Download Galaxy-History_4-Gene Expression Analysis

Uploaded gene expression data from Oncomine (Turashvili dataset) and compared genes with stable and
unstable regions as determined by copy number data (Hicks dataset).
Galaxy File:
Dataset
Dataset Description
Galaxy Tool
1
Uploaded the microarray platform data (Human U133 plus 2.0 array)
Upload File
2
Uploaded copy number data (gene symbols of genes in
unstable/stable regions)
Upload File
3
Joined microarray and copy number data indexed by gene symbol
Join two Queries on
data 1 and data 2
4
5
6
7
8
9
10
Uploaded list of stable genes that are measured on the microarray
platform
Uploaded list of unstable genes that are measured on the microarray
platform
Uploaded data from Oncomine (Turashvili et al.,) of top 10% genes
that are over- and under-expressed
Joined stable genes measured in microarray with expression dataset
indexed by gene symbol - excluded rows that did not join (i.e. Stable
genes that are not over/under-expressed)
Joined stable genes measured in microarray with expression dataset
indexed by gene symbol - included all rows (i.e. Stable genes that
are not over/under-expressed)
Joined unstable genes measured in microarray with expression
dataset indexed by gene symbol
Uploaded Entrez Ids of stable genes that are stable in copy number
and expression (to be used in pathway analysis: Webgestalt)
Upload File
Upload File
Upload File
Join two Queries on
data 4 and data 6
Join two Queries on
data 4 and data 6
Join two Queries on
data 5 and data 6
Upload File
11
Uploaded stable regions (812 regions)
Upload File
12
Counted regions based on chromosome (to determine how many
stable regions are present for each chromosome)
Count on data 11
13
Uploaded Entrez gene Ids of genes in stable regions
Upload File
14
15
Formatted the list of Entrez gene Ids and gene symbols of genes in
stable regions
Joined stable genes from copy number data and stable genes that
have are not differentially expressed
Cut on data 13
Join two Queries on
data 4 and data 14