Merged genome coordinates pertaining to probes that detected the same copy number abnormality to
create larger contiguous intervals of unstable regions. Used Galaxy tools to determine stable regions and
coding genes associated with each stable or unstable region.
Galaxy file: (insert)
Dataset
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Dataset Description
Uploaded CCDS gene track from UCSC table browser
(coding consensus genes)
Uploaded frequently deleted probes (data from Hicks et
al., supplementary file)
Uploaded frequently amplified probes (data from Hicks et
al., supplementary file)
Compared the amplified/deleted probe sets --> probes
that were similar to both sets
Compared the amplified/deleted probe sets --> probes
that are unique to amplified set
Compared the amplified/deleted probe sets --> probes
that are unique to deleted set
Uploaded file that numerically ordered probe Ids and
annotated each by: del, amp, or both
Uploaded file containing clustered coordinates of the
probes that belonged to detecting the same copy number
abnormality - i.e. Coordinates of unstable regions
Complemented the unstable regions to derive genomic
coordinates of stable regions
Intersected CCDS genes and unstable regions to get -->
coding genes in unstable regions
Intersected CCDS genes and stable regions to get -->
coding genes in stable regions
Determined level of coverage for each coding gene in
stable region (percentage of coverage is in column 8 of
table)
Built custom track to display unstable regions in UCSC
Genome Browser
Built custom track to display stable regions in UCSC
Genome Browser
Uploaded genomic coordinates of clustered intervals
based on probes that detected amplifications
Uploaded genomic coordinates of clustered intervals
based on probes that detected both amplifications and
deletions
Uploaded genomic coordinates of clustered intervals
based on probes that detected deletions
Intersected coding genes and amplified regions
Intersected coding genes and deleted regions
Intersected coding genes and both deleted/amplified
regions
Uploaded file containing coding genes that are 100%
covered by stable genomic regions
Uploaded 812 stable regions
Built custom track for UCSC Genome Browser based on
stable region coordinates
Galaxy Tool
UCSC Main Table Browser:
knownGene (genome)
Upload File
Upload File
Compare two Queries on data 2
and data 3
Compare two Queries on data 2
and data 3
Compare two Queries on data 2
and data 3
Upload File
Upload File
Complement on data 8
Intersect on data 1 and data 8
Intersect on data 1 and data 9
Coverage on data 9 and data 11
Build custom track on data 8
Upload File
Upload File
Upload File
Upload File
Intersect on data 1 and data 15
Intersect on data 1 and data 17
Intersect on data 1 and data 16
Upload File
Upload File
Build custom track on data 22