Genome Resources Workshop Genes Genome Sequence Map Homology Expression

1. Genome Resources WorkshopGenes Genome Sequence Map Homology Expression Lynn Schriml: NCBI, Judy Sprague: ZFIN, Kerstin Jekosch: Sanger Institute Tutorial: www.ncbi.nlm.nih.gov/genome/guide/zebrafish/Workshop2004 www.ncbi.nlm.nih.gov/genome/guide/zebrafish http://zfin.org www.sanger.ac.uk/Projects/D_rerio

2. Questions and Answers... a guide to genome resources 1. Where do I start ? 2. How do I find my gene ? 3. How do I find gene-related data ? 4. Where can I ask questions or submit suggestions ?

3. 1. Where do I start ? www.ncbi.nlm.nih.gov NCBI Home Page What kind of data is available ? • NCBI includes data from: • external resources • model organism databases, • genome projects, • PubMed and GenBank • submissions, and datasets • provided by the • research community • internal computation • ongoing curation • follow the “How to reach us” link to submit questions or submissions

4. 1. Where do I start ? www.ncbi.nlm.nih.gov NCBI Home Page • navigate to NCBI databases, resources and tools from links provided on NCBI’s home page • from NCBI’s home page you can submit a query against any of the databases in the pulldown menu

5. 1. Where do I start ? www.ncbi.nlm.nih.gov NCBI Home Page • begin searches from Entrez Home Page, the Genome Biology Page, or Taxonomy Page • navigate by links provided on the NCBI home page

6. 1. Where do I start ? www.ncbi.nlm.nih.gov NCBI Home Page • find out what is new at NCBI from the Highlights on the NCBI home page or from the NCBI newsletter

7. 1. Where do I start ? www.ncbi.nlm.nih.gov • the Genome Biology page provides links to organism specific resource pages

8. 1. Where do I start ? www.ncbi.nlm.nih.gov/Entrez • navigate to individual databases by clicking on database name or icon • NCBI pre-computes related records between each Entrez database • From the Entrez home page you can query all Entrez databases by a single text query • Text queries can include the Boolean terms AND, OR, NOT

9. 1. Where do I start ? www.ncbi.nlm.nih.gov/Database/datamodel • The NCBI Entrez integrated search and retrieval system provides pre-computed links between records in disparate databases.

10. 1. Where do I start ? www.ncbi.nlm.nih.gov/Entrez • view results and link to databases by clicking on the database name or icon • see examples of records in gene-related resources • see the summary results of the Entrez global query for the number of records in each Entrez database that matched the text query

11. 1. Where do I start ? www.ncbi.nlm.nih.gov/genome/guide/zebrafish • submit a text search in the top search box • the Zebrafish Genome Resources page includes links to NCBI and Community resources • click on provided Entrez queries to view the latest papers in PubMed, mRNAs in GenBank, or the complete set of ZGC clones in GenBank

12. 1. Where do I start ? www.ncbi.nlm.nih.gov/genome/guide/zebrafish zgc.nci.nih.gov • The ZGC home page provides inks to order clones and information on full-length clones and ZGC libraries

13. 1. Where do I start ? www.ncbi.nlm.nih.gov/Taxonomy • navigate to Zebrafish BLAST, Map Viewer, Trace Archive • view taxonomic lineage of over 150,000 organisms in sequence databases

14. 1. Where do I start ? www.sanger.ac.uk/Projects/D_rerio

15. 1. Where do I start ? www.sanger.ac.uk/Projects/D_rerio • whole genome shotgun assembly integrated with physical map • with • automated annotation in EnsEMBL • links to • pre-EnsEMBL database incl. BLAST/SSAHA server • EnsEMBL database incl. BLAST/SSAHA server • download assemblies • assembly information • mapsearch database • trace repository • clone mapping and sequencing • with • manual annotation in Vega • links to • mapping project incl. FPC database • Vega database with finished/annotated clones • BLAST server for (un-)finished clone sequences • clone status information

16. 1. Where do I start ? ZFIN Zebrafish Model Organism Database Gene Products Gene Expression Mutant Phenotypes Sequence Information Mapping Data Orthology

17. 1. Where do I start ?

18. 1. Where do I start ?

19. 2. How do I find my gene ? at ZFIN, NCBI and the Sanger Institute Gene xyz zebrafish

20. 2. How do I find my gene ?

21. Mapping Panels • Whole Genome Sequence 2. How do I find my gene ? Genomic Context

22. 2. How do I find my gene ? • by text search: in Entrez Gene • by sequence: find related sequences via BLAST • searches or by examining pre-computed sequence comparisons in HomoloGene or BLink (pre-computed protein comparisons) • (find links to BLink results on Entrez protein pages) • by map position: • query Entrez Gene by map position or query map data in Map Viewer Entrez Gene: www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene BLAST home page: www.ncbi.nlm.nih.gov/BLAST/ HomoloGene: www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene Map Viewer home page: www.ncbi.nlm.nih.gov/mapview/

23. 2. How do I find my gene ? www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene • search Entrez Gene by text • to find known (named) and unknown genes. Entrez Gene includes records based on uncharacterized cDNAs. These records may represent the gene you are looking for.

24. 2. How do I find my gene ? www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene • query Entrez Gene by gene attribute : identifier, name, symbol, accession, publication (PubMed ID), GO terms, LG or chromosome • view results of text query, view detailed results by clicking on the gene symbol • follow link to Gene Search for additional search options • Subscribe to resource mailing lists by following Subscriptions link

25. 2. How do I find my gene ? • Take advantage of the higher level of annotation available in other genome where your gene of interest has been indentified. • Beginning with a text search on the gene symbol, choose the Entrez Gene record for a homolog and then look at pre-computed related information. • Pre-computed nucleotide comparisons in HomoloGene or pre-computed protein comparisons in BLink may identify the homologous zebrafish sequence.

26. 2. How do I find my gene ? • for example: the SIX1 gene has been identified in human. • Look for related zebrafish sequences (from the Links menu) in HomoloGene (via related UniGene clusters) or Entrez Protein (via related proteins identified in BLink) • follow provided Links from Entrez Gene >> Entrez Protein or HomoloGene • The Entrez Protein record includes a link to the pre-computed protein comparisons in BLink (BLAST link)

27. BLink provides protein BLAST results between your query protein and all Entrez proteins • Look at the list of proteins, click on the “Best hits” button to view a list of the number of hits for each organism 2. How do I find my gene ? BLink: BLAST link

28. 2. How do I find my gene ? BLink: BLAST link • BLink results for the human SIX1 protein identifies • a highly similar (91% identical ) zebrafish protein • click on the protein Accession to go to Entrez Protein • click on the Score to view the BLAST2 protein alignment 91% Identical

29. 2. How do I find my gene ? • view the Entrez Protein record • from the pull-down Links menu, choose the Link to Entrez Gene to view the Gene record • associated with the zebrafish protein identified via the BLink comparison

30. 2. How do I find my gene ? • the Entrez Gene record details page provides links to external source of the data (e.g. ZFIN) and links to other Entrez databases (e.g. PubMed) • Entrez Gene records are continually updated. • This record was updated to six1 30-Jul-2004.

31. 2. How do I find my gene ? • functional information can be submitted to the Entrez Gene record via the GeneRIF submission form www.ncbi.nlm.nih.gov/RefSeq

32. 2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio • starting with cDNA/EST/peptide sequences • BLAST/SSAHA servers for Vega and EnsEMBL • BLAST server for (un-)finished clones

33. 2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio • starting with a gene name • text search in Vega and EnsEMBL

34. 2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio • starting with a homologuous gene • EnsEMBL gene from different species  ‘Orthologue Prediction’ • example: human FOXN4 gene

35. 2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio • starting with a marker or genomic position (clone) • in EnsEMBL via text search or ‘mapsearch’ • in Vega via text search

36. 2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio • how to obtain gene sequences • in Vega and EnsEMBL: mouse overs • in Vega and EnsEMBL: data downloads (‘Export Data’) • in EnsEMBL: general downloads (pre-computed datasets from mainpage)

37. 2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio • how to create on-the-fly datasets • in EnsEMBL: EnsMART at www.ensembl.org/Multi/martview

38. 2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio • available gene information • in EnsEMBL and Vega: GeneView with link to ZFIN

39. 3. How do I find gene-related data ? at the Sanger Institute, ZFIN and NCBI Gene abc zebrafish

40. 3. How do I find gene-related data ? www.sanger.ac.uk/Projects/D_rerio • inferring gene function • in EnsEMBL and Vega: GeneView textual entries (description, homologues, orthologues) • supporting evidence (‘Exon Information’)

41. 3. How do I find gene-related data? www.sanger.ac.uk/Projects/D_rerio • finding homologues in other species • in EnsEMBL: ‘Orthologue Prediction’ • in EnsEMBL: Compara tracks with sequence comparison

42. 3. How do I find gene-related data ? www.sanger.ac.uk/Projects/D_rerio • genomic context • in EnsEMBL and Vega: ContigView pages • with SNPs, affymetrix mapping, translated-BLAT comparisons to other species

43. 3. How do I find gene-related data ? www.sanger.ac.uk/Projects/D_rerio • physical map (FPC database) • mapping information, start with one clone and browse

44. 3. How do I find gene-related data ? www.sanger.ac.uk/Projects/D_rerio • ordering clones • help on ‘frequently asked questions’ page • can also be found on library details page (mapping)

45. 3. How do I find gene-related data ? Where do I find approved nomenclature ?

46. 3. How do I find gene-related data ? Where do I find approved nomenclature ?

47. 3. How do I find gene-related data ? How might I infer gene function ?

48. 3. How do I find gene-related data ? How might I infer gene function ?

49. 3. How do I find gene-related data ? How might I infer gene function ?

50. 3. How do I find gene-related data ? How might I infer gene function ?