Genome Exploration with the UCSC Genome Browser Hiram

Genome Exploration with the UCSC Genome Browser Hiram Clawson UCSC Genome Browser Engineering 23 July 2008

U. C. Santa Cruz David Haussler Genome Browser Jim Group Kent

UCSC Genome Browser • • A set of tools, more than just the browser: Genome Browser -> viewing annotations Blat Server -> find sequence Table Browser -> intersections, correlations Gene Sorter -> gene centric viewpoint In Silico PCR -> determine primer products Genome Graphs, Galaxy, Visi. Gene, etc … 6, 500 users/day 200, 000 pages/day ~200 Gb/day

today’s procedure: • Genome browser tracks display • Track controls to view annotations • Table browser intersections 6, 000 custom tracks/day 20 Gb My. SQL data/day

see also: • copy of this presentation: genomewiki. ucsc. edu - search for “Presentations” • Open Helix training: genome. ucsc. edu/training. html • Galaxy analysis workflow management system: galaxy. psu. edu • “Genomes, Browsers and Databases”, a recent book by Peter Schattner Cambridge University Press • “Powers of Ten” video by Charles & Ray Eames, 1977 • Genome browser documentation: genome. ucsc. edu/golden. Path/help/ • email help: genome at soe. ucsc. edu

http: //genome. ucsc. edu/ http: //genome. brc. mcw. edu/

from top level page 1. Select genome: or

default tracks display:

hide all, base position

it is a map with zoom out toonly view one morehighway

hide all, base position How does one operate the genome browser ?

track options

larger display size larger font size useful navigation options configure

900 width, medium font readjust to base due to font size change

UCSC gene track next gene Ensembl gene track next exon track controls

1 X 100 X 1, 000 X 100, 000 X 1, 000 X full chr. X navigation

zoom in on target position full chr. X, zoom in 3 X, 9 X, 27 X

item click

a gene item details page

position/search

design your experiment Task: find highly conserved non-coding regions 1. Select highly conserved regions from conservation track limit line at y = 0. 2 filter phast. Cons 28 way score > 0. 2 2. Intersect with NOT exons 3. result

table browser

ensembl exons

gene tracks output options: exons output (the ‘name=‘ string should be unique from other custom tracks)

same settings, get introns

select output introns output

measure results

visualize results

conservation track

conservation track settings set both on 100 on 0. 2 press Submit when ready

larger graph, with limit line at 0. 2 Go to the table browser via blue bar “Tables”

table browser filter (test small area first) select greater than filter > 0. 2 size of answer set

create custom track

create intersections primary table

secondary table base pair AND function NOT exons

output intersection results NOT exons AND phast. Cons 28 way > 0. 2

and the answer is:

thank you Angie Hinrichs Matt Schwartz Terry Furey Chuck Sugnet Heather Trumbower Kayla Smith Brooke Rhead Ann Zweig Daryl Thomas Robert Baertsch Jakob Peterson Katherine Pollard Adam Siepel Rachel Harte Mark Diekhans Fan Hsu Bob Kuhn Andy Pohl Kate Rosenbloom Galt Barber Archana Thakkapallayil Ali Sultan-Qurraie Jennifer Jackson Krishna Roskin Andrew Kern Brian Raney Craig Lowe Yontao Lu Ryan Weber Todd Lowe Josh Stewart Gill Bejerano Donna Karolchik David Haussler Jim Kent

The End

full chr 19 results

GC Percent

creating an intersection AND =

select intersecting tables primary table secondary table

get intersection output

view results why does it look different ? adjust graph parameters

adjusted graph parameters

same procedure for introns