Table 2 Comparison of different features of well-known programs with EpiMINE

Standard analyses

 Peak calling

FALSE

TRUE

TRUE

TRUE

FALSE

 Gene ontology

FALSE

FALSE

TRUE

FALSE

FALSE

 Motif analysis

FALSE

TRUE

TRUE

TRUE

FALSE

Peaks based analysis

 Enrichment of different samples in ROI

FALSE

FALSE

FALSE

FALSE

TRUE

 Coexistence of different samples in ROI

FALSE

FALSE

FALSE

FALSE

TRUE

 Correlation based on peaks

FALSE

FALSE

TRUE

FALSE

FALSE

 Predicting dependencies based on peaks

FALSE

FALSE

FALSE

FALSE

TRUE

 Introducing and analysing random regions

FALSE

FALSE

FALSE

FALSE

TRUE

Quantification-based analysis

 Number of samples can be processed in a run

1

1

NA

≥1 (applicable for few cases)

≥1 (applicable for all cases)

 Works with raw data (no processing required)

TRUE

FALSE

FALSE

FALSE

TRUE

 Signal within ROI

FALSE

FALSE

FALSE

FALSE

TRUE

 Spread of Signal around ROI

TRUE

TRUE

FALSE

TRUE

TRUE

 Profile generator

TRUE

TRUE

FALSE

TRUE

TRUE

 Genome-wide/ROI-specific correlation

FALSE

FALSE

FALSE

TRUE

TRUE

 Introducing and analysing random regions

FALSE

FALSE

FALSE

FALSE

TRUE

 Provision of k-means clustering on quantified data

TRUE

Not in build

FALSE

TRUE

TRUE

 Provision of hierarchical clustering on quantified data

FALSE

Not in build

FALSE

FALSE

TRUE

 Correlating clustered data with expression

FALSE

FALSE

FALSE

FALSE

TRUE

 Spike-in normalization

FALSE

FALSE

FALSE

FALSE

TRUE

 Predicting dependencies based on peaks

FALSE

FALSE

FALSE

FALSE

TRUE

 Filtering datasets on the basis of their importance wrt ROI

FALSE

FALSE

FALSE

FALSE

TRUE

 Classification studies

FALSE

FALSE

FALSE

FALSE

TRUE

Differential studies

 Identifying differential regions between two conditions without replicates

FALSE

TRUE

TRUE

 Identifying differential regions between two conditions with replicates

TRUE

TRUE

TRUE

 Identifying differential regions between more than two conditions with replicates

FALSE

FALSE

TRUE