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Section 2: Example dataset
The Example_DataSet.zip contains –
1.
Gene_Expr_Two_Conditions.txt
: An example gene expression dataset with samples
corresponding to two conditions – StateA and StateB
2.
Gene_Expr_Four_Conditions.txt
: An example gene expression dataset with samples
corresponding to four conditions – StateA, StateB, StateC, and StateD.
3.
Micro_Expr_Two_Conditions.txt
: An example microRNA expression dataset with
samples corresponding to two conditions – StateA and StateB.
4.
PPI_Map.txt
: An example protein-protein interactome file.
5.
Mirnome_Map.txt
: An example microRNA based interactome file.
6.
MiTabLite_Example.txt
: An example MiTabLite file downloaded from the website
http://wodaklab.org/iRefWeb/search/index
[1]
7.
Gene_Output_1.txt, Gene_Output_2.txt, Gene_Output_3.txt
: Three example output
files; each file contains the names of hubs and, for a given hub, the number of
interactors and the p-value for the test of significance. The test corresponds to the
null hypothesis that there is no change in association between a hub and its
interactors across biological states.
8.
Gene_Output_1_Cor.txt
: An example output file containing the correlations for all
hub-interactor pairs in two states, namely StateA and StateB.
9.
Gene_Output_2_Cor.txt
: An example output file containing the correlations for all
hub-interactor pairs in four states, namely StateA, StateB, StateC, and StateD.
10.
Micro_Output_1_Cor.txt
: An example output file containing the correlations for all
microRNA-target gene pairs in two states, namely StateA and StateB.
11.
Cancer_Gene_Census.xls
: An example file downloaded from the website
http://www.sanger.ac.uk/genetics/CGP/Census
. This file contains the catalogue of
genes
that have been causally linked to cancer(s)
.
12.
ExampleVisualStyle.props
: An example
Vizmap Property File
for use with Cytoscape [2]
to visualize the changes in hub-interactor associations across biological states. This
property file is independent of the dataset being analyzed, which implies that the
same property file can be used for visualizing any dataset.
Summary of Contents for GLSY22522
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