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The UCSC Genome Browser

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  1. The UCSC Genome Browser Peter Tsai, Bioinformatics Institute

  2. UCSC Genome Browser • University of California, Santa Cruz (UCSC) • A rapid and reliable display of any requested portion of genomes at any scale, together with dozens of aligned annotation tracks (known genes, predicted genes, ESTs, mRNAs, CpGislands, assemblygaps and coverage, chromosomal bands, mousehomologies, and more) • The Genome Browser stacks annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information.

  3. Overview • Simple search • Understanding displays • Get details and the actual sequence data • Table Browser & Custom tracks • Cancer Browser

  4. UCSC Homepage: http://genome.ucsc.edu

  5. A simple search EXAMPLES

  6. Basic search interface

  7. Search example: GPR87

  8. Overview • Simple search • Understanding displays • Get details and the actual sequence data • Table Browser & Custom tracks • Cancer Browser

  9. Genome viewer Scale UCSC genes RefSeq genes mRNA & EST Species comparison Single species comparison SNPs & repeats A gene in UCSC Exon Exon Exon 3’ UTR 5’ UTR

  10. Genome viewer Groups of data (Tracks) Mapping and Sequencing Tracks Phenotype and Disease Associations Genes and Gene Prediction Tracks mRNA and EST Tracks Expression Regulation Comparative Genomics Variation and Repeats

  11. navigate Zoom • Top navigation panel • “Base” zoom straight to nucleotide level • Re-arrange tracks by dragging it up or down

  12. Remember to click refresh Change track view

  13. Different types of track view • Hide – remove a track from view • Dense – Collapse all genes into a single line • Squish – each gene in separate line (50% height) • Pack - each gene in separate line (100% height)

  14. Overview • Simple search • Understanding displays • Get details and the actual sequence data • Table Browser & Custom tracks • Cancer Browser

  15. The human mRNA and spliced EST tracks show the nested gene structure of this region

  16. General description

  17. HGNC – HUGO Gene Nomenclature Committee, only worldwide authority that assigns standardisednomenclature to human genes. • BioGPS - Gene annotation portal, a complete resource for learning about gene and protein function.

  18. HGNC Catalogues of somatic mutation in cancer

  19. BioGPS

  20. Overview • Simple search • Understanding displays • Get details and the actual sequence data • Table Browser & Custom tracks • Cancer Browser

  21. Table browser • Use this program to retrieve the data associated with a track in text format, to calculate intersections between tracks, and to retrieve DNA sequence covered by a track. • Particularly useful for exporting large amount of information associated with different annotations. • Great tutorial in UCSC genome browser if you are interested in exporting data.

  22. Custom tracks • Provide a way of linking between databases • Integrate GeneCard annotation • Integrate COSMIC annotation • Provide a way of integrating your own data with UCSC • Customised data

  23. Export somatic mutations to UCSC

  24. Overview • Simple search • Understanding displays • Get details and the actual sequence data • Table Browser & Custom tracks • Cancer Browser

  25. Cancer Genomic Browser

  26. Tutorial

  27. Summary • UCSC collects information from many different types of data from multiple databases. • Gateway to massive amount of information, include link-out to other publicly available databases. • Visualise, compare and extract data of interest. • “Custom tracks” allow you to compare data against other database and supports many different formats, more and more databases are now supplying links to display their data in UCSC