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Sample Data

Affymetrix Exon 1.0 ST Array sample data for AltAnalyze

The following sample data compares human embryonic stem cells (control group) to cardiac progenitor cells (experimental group) and has been statistically analyzed via AltAnalyze. The AltAnalyze file can be selected for a general analysis, in which the data is automatically annotated with all affected genes and pathways for further analysis. Furthermore, the AltAnalyze data can be integrated into a DomainGraph network to highlight differential expression in the samples.

Please be aware: to analyze this data, you will need to install 'Homo sapiens' in the DomainGraph database, version 'ENS_52'.
If downloading the CEL files, please note: GSM335817-GSM335819 are the human embryonic stem cells, GSM335820-GSM335822 are the cardiac progenitors.

CEL files can be downloaded from GEO (human)
AltAnalyze data file (human)

The following sample data describes an Exon Array dataset where a splicing factor, the polypyrimidine tract binding protein (PTB), was knocked down in a mouse neuroblastoma cell line using short-hairpin RNAi (shRNA). The corresponding Affymetrix CEL files were divided into PTB-shRNA and empty-vector treated groups (experimental and control group, respectively) and processed by AltAnalyze using default parameters.
Please be aware: to analyze this data, you will need to install 'Mus musculus' in the DomainGraph database, version 'ENS_52'.

AltAnalyze data file (mouse)

Toy Interaction Networks

These are two toy sample networks, one gene and one protein interaction network. You can import these networks into Cytoscape via the DomainGraph plugin. The imported networks can then be overlaid with Affymetrix Exon Array data.

Gene interaction network - toy sample (human, Ensembl ids):
Protein interaction network - toy sample (human, UniProt accessions):

Affymetrix Human Exon 1.0 ST Array sample data for Single Experiments

The following sample datasets were provided by Affymetrix.

Please note that it is not allowed to redistribute this sample data!

These data can be integrated into the DomainGraph interaction networks to analyze occurrences of alternative splicing and their effects on the networks. The expression data was preprocessed using the rma-sketch method by APT (Affymetrix Power Tools), the p-value data was obtained using APT's dabg method.

Expression data files (human)
P-value data files (human)