with normal in each case. The gene expression output from differentially expressed genes with a B Ͼ 1 or isolated EMT-associated genes was subject to hierarchical clustering (Cluster 3.0 45 ), and results were visualized (TreeView 1.60 46 ).…”

Section: Discussionmentioning

confidence: 99%

Epithelial-to-Mesenchymal Transition in Early Transplant Tubulointerstitial Damage

Vitalone

O’Connell

Jimenez‐Vera

et al. 2008

Journal of the American Society of Nephrology

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It is unknown whether epithelial-to-mesenchymal transition (EMT) leads to tubulointerstitial fibrosis in renal transplants. In this study, interstitial fibrosis and markers of EMT were followed in protocol transplant biopsies in 24 patients. Tubulointerstitial damage (TID) increased from 34 to 54% between 1 and 3 mo after transplantation. Detection of EMT depended on the marker used; low levels of ␣-smooth muscle actin were found in 61% of biopsies, but the less specific marker S100 calcium binding protein-A4 (also known as Fsp1) suggested a higher incidence of EMT. The presence or development of TID did not correlate with EMT but instead significantly correlated with subclinical immune activity (P Ͻ 0.05). Among biopsies showing TID, microarray analysis revealed differential regulation of 127 genes at 1 mo and 67 genes at 3 mo compared with baseline; these genes were predominantly associated with fibrosis, tissue remodeling, and immune response. Of the 173 EMT-associated genes interrogated, however, only 8.1% showed an expression pattern consistent with EMT at 1 mo and 6.3% at 3 mo. The remainder were not differentially altered, or their changes in expression were opposite those expected to promote EMT. Quantitative reverse transcriptase-PCR revealed that the expression pattern of 12 EMT-associated genes was inconsistent over time, opposite that expected, or consistent with subclinical rejection or inflammation. In conclusion, EMT does not seem to play a significant role in the development of early allograft fibrosis.

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Section: Discussionmentioning

confidence: 99%

Epithelial-to-Mesenchymal Transition in Early Transplant Tubulointerstitial Damage

Vitalone

O’Connell

Jimenez‐Vera

et al. 2008

Journal of the American Society of Nephrology

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“…Retrieval from UniGene was performed in November, 1999. Additional information for selected genes was retrieved from GeneCards encyclopedia (Rebhan et al, 1997).…”

Section: Retrieval Of Information For Probe Setsmentioning

confidence: 99%

Microarray analysis of gene expression mirrors the biology of an ovarian cancer model

et al. 2001

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“…The biological functions of genes were assigned using the Gene Ontology (www.geneontology.org) and Genecards 26,27 (http://bioinformatics.weizmann.ac.il/cards) databases. Gene pathways were analyzed with the help of Gene Set Enrichment Analysis (GSEA) version 2.0.1.…”

Section: Statistical Analysesmentioning

confidence: 99%

Somatic hypermutation signature in B-cell low-grade lymphomas

Tracey

Aggarwal²,

García‐Cosío³

et al. 2008

Haematologica

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GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support.

Abstract: cards@bioinformatics.weizmann.ac.il

Cited by 427 publications

References 0 publications

Epithelial-to-Mesenchymal Transition in Early Transplant Tubulointerstitial Damage

Epithelial-to-Mesenchymal Transition in Early Transplant Tubulointerstitial Damage

Microarray analysis of gene expression mirrors the biology of an ovarian cancer model

Somatic hypermutation signature in B-cell low-grade lymphomas

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