Microarray Differential Expression Analysis
Load Data file
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Select type of file

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Load setup file
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Adjustment for multiple testing
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P-value cutoff (Venn diagram, Volcano plot)

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P-value Cutoff (Heatmap)

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Plots
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Email (Optional)
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Run

Adjustment method for multiple testing

Choose a method to adjust the differentially expressed genes.

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Input Data

To load a set of not normalized CEL files as raw data they should be compressed in a .zip archive with a name without spaces. It is also possible to load already normalized data in a text file, in which the first column should be the probeset IDs and correspond to the ones used in the annotation.

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Contact

Enter your E-mail Id for getting the result in your mail.

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Select comparisons

Click on 'Upload' in order to see the conditions that are assigned to each microarray. You are required to define at least two conditions that are to be compared, and genes that differ in expression between these conditions will be detected.

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P-value Cutoff (Heatmap)

Significance cutoff used (only) for the Heatmap. Will not affect analysis or results, just the visualization of top differentially expressed genes.

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Plots

The Venn diagram shows the number of differentially expressed genes for each contrast (by default at a significance level of 0.001). The Volcano plot shows the level of fold-change and significance for each gene. The heatmap shows the expression levels of significant genes for all microarrays and clusters them based on similar expression patterns.

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Input Setup

The setup file should describe the experimental setup assigning each sample to a specific condition. The format of the file should be as follows: The first column should contain the names of the CEL files (or the sample names used in the header of the normalized data file) and additional columns should assign attributes in some category to each array. See the example files under General instructions.

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P-value cutoff (Venn diagram, Volcano plot)

Significance cutoff used (only) for the Venn diagram and Volcano plot. Will not affect analysis or results, just the visualization of top differentially expressed genes.

(Back to General Instructions)

Microarray differential expression analysis

Raw or pre-normalized microarray data is used to detect genes that show changes in expression level between a pair of conditions or groups.

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General Instructions

Click "[?]" to display instructions here, or navigate through the links below.

Tool description
Input instructions
Output description

Example files to download

Normalized data
Raw data
setup file

Click load Example file and hit run

Input Instructions

Either raw CEL files (as a .zip archive) or prenormalized data can be used as input. A setup file is also needed to assign the samples into conditions or groups.

(Back to General Instructions)

Output file description

The tool produces three plots: a Venn diagram, heatmap and a volcano plot. It also produces gene statistics file in text tab delimited format for each set of conditions defined by the user.

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Citations
1) Väremo L, Nielsen J, Nookaew I ( 2013) Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods Nucleic Acids Res. Apr;41(8):4378-91
A * indicates that these authors contributed equally to the work.