Hypergeometric analysis for multiple inputs (workflow)

Workflow title

Hypergeometric analysis for multiple inputs

Provider

geneXplain GmbH

Workflow overview

Description

This workflow is designed to identify upregulated and downregulated genes for experimental data with any number of data points for each experiment and control. It can be used even for the cases with one data point in each experiment and control.

Input is a folder with multiple normalized tables. Each table is processed one after the other. Such normalized files are resulting from the output of the “Normalize data” procedure under “analyses/Methods/Data normalization/Normalize Affymetrix experiment and control”.

As the first step, for each normalized file p-value is calculated for up-and down-regulated probeset IDs. This workflow applies hypergeometric analysis for p-value calculation. Simultaneously, log fold change is calculated for each probeset ID, and as the result of this step, a table is produced in which both LogFoldChange and p-value are assigned to each probeset ID.

Further, this table is filtered by several conditions in parallel, to identify upregulated, downregulated, as well as a joint table of up- & downregulated Affymetrix probeset IDs.The filtering criteria are set as the following:

For upregulated probes: LogFoldChange>0.5 and -log_P_value_>3.

For downregulated probes: LogFoldChange<-0.5 and -log_P_value_<-3.

For up- & downregulated probes: (LogFoldChange>0.5 and -log_P_value_>3 & LogFoldChange<-0.5 and -log_P_value_<-3)

Resulting tables of the upregulated, downregulated, and up- & downregulated Affymetrix probeset IDs are annotated with additional information, gene description, gene symbols, species.Finally, these tables are converted into the tables of genes. Two tables are produced, with Ensembl Gene IDs and with Entrez IDs.

The same steps are repeated for the next input table, and several cycles are performed automatically corresponding to the number of tables in the input folder. 

 

Parameters

Input experiments

Input folder with all normalized CEL files (experiments)

Input controls

Input table with all normalized CEL files (controls)

Probe type

Species

Results folder