Peter Tsai, Bioinformatics Institute

 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, CpG islands, assembly gaps and coverage, chromosomal bands, mouse homologies, and more)  The Genome Browser stacks annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information.

 Simple search  Understanding displays  Get details and the actual sequence data  Table Browser & Custom tracks  Cancer Browser

EXAMPLES

 Simple search  Understanding displays  Get details and the actual sequence data  Table Browser & Custom tracks  Cancer Browser

Scale UCSC genes RefSeq genes mRNA & EST Species comparison Single species comparison SNPs & repeats Exon 5’ UTR3’ UTR A gene in UCSC

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

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

Remember to click refresh Change 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)

 Simple search  Understanding displays  Get details and the actual sequence data  Table Browser & Custom tracks  Cancer Browser

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

General description

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

Catalogues of somatic mutation in cancer

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

 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

Export somatic mutations to UCSC

 Simple search  Understanding displays  Get details and the actual sequence data  Table Browser & Custom tracks  Cancer Browser

 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