1. Spring 2006, v7 Copyright OpenHelix. No use or reproduction without express written consent 1 The UCSC Genome Browser Search, retrieve and display the data that you want UCSC Genome Browser Training Spring 2006 Part 1 Materials developed by: Warren C. Lathe, Ph.D. Mary Mangan, Ph.D.

2. Copyright OpenHelix. No use or reproduction without express written consent2 UCSC Genome Browser credits Led by David Haussler and Jim Kent Dozens of staff and students also work to bring you this software and data Development team: http://genome.ucsc.edu/staff.html http://genome.ucsc.edu/goldenPath/credits.html Funding, data sources, external contributors

3. Copyright OpenHelix. No use or reproduction without express written consent3 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 Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks Hands-on session for Sorter, Table Browser, and Custom Tracks

4. Copyright OpenHelix. No use or reproduction without express written consent4 The UCSC Home page: genome.ucsc.edu navigate General information Specific information— new features, current status, etc.

5. Copyright OpenHelix. No use or reproduction without express written consent5 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: chr11:1038475-1075482 Keywords: kinase, receptor IDs: NP, NM, OMIM, and more… See lower part of page for help with format

6. Copyright OpenHelix. No use or reproduction without express written consent6 The Genome Browser Gateway start page choices, February 2005 Make your Gateway choices: 1. Select Clade 2. Select species: search 1 species at a time 3. Assembly: the official backbone DNA sequence 4. Position: location in the genome to examine 5. Image width: how many pixels in display window; 5000 max 6. Configure: make fonts bigger + other choices 1 2 4 3 5 6

7. Copyright OpenHelix. No use or reproduction without express written consent7 The Genome Browser Gateway sample search for Human BRCA1 Sample search: human, May 2004 assembly, BRCA1 Often you will have to select the right gene from a results list Sometimes, you will go directly to a browser image (use an ID) AF005068, breast cancer 1, early onset select

8. Copyright OpenHelix. No use or reproduction without express written consent8 Overview of the whole Genome Browser page (first day, new human release) } Genome viewer section Track and image controls (day 1 = 40 tracks)

9. Copyright OpenHelix. No use or reproduction without express written consent9 Overview of the whole Genome Browser page (mature release) } Genome viewer section mRNA and EST Tracks Expression and Regulation Comparative Genomics ENCODE Tracks Variation and Repeats Groups of data Mapping and Sequencing Tracks Genes and Gene Prediction Tracks

10. Copyright OpenHelix. No use or reproduction without express written consent10 Different species, different tracks, same software

11. Copyright OpenHelix. No use or reproduction without express written consent11 Sample Genome Viewer image, BRCA1 region Genome backbone STS markers Known genes RefSeq genes Gene predictions GenBank mRNAs repeats GenBank ESTs conservation SNPs MGC clones

12. Copyright OpenHelix. No use or reproduction without express written consent12 Visual Cues on the Genome Browser 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 Tick marks; a single location (STS, SNP) Intron, and direction of transcription >> < exon < < << < ex 5' UTR3' UTR For some tracks, the height of a bar is increased likelihood of an evolutionary relationship

13. Copyright OpenHelix. No use or reproduction without express written consent13 Options for changing the images: upper section Change your view with controls at the top Use “base” to get right down to the nucleotides Configure: to change font, window size, more… Specify a position fonts, window, more Walk left or right Zoom in Zoom out click to zoom 3x and re-center

14. Copyright OpenHelix. No use or reproduction without express written consent14 Annotation Track display options Some data is ON or OFF by default Links to details and/or filters Menu links to info about the tracks: content, methods You change the view with pulldown menus enforce changes After making changes, REFRESH to enforce the change Change track view

15. Copyright OpenHelix. No use or reproduction without express written consent15 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

16. Copyright OpenHelix. No use or reproduction without express written consent16 Reset, Hide, Configure or Refresh to change settings You control the view Use pulldown menus Configure options page reset, back to defaults to start from scratch enforce the changes (hide, full, squish…)

17. Copyright OpenHelix. No use or reproduction without express written consent17 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

18. Copyright OpenHelix. No use or reproduction without express written consent18 Clicking an annotation line, new page of detailed information You will get detail for that single item you click Example: click on the BRCA1 Black “Known Genes” line Click the line New web page opens Many details and links to more data about BRCA1

19. Copyright OpenHelix. No use or reproduction without express written consent19 Click annotation track = BRCA1 “Known gene” detail page informative description other resource links microarray data mRNA secondary structure links to sequences protein domains/structure homologs in other species Gene Ontology™ descriptions mRNA descriptions pathways Not all genes have This much detail. Different annotation tracks carry different detail data. SNP detail page sample

20. Copyright OpenHelix. No use or reproduction without express written consent20 Getting the sequences Get DNA, with Extended Options; or Details pages Use the DNA link at the top Plain or Extended options Change colors, fonts, etc.

21. Copyright OpenHelix. No use or reproduction without express written consent21 Genomic (many options) mRNA Protein Getting the sequences Another way: from details pages Click a track, go to Sequence section of details page Click the line

22. Copyright OpenHelix. No use or reproduction without express written consent22 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 Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks Hands-on session for Sorter, Table Browser, and Custom Tracks

23. Copyright OpenHelix. No use or reproduction without express written consent23 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)

24. Copyright OpenHelix. No use or reproduction without express written consent24 In Silico PCR: results Genomic location shown, links to Genome Viewer locationyour primers Your primers displayed, flipped if necessary Predicted genomic sequence shown Tm for primers Primer melting temperatures provided size Product size shown

25. Copyright OpenHelix. No use or reproduction without express written consent25 Proteome Browser Access from homepage or Known Gene pages Exon diagram, amino acids Many protein properties (pI, mw, composition, 3D…) more protein data

26. Copyright OpenHelix. No use or reproduction without express written consent26 Gene Sorter Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser Hands-on session for Basic Searches Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks Table Browser Searches User-generated Data Externally Generated Data Hands-on session for Sorter, Table Browser, and Custom Tracks

27. Copyright OpenHelix. No use or reproduction without express written consent27 Gene Sorter From homepage select ‘Gene sorter’

28. Copyright OpenHelix. No use or reproduction without express written consent28 Gene Sorter interface Sorts genes by several criteria

29. Copyright OpenHelix. No use or reproduction without express written consent29 Choose genome Choose assembly Type in gene name or accession # Gene Sorter interface

30. Copyright OpenHelix. No use or reproduction without express written consent30 Gene Sorter interface Choose from 11 sorting options

31. Copyright OpenHelix. No use or reproduction without express written consent31 Gene Sorter interface Configure display view

32. Copyright OpenHelix. No use or reproduction without express written consent32 Gene Sorter interface Filter data by different criteria

33. Copyright OpenHelix. No use or reproduction without express written consent33 Gene Sorter results

34. Copyright OpenHelix. No use or reproduction without express written consent34 Gene Sorter results Obtain file of gene sequences or tab-delineated file of data

35. Copyright OpenHelix. No use or reproduction without express written consent35 Table Browser Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser Hands-on session for Basic Searches Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks Table Browser Searches User-generated Data Externally Generated Data Hands-on session for Sorter, Table Browser, and Custom Tracks

36. Copyright OpenHelix. No use or reproduction without express written consent36 The Table Browser Task: Download sequence of all simple repeats of copy number more than 10 from a position on chromosome 4.

37. Copyright OpenHelix. No use or reproduction without express written consent37 The Table Browser From the Genome Browser home page, select Table Browser

38. Copyright OpenHelix. No use or reproduction without express written consent38 Table browser: choose genome Choose genome and assembly

39. Copyright OpenHelix. No use or reproduction without express written consent39 Table browser: choose table to search Data tables are organized by group & annotation track.

40. Copyright OpenHelix. No use or reproduction without express written consent40 Table browser: choose region to search Choose entire genome, ENCODE regions, enter a single position or alternatively paste or upload a file of positions.

41. Copyright OpenHelix. No use or reproduction without express written consent41 Table browser: filter to refine search Filter is a form based sql query. Filters can be created for primary table and for related tables

42. Copyright OpenHelix. No use or reproduction without express written consent42 Table browser: Output formats Get fields of table data

43. Copyright OpenHelix. No use or reproduction without express written consent43 Table browser: Output formats Fasta file of sequence data

44. Copyright OpenHelix. No use or reproduction without express written consent44 Table browser: Output formats GTF or BED formated file

45. Copyright OpenHelix. No use or reproduction without express written consent45 Table browser: Output formats Custom track

46. Copyright OpenHelix. No use or reproduction without express written consent46 Table browser: Obtaining output Output as file or in browser. Also, obtain statistics. Adding name creates file on desktop, leaving blank creates output in browser. (exception: custom track) Obtain a summary of specified data

47. Copyright OpenHelix. No use or reproduction without express written consent47 Table browser: Output configuration

48. Copyright OpenHelix. No use or reproduction without express written consent48 The Table Browser Task: Find simple repeats (copy number > 10) within known genes and download the sequence.

49. Copyright OpenHelix. No use or reproduction without express written consent49 Table browser: Intersecting data Intersect table with another table of data

50. Copyright OpenHelix. No use or reproduction without express written consent50 Table browser: Intersecting data Filtered simple repeats Filtered simple repeats, intersected (overlapping) w/ known genes Obtaining summary shows how intersecting narrowed search

51. Copyright OpenHelix. No use or reproduction without express written consent51 Table browser: Intersecting data

52. Copyright OpenHelix. No use or reproduction without express written consent52 Table browser: Correlating data

53. Copyright OpenHelix. No use or reproduction without express written consent53 Custom Tracks Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser Hands-on session for Basic Searches Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks Table Browser Searches User-generated Data Externally Generated Data Hands-on session for Sorter, Table Browser, and Custom Tracks

54. Copyright OpenHelix. No use or reproduction without express written consent54 Custom Tracks: Table browser searches

55. Copyright OpenHelix. No use or reproduction without express written consent55 Custom Tracks: Table browser searches

56. Copyright OpenHelix. No use or reproduction without express written consent56 Custom Tracks: Table browser searches Custom Tracks can be viewed in the Genome Browser

57. Copyright OpenHelix. No use or reproduction without express written consent57 Custom Tracks: Table browser searches Custom tracks also are available for filtering and intersections on the Table Browser.

58. Copyright OpenHelix. No use or reproduction without express written consent58 Intersecting previously created custom track finds one simple repeat with copy number >10 in known genes that also overlaps a CpG island. Custom Tracks: Table browser searches

59. Copyright OpenHelix. No use or reproduction without express written consent59 Custom Tracks: Table browser searches Intersecting custom tracks with available data (or other custom tracks) can be a powerful discovery tool.

60. Copyright OpenHelix. No use or reproduction without express written consent60 Custom Tracks Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser Hands-on session for Basic Searches Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks Table Browser Searches User-generated Data Externally Generated Data Hands-on session for Sorter, Table Browser, and Custom Tracks

61. Copyright OpenHelix. No use or reproduction without express written consent61 Custom Tracks: User-generated Data

62. Copyright OpenHelix. No use or reproduction without express written consent62 Custom Tracks: User-generated Data

63. Copyright OpenHelix. No use or reproduction without express written consent63 Custom Tracks: User-generated Data Four steps in creating a custom annotation track Format your data Define Genome Browser characteristics Define annotation track characteristics Upload and view your track

64. Copyright OpenHelix. No use or reproduction without express written consent64 Custom Tracks: Format your Data Format Your Data (step 1) GFF GTF PSL BED WIG Browser Extensible Data chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512 chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601

65. Copyright OpenHelix. No use or reproduction without express written consent65 Custom Tracks: Format your Data Bed Extensible Data chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512 chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601 StartChromosomeEndNameScoreStrand Thick start Thick end ColorBlocks Block Sizes Block starts

66. Copyright OpenHelix. No use or reproduction without express written consent66 Custom Tracks: User-generated Data Define Genome Browser Characteristics (step 2) chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512 chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601 browser position chr22:1000-10000 browser pix 620 browser hide all browser full gap Default position Default image width Default track view

67. Copyright OpenHelix. No use or reproduction without express written consent67 Custom Tracks: User-generated Data Define Track Characteristics (step 3) chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512 chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601 browser position chr22:1000-10000 browser pix 620 browser full gap track name=pairedReads description="Clone Paired Reads" visibility=3 color=0,128,0 useScore=1 Default track visibility 0=hide 1=dense 2=full 3=pack 4=squish Default track color Score on (1) or off (0)

68. Copyright OpenHelix. No use or reproduction without express written consent68 Custom Tracks: User-generated Data Upload and View your Track (step 4)

69. Copyright OpenHelix. No use or reproduction without express written consent69 Custom Tracks: User-generated Data

70. Copyright OpenHelix. No use or reproduction without express written consent70 Custom Tracks: User-generated Data

71. Copyright OpenHelix. No use or reproduction without express written consent71 Custom Tracks: User-generated Data

72. Copyright OpenHelix. No use or reproduction without express written consent72 Custom Tracks: User-generated Data

73. Copyright OpenHelix. No use or reproduction without express written consent73 Custom Tracks: User-generated Data

74. Copyright OpenHelix. No use or reproduction without express written consent74 Custom Tracks Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser Hands-on session for Basic Searches Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks Table Browser Searches User-generated Data Externally Generated Data Hands-on session for Sorter, Table Browser, and Custom Tracks

75. Copyright OpenHelix. No use or reproduction without express written consent75 Custom Tracks from Outside Sources Custom tracks list shared by the community

76. Copyright OpenHelix. No use or reproduction without express written consent76 References for the UCSC Genome Browser General Browser topics: Hinrichs, A.S. et. al (2006). The UCSC Genome Browser Database: update 2006:. Nucl. Acids Res. 34(Database issue), D590-8. Kent, W.J., Sugnet, C. W., Furey, T. S., Roskin, K.M., Pringle, T. H., Zahler, A. M., and Haussler, D. (2002). The Human Genome Browser at UCSC. Genome Res. 12:996-1006. Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T., Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J., Weber, R.J., Haussler, D. and Kent, W.J. (2003). The UCSC Genome Browser Database. Nucl. Acids Res 31:51-54. BLAT: Kent, W.J. (2002). BLAT - The BLAST-Likse Alignment Tool. Genome Res. 12:656-664. Table Browser: Karolchik, D., Hinrichs, A.S., Furey, T.S., Roskin, K.M., Sugnet, C.W., Haussler, D. and Kent, W.J. (2004). The UCSC Table Browser data retrieval tool. Nucleic Acids Research, 2004, Vol. 32, Database issue D493-D496.

77. Copyright OpenHelix. No use or reproduction without express written consent77 Join the mailing list!

78. Copyright OpenHelix. No use or reproduction without express written consent78 Additional Materials available: www.openhelix.com UCSC sponsored material at www.openhelix.com/ucscmaterials.shtml Frequently updated training presentation and exercises Self-run tutorial Quick Reference Cards Tutorials and web seminars on a number of other tools Additional sponsored bioinformatics tools coming soon