Biomedical subjects

Donna Karolchik

Publications and source records attributed to Donna Karolchik.

4 recordsLinked to original sources

PubMed2006

The ENCODE Project at UC Santa Cruz.

The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome. The pilot phase is for comparison of existing methods and for the development of new methods to rigorously analyze a defined 1% of the human genome sequence. Experimental datasets are focused on the origin of replication, DNase I hypersensitivity, chromatin immunoprecipitation, promoter function, gene structure, pseudogenes, non-protein-coding RNAs, transcribed RNAs, multiple sequence alignment and evolutionarily constrained elements. The ENCODE project at UCSC website (http://genome.ucsc.edu/ENCODE) is the primary portal for the sequence-based data produced as part of the ENCODE project. In the pilot phase of the project, over 30 labs provided experimental results for a total of 56 browser tracks supported by 385 database tables. The site provides researchers with a number of tools that allow them to visualize and analyze the data as well as download data for local analyses. This paper describes the portal to the data, highlights the data that has been made available, and presents the tools that have been developed within the ENCODE project. Access to the data and types of interactive analysis that are possible are illustrated through supplemental examples.

Base Sequence↗

PubMed2005

The UCSC Proteome Browser.

The University of California Santa Cruz (UCSC) Proteome Browser provides a wealth of protein information presented in graphical images and with links to other protein-related Internet sites. The Proteome Browser is tightly integrated with the UCSC Genome Browser. For the first time, Genome Browser users have both the genome and proteome worlds at their fingertips simultaneously. The Proteome Browser displays tracks of protein and genomic sequences, exon structure, polarity, hydrophobicity, locations of cysteine and glycosylation potential, Superfamily domains and amino acids that deviate from normal abundance. Histograms show genome-wide distribution of protein properties, including isoelectric point, molecular weight, number of exons, InterPro domains and cysteine locations, together with specific property values of the selected protein. The Proteome Browser also provides links to gene annotations in the Genome Browser, the Known Genes details page and the Gene Sorter; domain information from Superfamily, InterPro and Pfam; three-dimensional structures at the Protein Data Bank and ModBase; and pathway data at KEGG, BioCarta/CGAP and BioCyc. As of August 2004, the Proteome Browser is available for human, mouse and rat proteomes. The browser may be accessed from any Known Genes details page of the Genome Browser at http://genome.ucsc.edu. A user's guide is also available on this website.

California↗

PubMed2005

Exploring relationships and mining data with the UCSC Gene Sorter.

In parallel with the human genome sequencing and assembly effort, many tools have been developed to examine the structure and function of the human gene set. The University of California Santa Cruz (UCSC) Gene Sorter has been created as a gene-based counterpart to the chromosome-oriented UCSC Genome Browser to facilitate the study of gene function and evolution. This simple, but powerful tool provides a graphical display of related genes that can be sorted and filtered based on a variety of criteria. Genes may be ordered based on such characteristics as expression profiles, proximity in genome, shared Gene Ontology (GO) terms, and protein similarity. The display can be restricted to a gene set meeting a specific set of constraints by filtering on expression levels, gene name or ID, chromosomal position, and so on. The default set of information for each gene entry-gene name, selected expression data, a BLASTP E-value, genomic position, and a description-can be configured to include many other types of data, including expanded expression data, related accession numbers and IDs, orthologs in other species, GO terms, and much more. The Gene Sorter, a CGI-based Web application written in C with a MySQL database, is tightly integrated with the other applications in the UCSC Genome Browser suite. Available on a selected subset of the genome assemblies found in the Genome Browser, it further enhances the usefulness of the UCSC tool set in interactive genomic exploration and analysis.

Computational Biology↗

PubMed2004

The UCSC Table Browser data retrieval tool.

The University of California Santa Cruz (UCSC) Table Browser (http://genome.ucsc.edu/cgi-bin/hgText) provides text-based access to a large collection of genome assemblies and annotation data stored in the Genome Browser Database. A flexible alternative to the graphical-based Genome Browser, this tool offers an enhanced level of query support that includes restrictions based on field values, free-form SQL queries and combined queries on multiple tables. Output can be filtered to restrict the fields and lines returned, and may be organized into one of several formats, including a simple tab- delimited file that can be loaded into a spreadsheet or database as well as advanced formats that may be uploaded into the Genome Browser as custom annotation tracks. The Table Browser User's Guide located on the UCSC website provides instructions and detailed examples for constructing queries and configuring output.

Animals↗