The UCSC Genome Browser
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1 The UCSC Genome Browser Search, retrieve and display the data that you want Materials prepared by Warren C. Lathe, Ph.D. Mary Mangan, Ph.D. Updated: Q Version_0906 Copyright OpenHelix. No use or reproduction without express written consent 1
2 DNA sequencing evolution techniques automation DATA Copyright OpenHelix. No use or reproduction without express written consent 2
3 Copyright OpenHelix. No use or reproduction without express written consent 3
4 Genome sequencing projects statistics: jan 2007 Organism Complete Draft In progress total Prokaryotes Archaea Bacteria Eukaryotes Animals Mammals Birds Fish Insects Flatworms 3 3 Roundworms Amphibians 1 1 Reptiles 0 Other animals Plants Land plants Green Algae 6 6 Fungi Ascomycetes Basidiomycetes Other fungi Protists Apicomplexans Kinetoplasts Other protists total: Copyright OpenHelix. No use or reproduction without express written consent 4
5 Genome information: more than sequences alone Genome structure: chromosomes? Annotation!! Sequence properties (GC content, folding, repeats ) Protein coding, introns, exons Gene functions Signal sequences, promotors etc Variable positions Comparisons Conservation between species? Links to other sources Literature Proteinstructure In situ experiments ect Copyright OpenHelix. No use or reproduction without express written consent 5
6 Genome Browsers Databases accessible through internet containing data, linking data internally and externally to other databases Filtering data Displaying data Retrieving data Ensembl: EMBL-EBI & Sanger center VISTA: Berkeley, Standford, Davis UCSC: University of California Santa Cruz Copyright OpenHelix. No use or reproduction without express written consent 6
7 Genome Browsing Explore chromosomal regions Look at features in and around specific genes Search and retrieve from whole genomes Investigate genome organization Compare to other genomes Link to other data sources Project your own data against what s known.. Copyright OpenHelix. No use or reproduction without express written consent 7
8 UCSC Genome Browser Agenda Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser, VisiGene Hands-on session for Basic Searches Gene Sorter Table Browser Custom Tracks Hands-on session for Sorter, Table Browser, and Custom Tracks UCSC Genome Browser: Mirror: Copyright OpenHelix. No use or reproduction without express written consent 8
9 The UCSC Home page: genome.ucsc.edu navigate navigate General information Specific information new features, current status, etc. Copyright OpenHelix. No use or reproduction without express written consent 9
10 The Genome Browser Gateway start page, basic search text/id searches Helpful search examples, suggestions below Use this Gateway to search by: Gene names, symbols Chromosome number: chr7, or region: chr11: Keywords: kinase, receptor IDs: NP, NM, OMIM, and more See lower part of page for help with format Copyright OpenHelix. No use or reproduction without express written consent 10
11 The Genome Browser Gateway start page choices, July Make your Gateway choices: Select Clade Select species: search 1 species at a time Assembly: the official backbone DNA sequence Position: location in the genome to examine Image width: how many pixels in display window; 5000 max Configure: make fonts bigger + other choices Copyright OpenHelix. No use or reproduction without express written consent 11
12 The Genome Browser Gateway sample search for Human TP53 Sample search: human, March 2006 assembly, tp53 select Select from results list ID search may go right to a viewer page, if unique Copyright OpenHelix. No use or reproduction without express written consent 12
13 Overview of the whole Genome Browser page (mature release) }Genome viewer section 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 Tracks Copyright OpenHelix. No use or reproduction without express written consent 13
14 Different species, different tracks, same software Species may have different data tracks Layout, software, functions the same Copyright OpenHelix. No use or reproduction without express written consent 14
15 Sample Genome Viewer image, TP53 region base position STS markers Known genes RefSeq genes GenBank seqs 17 species compared single species compared SNPs repeats Copyright OpenHelix. No use or reproduction without express written consent 15
16 Visual Cues on the Genome Browser Tick marks; a single location (STS, SNP) 3' UTR exon < < < exon < exon < < < <ex 5' UTR Intron, and direction of transcription <<< or >>> Track colors may have meaning for example, Known Gene track: If there is a corresponding PDB entry, = black If there is a corresponding NCBI Reviewed seq, = dark blue If there is a corresponding NCBI Provisional seq, = light blue For some tracks, the height of a bar is increased likelihood of an evolutionary relationship (conservation track) Copyright OpenHelix. No use or reproduction without express written consent 16
17 Options for changing the images: upper section Walk left or right Zoom in Zoom out click to zoom 3x and re-center Specify a position Change your view or location with controls at the top Use base to get right down to the nucleotides Configure: to change font, window size, more fonts, window, more Copyright OpenHelix. No use or reproduction without express written consent 17
18 Annotation Track display options enforce changes Links to info and/or filters Some data is ON or OFF by default Menu links to info about the tracks: content, methods You change the view with pulldown menus Change track view After making changes, REFRESH to enforce the change Copyright OpenHelix. No use or reproduction without express written consent 18
19 Annotation Track options, defined Hide: removes a track from view Dense: all items collapsed into a single line Squish: each item = separate line, but 50% height + packed Pack: each item separate, but efficiently stacked (full height) Full: each item on separate line Copyright OpenHelix. No use or reproduction without express written consent 19
20 Reset, Hide, Configure or Refresh to change settings enforce any changes (hide, full, squish ) reset, back to defaults start from scratch You control the views Use pulldown menus Configure options page Copyright OpenHelix. No use or reproduction without express written consent 20
21 Annotation Track options, if altered. important point: the browser remembers! Session information (the position you were examining) Track choices (squish, pack, full, etc) Filter parameters (if you changed the colors of any items, or the subset to be displayed) are all saved on your computer. When you come back in a couple of days to use it again, these will still be set. You may or may not intend this. To clear your cart or parameters, click default tracks OR Copyright OpenHelix. No use or reproduction without express written consent 21
22 Click Any Viewer Object for Details New web page opens Click the item Example: click your mouse anywhere on the TP53 line Many details and links to more data about TP53 Copyright OpenHelix. No use or reproduction without express written consent 22
23 informative description other resource links links to sequences Click annotation track item for details pages Not all genes have This much detail. microarray data Different annotation tracks carry different data. mrna secondary structure protein domains/structure homologs in other species Gene Ontology descriptions mrna descriptions pathways Copyright OpenHelix. No use or reproduction without express written consent 23
24 Get DNA, with Extended Case/Color Options Use the DNA link at the top Plain or Extended options Change colors, fonts, etc. Copyright OpenHelix. No use or reproduction without express written consent 24
25 Get Sequence from Details Pages Click a track, go to Sequence section of details page Click the line Click the item sequence section on detail page Copyright OpenHelix. No use or reproduction without express written consent 25
26 UCSC Genome Browser Agenda Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser, VisiGene Hands-on session for Basic Searches Gene Sorter Table Browser Custom Tracks Hands-on session for Sorter, Table Browser, and Custom Tracks UCSC Genome Browser: Copyright OpenHelix. No use or reproduction without express written consent 26
27 Accessing the BLAT tool BLAT = BLAST-like Alignment Tool Rapid searches by INDEXING the entire genome Works best with high similarity matches See documentation and publication for details Kent, WJ. Genome Res :656 Copyright OpenHelix. No use or reproduction without express written consent 27
28 BLAT tool overview: Make choices Paste one or more sequences DNA limit bases Protein limit aa 25 total sequences submit Or upload Copyright OpenHelix. No use or reproduction without express written consent 28
29 BLAT results, with links go to browser/viewer go to alignment detail sorting Results with demo sequences, settings default; sort = Query, Score Score is a count of matches higher number, better match Click browser to go to Genome Browser image location (next slide) Click details to see the alignment to genomic sequence (2 nd slide) Copyright OpenHelix. No use or reproduction without express written consent 29
30 BLAT results, browser link click to flip frame query From browser click in BLAT results A new line with your Sequence from BLAT Search appears! Watch out for reading frame! Click > to flip frame Base position = full and zoomed in enough to see amino acids Copyright OpenHelix. No use or reproduction without express written consent 30
31 BLAT results, alignment details Your query Genomic match, color cues Side-by-side alignment yours genomic Copyright OpenHelix. No use or reproduction without express written consent 31
32 UCSC Genome Browser Agenda Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser, VisiGene Hands-on session for Basic Searches Gene Sorter Table Browser Custom Tracks Hands-on session for Sorter, Table Browser, and Custom Tracks UCSC Genome Browser: Copyright OpenHelix. No use or reproduction without express written consent 32
33 In Silico PCR: find genomic sequence using primers Select genome Enter primers Minimum 15 bases Flip reverse primer? Submit (note: the tool does not handle ambiguous bases at this time don t use Ns) Copyright OpenHelix. No use or reproduction without express written consent 33
34 In Silico PCR: results location size your primers Tm for primers Genomic location shown, links to Genome Viewer Product size shown Your primers displayed, flipped if necessary Predicted genomic sequence shown Primer melting temperatures provided Copyright OpenHelix. No use or reproduction without express written consent 34
35 Proteome Browser Access from homepage or Known Gene pages Exon diagram, amino acids Many protein properties (pi, mw, composition, 3D ) more data Copyright OpenHelix. No use or reproduction without express written consent 35
36 VisiGene Image Browser VisiGene: Biological image data Expression in cells and tissues; mrna or protein Search by symbol, author, body parts, IDs, stages Copyright OpenHelix. No use or reproduction without express written consent 36
37 UCSC Genome Browser Agenda Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser, VisiGene Hands-on session for Basic Searches Gene Sorter Table Browser Custom Tracks Hands-on session for Sorter, Table Browser, and Custom Tracks UCSC Genome Browser: Copyright OpenHelix. No use or reproduction without express written consent 37
38 Tutorial exercise 1) Find out if the mouse TP53 gene has a gene expression data available from the The Genomics Institute of the Novartis Research Foundation, or GNF. Click on a tissue to examine the results in more detail. Other exercises will be handed out to complete yourselves! Copyright OpenHelix. No use or reproduction without express written consent 38
39 Exercise 1: walkthrough 1 Go to the UCSC Genome Browser homepage, genome.ucsc.edu or a faster mirror at: 2 Enter the Gateway, by clicking the Genome Browser link from thehomepage. 3 Select Vertebrate as the clade, Mouse as the genome. Choose the most current assembly. 4 Enter the text tp53 in the text box. Click Submit. 5 From the results list, click a link that appears to be the real tp53. We will choose (AY212017, Cellular tumor antigen p53) for this example. It is the 3rd item on the list at this time. 6 From the Genome Viewer page, scroll to the Expression and Regulation group of track controls. Open the menu for the track for GNF U74A. Choose Full mode. 7 You must click Refresh to enforce this change to the viewer. 8 Look back up in the Genome Viewer for the extensive list of tissues now present in the viewer. 9 Click on any GNF U74A track to go to the details page for thisdata. 10 Examine the color codes for the data. Note that higher expression is on the red scale, lower expression is on the green scale. 11 Scroll down the page to the Methods section. The Methods section provides additional information about the source and display of the data in the browser. Note that the details for this data are found in a publication which is also listed on this page. 12 Use the back button to go back to the Genome Viewer. Special note: there are several different microarray data sets, and the sets vary by species. UCSC presents the data, but they do not generate the data. It is provided by other labs. Copyright OpenHelix. No use or reproduction without express written consent 39
40 BREAK! Copyright OpenHelix. No use or reproduction without express written consent 40
41 The UCSC Gene Sorter, Table Browser & Custom Tracks Advanced searching and discovery using the UCSC Table Browser and Custom Tracks Materials prepared by: Warren C Lathe, Ph.D. Updated: Q Spring Version 2006, 7_0606 v7 Copyright OpenHelix. No use or reproduction without express written consent 41
42 Table Browser and Custom Tracks Agenda Gene Sorter Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Summary Exercises UCSC Table Browser: Copyright OpenHelix. No use or reproduction without express written consent 42
43 Gene Sorter From homepage select Gene Sorter Copyright OpenHelix. No use or reproduction without express written consent 43
44 Gene Sorter: Chose Genome and Gene Choose Assembly Type in gene name Choose Genome or accession number Copyright OpenHelix. No use or reproduction without express written consent 44
45 Gene Sorter: Similarity Sorting Options Choose from several similarity sorting options, varies by assembly & species Copyright OpenHelix. No use or reproduction without express written consent 45
46 Gene Sorter: Filters List genes Filter Filter data of columns displayed or those not displayed List all genes found with selected filters Copyright OpenHelix. No use or reproduction without express written consent 46
47 Gene Sorter: Submit Filters Submit Copyright OpenHelix. No use or reproduction without express written consent 47
48 Gene Sorter: Get Results Go to results Copyright OpenHelix. No use or reproduction without express written consent 48
49 Gene Sorter: Results Description Re-sort Re-sort genes based on gene clicked using same parameters. Copyright OpenHelix. No use or reproduction without express written consent 49
50 Gene Sorter: Results VisiGene Open UCSC VisiGene image page for gene. Copyright OpenHelix. No use or reproduction without express written consent 50
51 Gene Sorter: Results Alignment Amino acid alignment between reference gene and gene protein products Copyright OpenHelix. No use or reproduction without express written consent 51
52 Gene Sorter: Results Open Genome Browser to location of chosen gene Browser Copyright OpenHelix. No use or reproduction without express written consent 52
53 Gene Sorter: Results Open gene details page of chosen gene Description Copyright OpenHelix. No use or reproduction without express written consent 53
54 Gene Sorter: Gene Sequences Sequences Get sequences Choose sequence type, obtain FASTA file of all gene sequences Copyright OpenHelix. No use or reproduction without express written consent 54
55 Gene Sorter: Text File of Data Data text Obtain tab-delineated file of all displayed gene data Copyright OpenHelix. No use or reproduction without express written consent 55
56 Table Browser and Custom Tracks Agenda Gene Sorter Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Summary Exercises UCSC Table Browser: Copyright OpenHelix. No use or reproduction without express written consent 56
57 The Table Browser Copyright OpenHelix. No use or reproduction without express written consent 57
58 Genome Browser Database visualize search & download Underlying Database (MySQL) Primary table: positions, names, etc. Auxiliary table: related data Copyright OpenHelix. No use or reproduction without express written consent 58
59 Table Browser and Custom Tracks Agenda Gene Sorter Table Browser Introduction Table Browser: Set up and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Summary Exercises UCSC Table Browser: Copyright OpenHelix. No use or reproduction without express written consent 59
60 The Table Browser Open browser Open browser Copyright OpenHelix. No use or reproduction without express written consent 60
61 Table Browser: Choose Genome Choose Genome In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence. Copyright OpenHelix. No use or reproduction without express written consent 61
62 Table Browser: Choose Table to Search Choose Data Table In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence. Copyright OpenHelix. No use or reproduction without express written consent 62
63 Table Browser: Describe Table Describe table Copyright OpenHelix. No use or reproduction without express written consent 63
64 Table Browser: Choose Region to Search Choose Region to Search In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence. Copyright OpenHelix. No use or reproduction without express written consent 64
65 Table Browser: Upload Locations to Search Paste Upload Copyright OpenHelix. No use or reproduction without express written consent 65
66 Table Browser: Filter to Refine Search Create Filter Submit Filter In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence. Copyright OpenHelix. No use or reproduction without express written consent 66
67 Table Browser: Output Data Output data In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence. Copyright OpenHelix. No use or reproduction without express written consent 67
68 Table Browser: Output Formats Output formats Text Fields Copyright OpenHelix. No use or reproduction without express written consent 68
69 Table Browser: Fasta Sequence Output Sequence Copyright OpenHelix. No use or reproduction without express written consent 69
70 Table Browser: Database Format Outputs Database Copyright OpenHelix. No use or reproduction without express written consent 70
71 Table Browser: Custom Track Output Custom Track Copyright OpenHelix. No use or reproduction without express written consent 71
72 Table Browser: Custom Track Output Hyperlinks Copyright OpenHelix. No use or reproduction without express written consent 72
73 Table Browser: Obtaining Output Adding name creates file on desktop, leaving blank creates output in browser. (exception: custom track) Data Summary Copyright OpenHelix. No use or reproduction without express written consent 73
74 Table Browser: Output configuration Sequence Format Get Sequence Copyright OpenHelix. No use or reproduction without express written consent 74
75 Table Browser Agenda Gene Sorter Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Summary Exercises UCSC Table Browser: Copyright OpenHelix. No use or reproduction without express written consent 75
76 Table Browser: Intersecting Data 2nd Table Any Overlap Intersect Submit Find simple repeats (copy number > 10) within known genes and download the sequence. Copyright OpenHelix. No use or reproduction without express written consent 76
77 Table Browser: Intersecting Data Narrows Search Filtered simple repeats Summary Filtered simple repeats, intersected (overlapping) w/ known genes Copyright OpenHelix. No use or reproduction without express written consent 77
78 Table Browser: Downloading Sequence Data Sequence Format Get Sequence Copyright OpenHelix. No use or reproduction without express written consent 78
79 Table Browser: Correlating Data Tables Get Results Correlate 2 Datasets Copyright OpenHelix. No use or reproduction without express written consent 79
80 Table Browser and Custom Tracks Agenda Gene Sorter Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Summary Exercises UCSC Table Browser: Copyright OpenHelix. No use or reproduction without express written consent 80
81 Custom Tracks: Table Browser Searches Create Track Get Output Copyright OpenHelix. No use or reproduction without express written consent 81
82 Custom Tracks: Name and Configure Track Name Track: SRepeatKGenes Describe Track: Intersection Choose default view in browser Download track file to desktop In Genome Browser Copyright OpenHelix. No use or reproduction without express written consent 82
83 Custom Tracks: Open Track in Genome Browser Open Details Compare caused by an expanded, unstable trinucleotide repeat Copyright OpenHelix. No use or reproduction without express written consent 83
84 Custom Tracks: Track in Table Browser Custom tracks also are available for filtering and intersections on the Table Browser Copyright OpenHelix. No use or reproduction without express written consent 84
85 Custom Tracks: User-generated Data in Track Custom Track How-to Custom Tracks Link Copyright OpenHelix. No use or reproduction without express written consent 85
86 Custom Tracks: Four Steps to Create Track Four steps to create a custom track Define track characteristics Define browser characteristics Format your data Upload and view your track Copyright OpenHelix. No use or reproduction without express written consent 86
87 Custom Tracks: Track Appears in Genome Browser Copyright OpenHelix. No use or reproduction without express written consent 87
88 Custom Tracks: Track Appears in Table Browser Custom Track also appears in Table Browser Copyright OpenHelix. No use or reproduction without express written consent 88
89 Custom Tracks from Outside Sources Contributed Track Custom Tracks Link Copyright OpenHelix. No use or reproduction without express written consent 89
90 Table Browser and Custom Tracks Agenda Gene Sorter Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Summary Exercises UCSC Table Browser: Copyright OpenHelix. No use or reproduction without express written consent 90
91 The Table Browser Open browser Open browser Copyright OpenHelix. No use or reproduction without express written consent 91
92 Table Browser: Advanced Searching Genomes Data Location Filter and Intersect Output Copyright OpenHelix. No use or reproduction without express written consent 92
93 Custom Tracks: Table Browser Searches Create Track Copyright OpenHelix. No use or reproduction without express written consent 93
94 Custom Tracks: User-generated Data in Track Custom Track How-to Custom Tracks Link Copyright OpenHelix. No use or reproduction without express written consent 94
95 Table Browser and Custom Tracks Agenda Gene Sorter Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Summary Exercises UCSC Table Browser: Copyright OpenHelix. No use or reproduction without express written consent 95
96 Exercise: gene sorting & table browser 1) Find genes that are predominately expressed in the mouse adrenal gland, determine the expression pattern of the human ortholog of one such gene and obtain the genomic sequence of the human gene. More exercises will be handed out for you to complete yourselves! Copyright OpenHelix. No use or reproduction without express written consent 96
97 Exercise 1: walkthrough 1 Go to the UCSC Genome Browser homepage, genome.ucsc.edu or a faster mirror at: 2 Enter the Gene Sorter, by clicking either of the Gene Sorter links from the homepage. 3 Select mouse as the species. Leave as August 2005 assembly 4 Enter a mouse gene (example: hoxa11) in the search box. 5 Sort by expression (GNF Atlas 2) 6 Click configure, leaving rest of default configuration, choose median of all replicas from the TISSUES pull down menu of Expression (GNF Atlas 2) and then 7 while still in configure menu, scroll down and click the checkbox for human ortholog. (If you wish, you can click on the up arrow of the human ortholog column till it is listed before GNF Atlas 2 column, for later ease of viewing, though this my take some time). Click submit. 8 Click the filter button and filter for genes highly expressed in the adrenal gland by putting 2.5 in the minimum box for the adrenal gland. (to obtain genes that are expressed in the adrenal gland to at least this level). Click submit. 9 The resulting browser page will show genes expressed in the adrenal gland (and other tissues as shown in red) 10 To narrow down the field to genes predominately expressed in the adrenal gland, click again on the filter button and add a maximum expression value (.5 is a good number) for the following tissues: frontal cortex, olfactory bulb, mammary gland, brown fat, and ovary. This will filter out these genes which are expressed in multiple tissues. Click submit. 11 The resulting page gives 12 genes expressed in the adrenal gland, you will notice that at least one of these genes is expressed predominately in the adrenal gland. (AK143928) is one strong possibility) 12 Click on the human ortholog name of the gene you ve chosen (hint: NM_053279) taking you to a choice between the Known Gene record or the RefSeq record. Choose the Known Gene record link which will take you to the genome graphical browser view. Find out more about this human ortholog now by clicking on the gene name in the known gene track. Two links will be of interest to you on this page: The Gene Sorter link under Quick Links to Tools and Databases heading and the sequence link under Human Gene C8orf13 Description and Page Index heading, clicking the former link will take you back to the Gene Sorter with the human ortholog as the entry. Here you can view the expression pattern. Clicking the latter sequence link will give you options to download the sequence of this gene (genomic, RNA, etc). Copyright OpenHelix. No use or reproduction without express written consent 97
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