The UCSC Genome Browser Database

Karolchik, Donna; Baertsch, Robert; Diekhans, Mark; Furey, Terrence S.; Hinrichs, Angie S.; Lu, Yontao; Roskin, Krishna M.; Schwartz, M.; Sugnet, Charles W.; Thomas, Daniel; Weber, Ryan; Haussler, David; Kent, W. James

doi:10.1093/nar/gkg129

Cited by 1,491 publications

(1,363 citation statements)

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“…The alignment data was taken from the UCSC genome browser (http://genome.ucsc.edu) [16]. We excluded 322 genes that do not have a unique alignment, as well as 1242 genes that…”

Section: Length Analysis Of Hk Genesmentioning

confidence: 99%

Human housekeeping genes are compact

2003

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We identify a set of 575 human genes that are expressed in all conditions tested in a publicly available database of microarray results. Based on this common occurrence, the set is expected to be rich in "housekeeping" genes, showing constitutive expression in all tissues. We compare selected aspects of their genomic structure with a set of background genes. We find that the introns, untranslated regions and coding sequences of the housekeeping genes are shorter, indicating a selection for compactness in these genes. 1The amazing diversity of the human body stems from the different expression patterns of genes in different tissues. Although most genes show constitutive expression in only a subset of tissues, some gene products are required for the maintenance of the basal cellular function and are constitutively found in all human cells. These genes are called housekeeping genes (HK genes) [1]. HK genes can be used to calibrate measurements of gene expression [2].They might also help to define the minimal gene complement needed for a human cell [1].Several attempts have been made recently to define the complete set of HK genes [3,4].Microarrays are often used to identify sets of genes that are expressed either ubiquitously or in specific tissues or conditions. However, the technique is technically demanding and prone to artifacts, so independent evidence is often required to confirm the results. In principle, identifying the set of HK genes using microarray data is straightforward; one need only look for genes that are expressed in all tissues and all experimental conditions.Employing such an approach has so far resulted in two lists of HK genes [3,4]. However, problems in probe design, measurement noise and other artifacts introduce inevitable errors in such lists. Because a northern blot experiment for each gene in each tissue is impractical, an independent test is needed to validate any list of HK genes. Here, we report a validation test that uses a recently discovered property of highly expressed genes.The transcription process is both slow and costly; it takes 50 milliseconds [5,6] and two ATP molecules [7] approximately to transcribe a nucleotide. This might be expected to provide selective pressure to make genes as short as functionally possible. The more copies of a gene required for the organism, the stronger this pressure should be. The first demonstration of this principle [8] showed that genes with a large number of expressed sequence tags (ESTs) in public libraries (and hence most mRNAs) have a significantly shorter average intron length than those with fewer ESTs.Here, an implication of this principle is used to validate a set of HK genes. The HK genes, which are transcribed in all somatic cells and under all circumstances, are by nature highly expressed, and therefore should be selected to have shorter introns. We used a recently published database of microarray experiments [9] to identify a set of HK genes. As a further validation step, we checked the Gene Ontology (GO) annotation of thes...

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“…The alignment data was taken from the UCSC genome browser (http://genome.ucsc.edu) [16]. We excluded 322 genes that do not have a unique alignment, as well as 1242 genes that…”

Section: Length Analysis Of Hk Genesmentioning

confidence: 99%

Human housekeeping genes are compact

2003

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“…PCR primers were designed using ExonPrimer (http://ihg.gsf.de/ihg/ExonPrimer.html) and Primer3 [12] accessed via an interface with the UCSC Genome Browser [13] to amplify OTC exons 1, 9, and 10, RPGR exon 1, SYTL5 exon 16, CYBB exon 13, XK exon 2, PRRG1 exon 3, TMEM47 exon 2, and DMD exon 3. Primer sequences are available upon request.…”

Section: Genomic Analysismentioning

confidence: 99%

Complex management of a patient with a contiguous Xp11.4 gene deletion involving ornithine transcarbamylase: A role for detailed molecular analysis in complex presentations of classical diseases

Deardorff

Gaddipati

Kaplan

et al. 2008

Molecular Genetics and Metabolism

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A male infant was diagnosed prenatally with a partial ornithine transcarbamylase (OTC) gene deletion and managed from birth. However, he displayed neurological abnormalities and developed pleural effusions, ascites and anasarca not solely explained by OTC deficiency (OTCD). Further evaluation of the gene locus using exon-specific PCR and high density SNP array copy number analysis revealed a 3.9Mb deletion from Xp11.4 to Xp21.1 including five additional gene deletions, three causing the known genetic diseases: Retinitis pigmentosa (RP3), X-linked chronic granulomatous disease (CGD) and McLeod syndrome. The case illustrates (1) the complexities of managing a patient withneonatal onset OTCD, CGD, RP3 and McLeod syndrome, (2) the need for detailed evaluation in seemingly "isolated" gene deletions and (3) the clinical utility of high density copy number analysis for rapidly characterizing chromosomal lesions.

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“…Pairwise comparisons have helped to predict functionally conserved regions, however the statistical accuracy of these predictions is increased when more than two sequences are used (Dubchak et al 2000). Several studies suggest that comparative analysis of multiple evolutionarily diverse organisms facilitate the prediction of functionally important non-coding regions (Dubchak et al 2000;Matys et al 2003;Thomas et al 2003). Comparisons of genome sequences from evolutionarily diverse organisms also elucidate regulatory regions that are specific to a particular species or group of species.…”

Section: Applied Aspects Of Vertebrate Comparative Genomics and Predimentioning

confidence: 99%

“…The identification of conserved coding and regulatory regions is enhanced by including divergent sequences in comparative studies (Thomas et al 2003) because these sequences provide more stringent filters for detecting conserved, and presumably functionally important elements (Dubchak et al 2000;Thomas et al 2003;Ahituv et al 2004). Consequently, sequences from evolutionarily distant marine vertebrates and protovertebrates are being used in comparative studies with increasing frequency.…”

Section: The Contributions Of Marine and Freshwater Organisms To Compmentioning

confidence: 99%

“…The University of California Santa Cruz Genomic Browser (http://genome.ucsc.edu/; Karolchik et al 2003) is among the most popular databases for querying and retrieving genomic sequences of interest. It currently provides access to genomic assemblies from 23 organisms, including 10 vertebrates, 8 insects, 2 nematodes, a sea squirt, baker's yeast, and the SARS virus.…”

Section: The Contributions Of Marine and Freshwater Organisms To Compmentioning

confidence: 99%

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Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics

et al. 2004

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The use of bioinformatics to integrate phenotypic and genomic data from mammalian models is well established as a means of understanding human biology and disease. Beyond direct biomedical applications of these approaches in predicting structure-function relationships between coding sequences and protein activities, comparative studies also promote understanding of molecular evolution and the relationship between genomic sequence and morphological and physiological specialization. Recently recognized is the potential of comparative studies to identify functionally significant regulatory regions and to generate experimentally testable hypotheses that contribute to understanding mechanisms that regulate gene expression, including transcriptional activity, alternative splicing and transcript stability. Functional tests of hypotheses generated by computational approaches require experimentally tractable in vitro systems, including cell cultures. Comparative sequence analysis strategies that use genomic sequences from a variety of evolutionarily diverse organisms are critical for identifying conserved regulatory motifs in the 5¢-upstream, 3¢-downstream and introns of genes. Genomic sequences and gene orthologues in the first aquatic vertebrate and protovertebrate organisms to be fully sequenced (Fugu rubripes, Ciona intestinalis, Tetraodon nigroviridis, Danio rerio) as well as in the elasmobranchs, spiny dogfish shark (Squalus acanthias) and little skate (Raja erinacea), and marine invertebrate models such as the sea urchin (Strongylocentrotus purpuratus) are valuable in the prediction of putative genomic regulatory regions. Cell cultures have been derived for these and other model species. Data and tools resulting from these kinds of studies will contribute to understanding transcriptional regulation of biomedically important genes and provide new avenues for medical therapeutics and disease prevention.

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The UCSC Genome Browser Database

Cited by 1,491 publications

References 10 publications

Human housekeeping genes are compact

Human housekeeping genes are compact

Complex management of a patient with a contiguous Xp11.4 gene deletion involving ornithine transcarbamylase: A role for detailed molecular analysis in complex presentations of classical diseases

Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics

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