DAVID: Database for Annotation, Visualization, and Integrated Discovery

Dennis, Glynn; Sherman, Brad T.; Hosack, Douglas A; Yang, Jun; Gao, Wei; Lane, H. Clifford; Lempicki, Richard A.

doi:10.1186/gb-2003-4-9-r60

Cited by 1,619 publications

(745 citation statements)

References 11 publications

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“…DAVID is a web-based application that allows users to access relational databases for functional annotations. 47 Real-time PCR Total RNA was re-extracted from 10-20 mg of frozen tissue in the four areas examined using Trizol (Invitrogen Corp, Carlsbad, CA, USA). These samples were independent from those used in the microarray assays, and were obtained from adjacent tissue dissections.…”

Section: Resultsmentioning

confidence: 99%

Patterns of gene expression in the limbic system of suicides with and without major depression

et al. 2007

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The limbic system has consistently been associated with the control of emotions and with mood disorders. The goal of this study was to identify new molecular targets associated with suicide and with major depression using oligonucleotide microarrays in the limbic system (amygdala, hippocampus, anterior cingulate gryus (BA24) and posterior cingulate gyrus (BA29)). A total of 39 subjects were included in this study. They were all male subjects and comprised 26 suicides (depressed suicides = 18, non depressed suicides = 8) and 13 matched controls. Brain gene expression analysis was carried out on human brain samples using the Affymetrix HG U133 chip set. Differential expression in each of the limbic regions showed group-specific patterns of expression, supporting particular neurobiological mechanisms implicated in suicide and depression. Confirmation of genes selected based on their significance and the interest of their function with reverse transcriptase-polymerase chain reaction showed consistently correlated signals with the results obtained in the microarray analysis. Gene ontology analysis with differentially expressed genes revealed an overrepresentation of transcription and metabolism-related genes in the hippocampus and amygdala, whereas differentially expressed genes in BA24 and BA29 were more generally related to RNA-binding, regulation of enzymatic activity and protein metabolism. Limbic expression patterns were most extensively altered in the hippocampus, where processes related to major depression were associated with altered expression of factors involved with transcription and cellular metabolism. Additionally, our results confirm previous evidence pointing to global alteration of gabaergic neurotransmission in suicide and major depression, offering new avenues in the study and possibly treatment of such complex disorders. Overall, these data suggest that specific patterns of expression in the limbic system contribute to the etiology of depression and suicidal behaviors and highlight the role of the hippocampus in major depression.

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Section: Resultsmentioning

confidence: 99%

Patterns of gene expression in the limbic system of suicides with and without major depression

et al. 2007

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show abstract

Section: Resultsmentioning

confidence: 99%

“…31 This program uses a modified Fisher's exact P-value (EASE score) to rank gene clusters by statistical overrepresentation of individual genes, based on the cooccurrence/enrichment of the category within the gene list relative to all genes in the same category on the array. 31 Pathway analysis maps gene products from the lists to BioCarta and KEGG pathways, and GO analysis maps gene products GO to categories as provided by Gene Ontology Consortium. To avoid potentially spurious associations when categories had low numbers of members, we only considered categories in which more than two genes were found to be significantly differentially expressed, that is, using the default EASE-score cutoff of 0.1 for DAVID 2006 analysis.…”

Section: Resultsmentioning

confidence: 99%

Expression profiling in monozygotic twins discordant for bipolar disorder reveals dysregulation of the WNT signalling pathway

et al. 2007

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To identify genes dysregulated in bipolar disorder (BD1), we carried out global gene expression profiling using whole-genome microarrays. To minimize genetic variation in gene expression levels between cases and controls, we compared expression profiles in lymphoblastoid cell lines from monozygotic twin pairs discordant for the disease. We identified 82 genes that were differentially expressed by X1.3-fold in three BD1 cases compared to their co-twins, and which were statistically (Pp0.05) differentially expressed between the groups of BD1 cases and controls. Using quantitative reverse transcriptasepolymerase chain reaction, we confirmed the differential expression of some of these genes, including: KCNK1, MAL, PFN2, TCF7, PGK1 and PI4KCB, in at least two of the twin pairs. In contrast to the findings of a previous study by Kakiuchi and colleagues with similar discordant BD1 twin design, our data do not support the dysregulation of XBP1 and HSPA5. From pathway and gene ontology analysis, we identified upregulation of the WNT signalling pathway and the biological process of apoptosis. The differentially regulated genes and pathways identified in this study may provide insights into the biology of BD1.

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“…The functional classification of the 88 IP-VE target genes using Database for Annotation, Visualization and Integration Discovery (DAVID), http://david.niaid.nih.gov), (69) a tool that implements Gene Ontology (GO) term clustering, indicated that the IP-VE target genes are predominantly involved in biological processes of development and neurophysiology. In molecular function, the major category is transcription regulation ( Table 3).…”

Section: Functional Classification Of Ip-ve Genesmentioning

confidence: 99%

“…DAVID (69) was applied for functional classification and clustering of genes. Default cut-offs given at DAVID and p value 0.01 was considered for gene enrichment, at levels 3 and 4.…”

Section: Functional Clusteringmentioning

confidence: 99%

Incomplete penetrance and variable expressivity: is there a microRNA connection?

et al. 2009

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Incomplete penetrance and variable expressivity are non‐Mendelian phenomena resulting in the lack of correlation between genotype and phenotype. Not withstanding the diversity in mechanisms, differential expression of homologous alleles within cells manifests as variations in penetrance and expressivity of mutations between individuals of the same genotype. These phenomena are seen most often in dominantly inherited diseases, implying that they are sensitive to concentration of the gene product. In this framework and the advances in understanding the role of microRNA (miRNA) in fine‐tuning gene expression at translational level, we propose miRNA‐mediated regulation as a mechanism for incomplete penetrance and variable expressivity. The presence of miRNA binding sites at 3′ UTR, co‐expression of target gene–miRNA pairs for genes showing incomplete penetrance and variable expressivity derived from available data lend support to our hypothesis. Single nucleotide polymorphisms in the miRNA target site facilitate the implied differential targeting of the transcripts from homologous alleles.

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DAVID: Database for Annotation, Visualization, and Integrated Discovery

Cited by 1,619 publications

References 11 publications

Patterns of gene expression in the limbic system of suicides with and without major depression

Patterns of gene expression in the limbic system of suicides with and without major depression

Expression profiling in monozygotic twins discordant for bipolar disorder reveals dysregulation of the WNT signalling pathway

Incomplete penetrance and variable expressivity: is there a microRNA connection?

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