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The UCSC (University of California Santa Cruz) Genome Browser “the golden path” genome.ucsc.edu Stephen Baird Apoptosis Research Centre Children’s Hospital of Eastern Ontario [email protected] Lecture/Lab 7.2 1 Jim Kent • First assembly of the human genome as a graduate student with his program GigAssembler • Catalog of software includes: • blat - Fast alignment of similar sequences. • autoSql - create SQL and C code for permanently storing a structure in database and loading it back into memory based on a specification file • ameme - Find motifs in DNA sequence. • 40 other command line programs for genome browser • The Intronerator - to look at C. elegans genes and splicing patterns. • cis-Site Seeker - Look for regulatory regions in RNA or DNA sequences Lecture/Lab 7.2 2 UCSC Genome Gateway Structure Custom tracks Genome browser Table browser Your sequence BLAT Database in silico PCR Downloadable data files Lecture/Lab 7.2 Gene sorter Proteome browser Public MySQL server Your query 3 The UCSC Home page: genome.ucsc.edu navigate navigate Lecture/Lab 7.2 4 UCSC Genome Browser Gateway - start page, basic search Lecture/Lab 7.2 5 Lecture/Lab 7.2 6 } Genome viewer section Overview of the whole Genome Browser page Groups of data Mapping and Sequencing Tracks Genes and Gene Prediction Tracks mRNA and EST Tracks Expression and Regulation Comparative Genomics Variation and Repeats ENCODE Regions and Genes ENCODE Transcript Levels ENCODE Chromatin Immunoprecipitation, Chromosome, Chromatin and DNA Structure, Variation Lecture/Lab 7.2 7 Lecture/Lab 7.2 8 Configure Tracks – Spliced ESTs, Microarray Expression, Repeats, etc Lecture/Lab 7.2 9 Known Genes Spliced ESTs By UCSC Simple Repeats Lecture/Lab 7.2 10 Gene Description Links to Tools/DBs UniProt Description Links to output Sequence “Known Gene” Details page for Clock gene Microarray data mRNA secondary structure Protein domains/structure Homologs Gene Ontology ™ (GO) mRNA descriptions Lecture/Lab 7.2 pathways 11 Proteome Browser Genome Browser Superfamily Domin Db Lecture/Lab 7.2 12 Genome Gateway Help/User’s Guide Lecture/Lab 7.2 13 BLAT – Blast Like Alignment Tool Lecture/Lab 7.2 14 In Silico PCR Lecture/Lab 7.2 15 “Gene Sorter” and “Table Browser” • Query database by filtering and cross references all of the data tables of the database to output sequence, genomic positions or text data. • What are in all the tables? – genome.ucsc.edu/goldenPath/gbdDescriptions.html Lecture/Lab 7.2 16 Gene Sorter • “display a sorted table of genes that are related to one another” • EXAMPLE 1: Make a list of genes of membrane proteins that are highly expressed in pancreatic islet cells to possibly explore the role of autoimmunity in Type 1 Diabetes. Lecture/Lab 7.2 17 Gene Sorter - Configure Lecture/Lab 7.2 18 Gene Sorter - Filter Lecture/Lab 7.2 19 Gene Sorter - Output Sequence- genomic, protein or mRNA Lecture/Lab 7.2 Text – Tab delimited 20 Gene Sorter - To Try Now • EXAMPLE 2: Find genes expressed predominately in the mouse adrenal gland that have human ‘homologs’. Get the sequence data and examine the expression of the human orthologs. • Enter any gene to start. • In configure menu: (a) Expand tissue selection of GNF Atlas 2 to “median of replicas”, (b) click on human homologs • In filter menu: (a) set adrenal gland minimum box to 2.5, (b) look at results and set maximum box of other commonly expressed tissues to 0.5 • Complete solution in notes 7.2 UCSC. Lecture/Lab 7.2 21 Table Browser Groups as in Browser Tracks within Group Filter fields in Table and connecting Tables Intersect non-connecting Tables by position RESET! Lecture/Lab 7.2 22 Table Browser – table schema Lecture/Lab 7.2 23 Table Browser – Example • EXAMPLE 3: Find CpG islands in known genes on the last part of chromosome 22 of the human genome. Obtain the genes sequences as one fasta record per region. Change to Lecture/Lab 7.2 24 Table Browser – CpG Example Click on ‘intersection’ Lecture/Lab 7.2 Set group for ‘Expression and Regulation’ and track for ‘CpG’ Islands 25 Table Browser – CpG Example Lecture/Lab 7.2 26 Table Browser – CpG Example Copy and paste sequences or Set up an ‘output file’ in the Table Browser Lecture/Lab 7.2 27 Table Browser – Example To Try • EXAMPLE 4: Find trinucleotide repeats of more than 10 copies within mRNA sequence on human chromosome 4. How many are there? How many are linked to known disease genes? • Hints • Period = 3, copies > 10. • Intersect tables and custom track. • Tables: knownGene, simpleRepeats, spDisease Lecture/Lab 7.2 28 VisiGene -in situ mRNA and protein images in mice and frogs Lecture/Lab 7.2 29 Data Downloads ... - from download link on homepage Lecture/Lab 7.2 30 Example: simpleRepeats table Lecture/Lab 7.2 31 Public MySQL Server See the Data and Downloads FAQ: Direct MySQL access to data http://genome.ucsc.edu/FAQ/FAQdownloads#download29 Command from local MySQL client: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A Lecture/Lab 7.2 32