GALA, a Database for Genomic Sequence Alignments and Annotations

Giardine, Belinda; Elnitski, Laura; Riemer, Cathy; Makałowska, Izabela; Schwartz, Scott; Miller, Webb; Hardison, Ross C.

doi:10.1101/gr.603103

Cited by 46 publications

(34 citation statements)

References 36 publications

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“…The link between the HbVar and GALA databases (Giardine et al, 2003, Patrinos et al, 2004, coupled with the UCSC Genome Browser (Hinrichs et al, 2006), was the first step towards integrating the available resources at the Globin Gene Server (Hardison et al, 1994). A step further is PhenCode (Giardine et al, submitted), which connects the phenotype and clinical data in a variety of LSDBs, including HbVar and GenPhen, to the data on genome sequences, evolutionary history, and function available at the Genome Browser.…”

Section: Future Prospectsmentioning

confidence: 99%

“…HbVar has rapidly become an important aid in the globin research community and is considered to be one of the premier LSDBs available to date (Claustres et al, 2002, Beroud, 2005. The major advantages of HbVar compared to other LSDBs, are the mutation information quality and depth of coverage, its regular updates and upgrades, and, most importantly, its interrelation with other databases, such as GALA (Giardine et al, 2003), GenPhen and PhenCode (Giardine et al, submitted). Minor disadvantages were the lack of information on the available experimental protocols to screen for globin gene mutations and the database's lengthy query page.…”

Section: Introductionmentioning

confidence: 99%

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HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update

et al. 2007

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Communicated by Stylianos E. AntonarakisHbVar (http://globin.bx.psu.edu/hbvar) is a locus-specific database (LSDB) developed in 2001 by a multi-center academic effort to provide timely information on the genomic sequence changes leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology, and ethnic occurrence, accompanied by mutation frequencies and references. In addition to the regular updates to entries, we report significant advances and updates, which can be useful not only for HbVar users but also for other LSDB development and curation in general. The query page provides more functionality but in a simpler, more user-friendly format and known single nucleotide polymorphisms in the human α-and β-globin loci are provided automatically. Populationspecific β-thalassemia mutation frequencies for 31 population groups have been added and/or modified and the previously reported δ-and α-thalassemia mutation frequency data from 10 population groups have also been incorporated. In addition, an independent flat-file database, named XPRbase (http://www.goldenhelix.org/xprbase), has been developed and linked to the main HbVar web page to provide a succinct listing of 51 experimental protocols available for globin gene mutation screening. These updates significantly augment the database profile and quality of information provided, which should increase the already high impact of the HbVar database, while its combination with the UCSC powerful genome browser and the ITHANET web portal paves the way for drawing connections of clinical importance, that is from genome to function to phenotype.

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Section: Future Prospectsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update

et al. 2007

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“…We evaluated the biological relevance of the pCRMs by measuring the extent to which they overlap known regulatory elements such as those compiled in the TRRD (Kolchanov et al 2002), Transfac (Matys et al 2003), and GALA (Giardine et al 2003) databases. We also measured the overlap between the pCRMs and other putative regulatory elements, such as "promoter" regions (defined as the 1-kb region upstream of the transcription start sites [TSS] of all known genes), CpG islands (based on the UCSC Genome Browser annotation [Karolchik et al 2003]), and DNaseI hypersensitive sites Sabo et al 2004;) from the Encode regions .…”

Section: In Silico Validation Of Predicted Modulesmentioning

confidence: 99%

Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression

Blanchette

Bataille²,

Chen³

et al. 2006

Genome Res.

243

217

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The identification of regulatory regions is one of the most important and challenging problems toward the functional annotation of the human genome. In higher eukaryotes, transcription-factor (TF) binding sites are often organized in clusters called cis-regulatory modules (CRM). While the prediction of individual TF-binding sites is a notoriously difficult problem, CRM prediction has proven to be somewhat more reliable. Starting from a set of predicted binding sites for more than 200 TF families documented in Transfac, we describe an algorithm relying on the principle that CRMs generally contain several phylogenetically conserved binding sites for a few different TFs. The method allows the prediction of more than 118,000 CRMs within the human genome. A subset of these is shown to be bound in vivo by TFs using ChIP-chip. Their analysis reveals, among other things, that CRM density varies widely across the genome, with CRM-rich regions often being located near genes encoding transcription factors involved in development. Predicted CRMs show a surprising enrichment near the 3′ end of genes and in regions far from genes. We document the tendency for certain TFs to bind modules located in specific regions with respect to their target genes and identify TFs likely to be involved in tissue-specific regulation. The set of predicted CRMs, which is made available as a public database called PReMod (http://genomequebec.mcgill.ca/PReMod), will help analyze regulatory mechanisms in specific biological systems.

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“…The assembly of genome-wide data sets has been facilitated by the introduction of tools such as the UCSC Table Browser, which is intended to retrieve specific subsets of coordinate-based data, and the Genome Alignment and Annotation Databases (GALA), which merge genome annotations with multi-species alignment data (Giardine et al 2003). Once a genome-wide data set has been generated, highthroughput analysis can be performed using tools such as Galaxy, a simple Web portal that enables users to combine data from independent queries; visualize results; perform operations such as intersections, unions, and subtractions; and submit data to numerous computational tools that are useful in genomic analysis (Giardine et al 2005).…”

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confidence: 99%

The ENCODEdb portal: Simplified access to ENCODE Consortium data

Elnitski

Shah²,

Moreland³

et al. 2007

Genome Res.

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The Encyclopedia of DNA Elements (ENCODE) project aims to identify and characterize all functional elements in a representative chromosomal sample comprising 1% of the human genome. Data generated by members of The ENCODE Project Consortium are housed in a number of public databases, such as the UCSC Genome Browser, NCBI's Gene Expression Omnibus (GEO), and EBI's ArrayExpress. As such, it is often difficult for biologists to gather all of the ENCODE data from a particular genomic region of interest and integrate them with relevant information found in other public databases. The ENCODEdb portal was developed to address this problem. ENCODEdb provides a unified, single point-of-access to data generated by the ENCODE Consortium, as well as to data from other source databases that lie within ENCODE regions; this provides the user a complete view of all known data in a particular region of interest. ENCODEdb Genomic Context searches allow for the retrieval of information on functional elements annotated within ENCODE regions, including mRNA, EST, and STS sequences; single nucleotide polymorphisms, and UniGene clusters. Information is also retrieved from GEO, OMIM, and major genome sequence browsers. ENCODEdb Consortium Data searches allow users to perform compound queries on array-based ENCODE data available both from GEO and from the UCSC Genome Browser. Results are retrieved from a specific genomic area of interest and can be further manipulated in a variety of contexts, including the UCSC Genome Browser and the Galaxy large-scale genome analysis platform. The ENCODEdb portal is freely accessible at http://research. nhgri.nih.gov/ENCODEdb.

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GALA, a Database for Genomic Sequence Alignments and Annotations

Cited by 46 publications

References 36 publications

HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update

HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update

Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression

The ENCODEdb portal: Simplified access to ENCODE Consortium data

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