Compute differentially expressed genes (Illumina probes) (workflow)

Workflow title

Compute differentially expressed genes (Illumina probes)

Provider

geneXplain GmbH

Workflow overview

Description

This workflow is designed to identify upregulated, downregulated and non-changed genes for experimental data with three and more data points for each experiment and control. 

As input, the normalized data with Illumina probe IDs or Illumina gene IDs can be submitted, both types of IDs can be treated.

Such normalized files are resulting from the output of the “Normalize data” procedure under  “analyses/Methods/Data normalization/Normalize Illumina experiment and control”.

At the next step, p-value is calculated for up-and down-regulated Illumina IDs. This workflow applies Student T-test for p-value calculation, and therefore the number of data points should be at least three for each experiment and control.

Simultaneously, log fold change is calculated for Illumina IDs, and as the result of this step, a table is produced in which both LogFoldChange and p-value are assigned to each row.

Further, this table is filtered by several conditions in parallel, to identify upregulated, downregulated, and non-changed Agilent 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 non-changed probes: LogFoldChange<0.01 and LogFoldChange>-0.01

Resulting tables of the upregulated, downregulated, and non-changed Illumina 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.

Parameters

Experiment normalized

Control normalized

Species

Results folder