ZFIN NEWS In this issue: • ZFIN - A valuable resource for the research The Zebrafish Information Network community (pg. 1) • Zebrafish Gene Collection now available in ZFIN (pg. 1) http://zfin.org • What’s new on the ZFIN Gene Page? (pg. 2) • Easier Access to Gene Expression & Anatomy (pg. 3) Volume 1, Number 1 • Phenotype Futures (pg. 3) Summer 2004 • Gene Ontology Annotation of Zebrafish Genes (pg. 4)
ZFIN - A valuable resource for the Zebrafish Gene Collection now available in ZFIN zebrafish research community We have incorporated full length cDNA clones from the Zebrafish Gene Collec- What is ZFIN? tion (ZGC) initiative into ZFIN. ZGC cDNA clones are available to the scien- The Zebrafish Information Network, developed by the Gene Ontology (GO) tific community without restriction. Pur- ZFIN, serves as your zebrafish model consortium to describe and classify chasing information is available at http:// organism database by providing a genes and gene products, and increasing zgc.nci.nih.gov/Info/Buy. central location for the curation and support for whole genome sequence integration of zebrafish genetic, data. Many cDNA sequences are curated and genomic and phenotypic data. Web associated with their encoding genes, and accessible query interfaces for mutant, ZFIN - The Future we will add more as data become avail- gene, marker, clone, mapping and able. For sequences that represent genes expression data facilitate integrated Communication from the zebrafish novel to ZFIN, we make the association studies of zebrafish functional research community is invaluable in after the creation of a new gene record. genomics. helping us maximize the utility and These novel genes have nomenclature usability of ZFIN. We encourage you based upon the ZGC clone accession ID. ZFIN - Past & Present to send your comments and suggestions ZFIN will continue to revise and update to [email protected] nomenclature for these genes as informa- ZFIN is a dynamic resource with new tion from paralogous and orthologous data added daily and new features added We will publish ZFIN News genes becomes available. Electronic Gene frequently. Scientific curators extract periodically to help keep you abreast of Ontology (GO) annotations based upon and attribute pertinent information from new ZFIN resources. Watch for it on Swiss-Prot keyword, enzyme commission the literature. Collaborations with our website (http://zfin.org) in PDF number and InterPro domain translations zebrafish laboratories, data exchanges format. are also available for some of these genes. with other bioinformatics organizations such as NCBI, the Sanger Institute, the Table 1: ZFIN growth - 1998 to 2004 Zebrafish Gene Collection (ZGC) 1998 1999 2000 2001 2002 2003 2004 and Swiss-Prot, and personal (thru June) communications from you regularly Genes & Genetics: provide data to ZFIN. Table 1 depicts Genes 220 608 974 1384 1715 12205 14517 Alleles 1896 1951 2018 2088 2278 2343 2484 the growth of ZFIN over the years. ESTs 0 97 5845 9169 10493 11847 12134 Genes with GO Annotations 0 0 0 0 0 1353 2790 We are currently expanding curation of zebrafish phenotypes and expression Expression & Phenotypes Gene expression patterns 0 0 0 83 739 1295 1364 data, annotating ZFIN gene records Images (phenotypes, expression patterns) 1851 1858 1866 2598 8473 16874 17650 using the structured vocabularies Anatomical structures 0 0 0 747 1112 1132 1132
Genomics: Mapping panels 3 5 5 7 7 7 7 Marker mappings 3138 2942 10509 14891 25483 26858 31017 Be sure to visit the ZFIN Links to other databases 0 8621 31589 46522 60417 99118 116931
exhibit at the Zebrafish Community Information: Meeting in Madison! Publications 1913 2415 2856 3517 4246 4986 5385 Researchers 1403 1640 2092 2431 2683 2916 3033 Laboratories 190 228 280 324 329 372 391 http://zfin.org
What’s new on the ZFIN gene page?
In ZFIN, the gene page is a central hub from which a variety of information is accessible (Figure 1). This wealth of summarized information has made gene pages the most accessed in ZFIN. We update the gene pages frequently due to ongoing development of existing data types, as well as the addition of new data. Keeping abreast of these changes can present a challenge to even the most seasoned users. The most recent changes to the ZFIN gene pages include:
GENE PRODUCTS: This section contains a list of Gene Ontology terms (GO) as well as links to external databases storing information on protein families, domains, and sites. Gene Ontology information and its display are explained in more detail in a companion article in this issue (see page 4).
SEGMENT(CLONE and PROBE) RELATIONSHIPS: This section provides links to ZFIN cDNA and genomic DNA segment records. The relationship between the gene and the DNA segment is also indicated. ZFIN has recently incorporated clones from the Zebrafish Gene Collection (ZGC) and genome sequencing project. Links to DNA segment pages supporting ZFIN mapping and expression data can also be found in this section.
SEQUENCE INFORMATION: Figure 1: ZFIN gene page example The redesigned sequence information section better summarizes sequences, Additional information such as length LocusLink and in the Sanger provides more information, and and sequence type has been added to Institute’s Vertebrate Genome increases functionality. Sequences each sequence. We have increased the Annotation database (Vega). are summarized by links to functionality of the sequence Researchers can also access marker representative cDNA, genomic, and information section by adding pages from The Sanger Institute’s polypeptide sequences as well as the “BLAST IT!” or “MegaBLAST IT!” fingerprinting map of the zebrafish UniGene cluster on the gene page. All buttons that bring up the sequence in genome (Fingerprint Contig or FPC) cDNA, genomic, polypeptide, and a NCBI BLAST query form. from this location. cluster sequences associated with the gene are found on a separate page OTHER ... GENE/MARKER ORTHOLOGUES: The redesigned accessed by selecting the “All PAGES: We now provide links orthology display has evidence codes Sequence Information” link. directly to zebrafish gene pages in to indicate the types of evidence
ZFIN News - Summer 2004 2 http://zfin.org
Easier Access to Gene Expression and Anatomy (continued from page 2) Patterns of gene expression in Currently ZFIN has a large database used to support assertions of developing zebrafish embryos of directly-submitted, annotated orthology. Evidence includes amino contribute vitally to the understanding expression patterns (Figure 3). In acid comparison, nucleotide sequence of vertebrate gene function. ZFIN is addition, ZFIN curators have indexed comparison, and conserved location. expanding its coverage of gene hundreds of recent publications Multiple columns in a single evidence expression and has significantly reporting gene expression, which can code section indicate that different changed its expression query page to be found with the new search publications use that particular type make searching faster and easier. interface. We are developing the of evidence to support orthology means to add figures to ZFIN from between different sets of species. Researchers may search ZFIN for the literature, to associate them with expression patterns by gene name, anatomical structures, and to make mutant background, developmental them fully searchable. With time, we stage, and other criteria, as well as by will populate anatomical structure entering anatomical structures. descriptions with definitions, related Phenotype Futures Researchers may also use an structures, images, links to expression anatomical hierarchy to browse for and phenotypic data, and homologous structures of other model organisms. ZFIN is improving its support of data of interest or to find descriptions zebrafish phenotypes with the goal of specific structures (Figure 2). of providing comprehensive information about mutants and morpholinos. We offer annotation Fig 2 tools to laboratories that are generating phenotype data. These tools promote the use of approved nomenclature for anatomical structures, biological processes, and phenotypic attributes that are consistent with the structured vocabularies (ontologies) in ZFIN. We encourage investigators who are interested in these tools to contact us at [email protected]. Figure 2: Hierarchic list of structures from the ZFIN anatomical browser. ZFIN curators are beginning to curate phenotypes reported in the literature using these same vocabularies. In the Fig 3 meantime, we are developing new query forms and page displays that will fully integrate phenotypes with other ZFIN data.
Keep your ZFIN personal and lab records up to date!
For assistance, or to request a new ZFIN record, contact:
[email protected] Figure 3: Expression pattern of clone cb918 annotated with structures from the anatomical dictionary. Source:Direct data submission, Thisse Laboratory, Strasbourg, FR 3 ZFIN News - Summer 2004 http://zfin.org
Gene Ontology Annotation of Zebrafish Genes Number of Genes with GO Annotation Electronic Annotations Manual Annotations
3000 Biological ontologies are constrained by a curator. All other evidence codes and structured vocabularies used to indicate that an annotation has been 2500 reviewed by a curator and reflect the describe a specific biological domain 2000 such as anatomy, nucleotide nature and quality of the data backing sequence features, phenotypes, or that annotation. To learn more about 1500 GO annotation, click on an evidence protein functions. In recent years Gene Count 1000 there has been an increased effort to code from within ZFIN, or visit the produce and employ such ontologies. Gene Ontology Consortium website. 500
The shared use of these biological 0 ontologies promotes consistent usage How can I make GO-based gene queries? Jan. '04 May '04 of terms and their meaning across Sep. '03 Feb. '04 Apr. '04 databases, supporting cross-species Annotation of zebrafish gene records with GO terms is now an integral part genomics studies and computational characterized and novel genes. GO- aspects of data storage and retrieval. of the ZFIN literature curation effort. Many uncharacterized genes, such as based queries for zebrafish genes can those solely represented by a cDNA be made using AmiGO (http:// What is the Gene Ontology? www.godatabase.org/cgi-bin/amigo/ The Gene Ontology (GO) is a set of sequence, also get GO annotation through our electronic annotation go.cgi), a web based query tool three orthogonal ontologies developed by the GO consortium. describing the Cellular Components, methods. Thus, GO annotation is an Biological Processes, and Molecular exciting method for describing both Functions of gene products (Table 2). Table 2: Orthogonal components of Gene Ontology (GO). These ontologies are produced and utilized by members of the Ontology Content Example • carbohydrate Gene Ontology Consortium (http:// binding Molecular Function The tasks performed by individual gene products • ATPase activity www.geneontology.org), including • protein kinase ZFIN. Terms from these ontologies activity • mitosis Broad biological goals generally accomplished by ordered retinoid are associated with gene records in Biological Process • assemblies of Molecular Functions metabolism ZFIN as a routine part of literature • gastrulation curation, as well as by automated • nucleus • telomere cap Cellular Component Subcellular structures, locations and macromolecular complex computational methods. complexes • connexon complex Where are the GO annotations in ZFIN? A. GO annotations are located in the Gene Products section of gene pages in ZFIN (Figure 4A). The total number of GO annotations applied to a gene is listed below the GO categories. The “All GO Terms” hyperlink brings up the GO details page, where all the GO terms and B. their details can be reviewed (Figure 4B). The GO annotation details include evidence codes, inference data and publications. Evidence codes indicate what type of experimental support exists for an annotation. For example, the IEA (Inferred from Electronic Annotation) evidence code indicates that the annotation was produced through automated electronic methods, and has not been reviewed Figure 4: Example of GO annotations in ZFIN gene pages.
4 ZFIN News - Summer 2004