Determined which drugs have targets that are encoded by genes in stable regions (for all breast cancer
drugs and comprehensive list of all drugs from DrugBank).
Galaxy File:
Dataset Dataset Description
Uploaded all drugs and drug targets from DrugBank
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database
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Uploaded all coding genes associated with stable regions
Compared drug targets of drugs with stable genes (which
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genes are similar between both sets)
Joined both drug data and stable gene data indexed by
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gene symbol, keeping all lines from both queries to retrieve
drug information of a stable drug target
Joined both drug data and stable gene data indexed by
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gene symbol, excluding rows that do not join to retrieve
drug information of a stable drug target
Uploaded all drugs and related diseases from PharmGKB
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database
Uploaded drug file that contained stable drug targets and
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drug (text in lower case)
Joined drug target file with PharmGKB drug relationship file
to retrieve more information about the drugs that are
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associated with stable drug targets (i.e. Pathways and
disease information)
Removed duplicates based on stable drug target, the drug
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target (gene name) and the drug. The result was 2,984
unique drugs targeting unique stable genes
Counted the number of occurrences of each drug - i.e.
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How many stable drug targets for each drug
Joined the count of all drugs with data of drug targets
indexed by drug name – result: all stable drug targets with
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associated drug that has a count based on how many
stable drug targets it is associated with
Uploaded all stable genomic regions (genomic
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coordinates)
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Uploaded all known UCSC genes
Determined which genes were 100% covered by stable
regions
Filtered based on the coverage amount (i.e. Genes only
that covered 100% by stable regions)
Uploaded kgXref data from UCSC Table Browser to
retrieve gene names/symbols of each known UCSC gene
Uploaded data from DrugBank database which contained a
list of all drugs and drug targets
Uploaded the list of genes that were found to be stable in
copy number as well as expression
Joined (including rows that do not join) stable genes with
drug targets from drug bank to determine which targets are
encoded by stable genes
Joined (excluding rows that do not join) stable genes with
drug targets from drug bank to determine which targets are
encoded by stable genes
Counted the number of stable drug targets for each drug
Counted the number of all drug targets for each drug
Galaxy Tool
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Compare two Queries on data 1
and data 2
Join two Queries on data 1 and
data 2
Join two Queries on data 1 and
data 2
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Join two Queries on data 6 and
data 7
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Count on data 9
Join two Queries on data 9 and
data 10
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UCSC Main Table Browser:
knownGene (genome)
Coverage on data 12 and data
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Filter on data 14
UCSC Main Table Browser:
kgXref (genome)
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Join two Queries on data 17 and
data 18
Join two Queries on data 17 and
data 18
Count on data 20
Count on data 19
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Joined counts of drug targets and stable drug targets
indexed by drug name to determine of how many drug
targets per drug and how many are stable
Uploaded specifically breast cancer drugs and targets that
were joined with stable genes to determine which drug
targets are stable for each breast cancer drug
Uploaded all breast cancer drug targets and associated
pathways (KEGG pathway analysis by Webgestalt)
Joined pathway information with breast cancer drugs that
have stable drug targets
Joined list of stable genes with kgXref data to determine
gene symbols of each stable gene
Formatted list of stable genes (list of gene symbols with
associated UCSC Id)
Joined UCSC Ids of stable genes with genomic
coordinates of all genes to determine genomic coordinates
of stable genes
Used the count tool on list of stable genes (coordinates) to
determine how many stable genes occurred for each
autosome
Uploaded all stable genes (gene names)
Uploaded breast cancer drugs with associated drug targets
Joined drug data with stable genes to determine which
drugs have stable drug targets
Uploaded formatted list of breast cancer drugs with stable
drug targets
Uploaded drug information from DrugBank which included
drugs and drug targets
Uploaded all stable protein-coding genes (those genes
encoded by stable regions)
Joined drug information with stable genes to determine all
drugs (not solely those to treat breast cancer) that have
targets encoded by stable regions
Join two Queries on data 21 and
data 22
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Join two Queries on data 24 and
data 25
Join two Queries on data 16 and
data 18
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Join two Queries on data 13 and
data 28
Count on data 29
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Join two Queries on data 31 and
data 32
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Join two Queries on data 35 and
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