Independent datasets were used for determining stable and unstable regions (Chin et al.,) and stable and
unstable genes (Naderi et al.,) as a replication study. This Galaxy history includes analyses of deriving
stable regions, stable gene expression, as well as, common pathways, gene ontologies, and drugs
enriched by stable genes from the original analysis (based on datasets of Hicks et al., and Turashvili et
al.,).
Galaxy File:
Dataset
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Dataset Description
Uploaded frequently amplified regions from supplementary
file 3 (Chin et al.,)
Uploaded frequently deleted regions from supplementary
file 3 (Chin et al.,)
Uploaded stable regions (Hicks et al.,)
Uploaded clustered intervals of unstable regions (Chin et
al.,)
Complemented on unstable regions to derive genomic
coordinates of stable regions
Determined level of coverage between stable regions based
on Hicks and Chins data
Intersected stable regions (Chin et al.,) with that of stable
regions (Hicks et al.,) to derive genome coordinates of
overlapping stable intervals
Uploaded RefSeq genes that intersected with stable regions
based on Chin et al., dataset
All CCDS protein-coding genes that intersected with stable
regions based on Chin et al., dataset
Uploaded gene symbols of stable protein-coding genes
(removed duplicates only unique genes remain)
Uploaded platform of the array used for expression study
(Naderi et al.,)
Uploaded probes that detected significant over- and underexpression (top 10% of probes)
Joined the probe dataset with the platform dataset to
retrieve corresponding gene IDs to probe IDs
Genes that were not significantly changed in expression
levels based on gene expression study Naderi et al.,
Determined which protein-coding genes were stable in
copy-number as well as expression
Results of the pathway analysis were uploaded (stable
genes based on data by Chin et al.,)
Results of the pathway analysis were uploaded (stable
genes based on data by Hicks et al.,)
Joined results of both pathway analyses to determine
common pathways enriched by stable genes
Results of gene ontology analysis (DAVID) were uploaded
(stable genes based on data by Chin et al.,)
Results of gene ontology analysis (DAVID) were uploaded
(stable genes based on data by Hicks et al.,)
Joined results of both gene ontology analyses to determine
common functions enriched by stable genes
Results of drug target analysis were uploaded (stable genes
based on data by Hicks et al.,)
Galaxy Tool
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Complement on data 4
Coverage on data 3 and data 5
Intersect on data 3 and data 5
UCSC Main Table Browser:
refGene (genome)
UCSC Main Table Browser:
ccdsGene (genome)
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Join two Datasets on data 11
and data 12
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Join two Datasets on data 10
and data 14
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Join two Datasets on data 16
and data 17
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Join two Datasets on data 19
and data 20
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Uploaded list of stable genes (stable in copy number as well
as expression based on data by Chin and Naderi et al.,)
Determined which stable genes were targets of drugs based
on previous drug analysis (Hicks et al.,)
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Join two Datasets on data 22
and data 23