Lukas Wagner

Database resources of the National Center for Biotechnology Information.

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website. NCBI resources include Entrez, PubMed, PubMed Central, LocusLink, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SARS Coronavirus Resource, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD) and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.

The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene. ESTs were generated from libraries enriched for full-length cDNAs and analyzed to identify candidate full-ORF clones, which then were sequenced to high accuracy. The MGC has currently sequenced and verified the full ORF for a nonredundant set of >9,000 human and >6,000 mouse genes. Candidate full-ORF clones for an additional 7,800 human and 3,500 mouse genes also have been identified. All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http://mgc.nci.nih.gov).

Database resources of the National Center for Biotechnology

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBIs Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Functional annotation of a full-length mouse cDNA collection

The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.

Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative.

The NIH Xenopus Initiative is establishing many of the genetic and genomic resources that have been recommended by the Xenopus research community. These resources include cDNA libraries, expressed sequence tags, full‐length cDNA sequences, genomic libraries, pilot projects to mutagenize and phenotype X. tropicalis, and sequencing the X. tropicalis genome. This review describes the status of these projects and explains how to access their data and resources. Current information about these activities is available on the NIH Xenopus Web site (http://www.nih.gov/science/models/xenopus/). Published 2002 Wiley‐Liss, Inc.

A radiation hybrid map of mouse genes.

A comprehensive gene-based map of a genome is a powerful tool for genetic studies and is especially useful for the positional cloning and positional candidate approaches. The availability of gene maps for multiple organisms provides the foundation for detailed conserved-orthology maps showing the correspondence between conserved genomic segments. These maps make it possible to use cross-species information in gene hunts and shed light on the evolutionary forces that shape the genome. Here we report a radiation hybrid map of mouse genes, a combined project of the Whitehead Institute/Massachusetts Institute of Technology Center for Genome Research, the Medical Research Council UK Mouse Genome Centre, and the National Center for Biotechnology Information. The map contains 11,109 genes, screened against the T31 RH panel and positioned relative to a reference map containing 2,280 mouse genetic markers. It includes 3,658 genes homologous to the human genome sequence and provides a framework for overlaying the human genome sequence to the mouse and for sequencing the mouse genome.

The ORFeome Collaboration: a genome-scale human ORF-clone resource

To the Editor: Here we describe the ORFeome Collaboration (OC) open reading frame (ORF) clone collection, created by the OC (http://www.orfeomecollaboration.org/), an international collaboration of academic and commercial groups committed to providing genome-scale clone resources for human genes via worldwide commercial and academic clone distributors. Proteins are the predominant functional modules determining the fate of cells, tissues and organisms. An encyclopedic understanding of cellular physiology requires protein expression for proteinprotein interaction screening, cellular functional screening, validation of knockout and knockdown phenotypes, and numerous other approaches. Performing such studies on individual proteins or at the proteome scale requires a comprehensive collection of human protein expression clones. Our collection comprises ORF clones (Supplementary Note) and covers 17,154 RefSeq and Ensembl genes, nearly 73% of human RefSeq genes (http://www.ncbi.nlm.nih.gov/refseq/rsg/) and 79% of the highly curated Consensus Coding DNA Sequence Project (CCDS) human genes (http://www.ncbi.nlm.nih.gov/CCDS/ CcdsBrowse.cgi) (Fig. 1a and Supplementary Data). The collection includes clones of transcript variants for 6,304 (37%) of those genes. All major functional categories of human genes are substantially represented (Fig. 1b). All clones are provided in the Gateway vector format (Life Technologies), permitting high-throughput, precise and directional transfer of ORFs to a large variety of vectors for protein expression in biological systems such as Escherichia coli, yeast and mammals or using cell-free protein expression1 (Supplementary Note). OC clones were generated primarily by PCR amplification of the ORF from full-length, sequence-verified human cDNA clones of the Mammalian Gene Collection2 or the German cDNA Consortium3; ORFs were also prepared by directed RT-PCR cloning4 or DNA synthesis2. All 5′ and 3′ untranslated regions were excluded, permitting direct expression of ORFs as fusions to aminoor carboxy-terminal polypeptides, or as native protein, after transfer to a Gatewayexpression vector1. The clones are designed to maintain the correct reading frame for both aminoand carboxy-fusion proteins. Among all genes represented in the OC collection, 64% of clones are without stop codons, 5% have stop codons, and 31% are present in both versions. Each OC clone was isolated from a single colony and is fully sequenced. Individual clone sequences have been deposited in the GenBank, EMBL and DDBJ databases. The OC website provides a searchable database with annotation of all OC clones, their respective genes, and clone confidence levels based on CCDS and RefSeq annotations (Supplementary Note) along with links to the UCSC and RIKEN browsers (http://genome.ucsc.edu/cgi-bin/hgGateway and http://fantom.gsc.riken.jp/zenbu/gLyphs/#config), which provide graphical representations of the gene structures and transcripts. OC clones are distributed via a good faith agreement, giving unrestricted clone access to all scientists worldwide. The OC website lists OC clone distributors. The value of the OC resource has been demonstrated in numerous studies covering a broad range of applications. These include large-scale binary protein-protein interaction mapping5, production of recombinant human proteins6, mapping of co-complex associations, fluorescent protein tagging for human protein localization in mammalian cells and microscopy-based functional screening of proteins, development of disease-specific protein interaction Figure 1 | RefSeq and Ensembl genes and functional gene categories represented in the OC. (a) Numbers of protein-coding genes represented in the OC collection from RefSeq (blue) and Ensembl (green) gene catalogs. The table summarizes these numbers, together with OC coverage for RefSeq-only and Ensembl-only genes. (b) Numbers of human RefSeq genes represented in the OC collection versus in the human genome, compared in nine functional categories; percentages of genes in the OC are presented above the bars. The methods used to calculate the gene numbers in each category are explained in the Supplementary Note and contrasted to the standard Gene Ontology categories. An expanded list of the top Gene Ontology categories is also provided in the Supplementary Note. The data underlying the graphs are provided as Supplementary Data. a

Resources for Genetic and Genomic Studies of Xenopus

The National Institutes of Health Xenopus Initiative is a concerted effort to interact with the Xenopus research community to identify the communitys needs; to devise strategies to meet those needs; and to support, oversee, and coordinate the resulting projects. This chapter provides a brief description of several genetic and genomic resources generated by this initiative and explains how to access them. The resources described in this chapter are (1) complementary deoxyribonucleic acid (cDNA) libraries and expressed sequence tag (EST) sequences; (2) UniGene clusters; (3) full-insert cDNA sequences; (4) a genetic map; (5) genomic libraries; (6) a physical map; (7) genome sequence; (8) microarrays; (9) mutagenesis and phenotyping; and (10) bioinformatics. The descriptions presented here were based on data that were available at the time of manuscript submission. Because these are ongoing projects, they are constantly generating new data and analyses. The Web sites cited in each subheading present current data and analyses.