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Input Format
The reference gene expression data-set used by MANTRA is part of the
Connectivity Map (cmap) project based at the Broad Institute of MIT and Harvard
in Cambridge, Massachusetts (USA).
In order to classify a novel drug X, there are two input formats available:
1) A Microarray Analysis pipeline allows to analyze raw data from microarray experiments with the Affymetrix platform.
Supported Chips:
> HG-U133A
> HT_HG-U133A
> HG-U133A_2
> HG-U133_Plus_2
Coming soon:
> HuEx-1_0-st
> Human Agilent 4x44k
The experiment folder should contain Affymetrix .cel files only and nothing else.
2) It is possible to upload one or more txt files containing all the 22,283 affymetrix probe-set identifiers (platform HG-U133A) sorted according to their differential expression (in ascending order) following treatment with the testing drug.
The current version of MANTRA can be used only with data coming from Affymetrix HG-U133A hybridizations.
Sample data ready to be analyzed with MANTRA can be downloaded by using the following links:
SampleData1: MCF7 (Human Breast Cancer) cell line at 6hr treated with Tanespimycin
SampleData2: MCF7 (Human Breast Cancer) cell line at 6hr treated with Doxorubicin
SampleData1.txt and SampleData2.txt contain the complete set of Probe Set Id in the Affymetrix Human Genome U133A gene Chip.
These Probe Set are sorted according their differential expression values.
If upload this two files as input to MANTRA, the classification result that should be obtained is described in Iorio et al. PNAS 2010.
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