Table 2.

Output of DEP analysis

Output name	Description
Differential Expression Profile (DEPs)	A file containing analysis result statistics of each gene or probe from condition 1 vs. condition 2 comparison. The statistics returned depend on the statistical method used. For example, if using the limma method, results include log(fold change), average expression, t-statistic, p-value, adjusted p-value, and b-statistic.
Differentially Expressed Gene or Probe List	A list of differentially expressed genes or probes determined based on the defined statistical cut-off. This list can be used to perform gene-set enrichment analysis.
Heatmap (100 most DE genes/probes)	A heatmap of the top 100 differentially expressed genes or probes showing all samples in the CGP. The values shown in the heatmap reflect the data source the user selected. If the “one-button” approach was used, by default the “Normalized GEO Data” is shown.
GenePattern Input Files	Two files (GCT and CLS formatted) are provided containing gene expression values and sample grouping information for down-stream analysis outside of OMiCC. This format is supported by tools such as Gene Pattern, Gene Set Enrichment Analysis, and Integrative Genomics Viewer.