Table 1 Overview comparison of functionalities of Cistrome, CisGenome and SeqMINER

Data preprocessing

   ChIP-chip preprocessing

Yes. Affymetrix or NimbleGen platform

Yes. Affymetrix or other platform through conversions

Not available

   ChIP-seq preprocessing

Yes

Yes. No support for SAM/BAM

Not available

   General peak calling

Yes. Through wiggle file for signals

No direct solution

Not available

   Cross-platform analysis

Yes. Across different ChIP-chip platforms, or across different ChIP-seq libraries

Not available

Not available

Expression analysis

   From normalization, differential expression, to gene ontology

Yes. Affymetrix or NimbleGen platform

Not available

Not available

Integrative analysis

   Genome association study

Yes. Chromosome or gene feature enrichment; aggregation plot; genes or peaks centered annotation; conservation plot; k-means clustering heatmap

Yes. Closest genes around peaks

Yes. K-means clustering at peak sites; interactive heatmap; aggregation plot

   Correlation between samples

Yes. Whole genome or peak centered Pearson correlation; Venn diagram

Not available

Yes. Pearson correlation at enriched regions

   Motif analysis

Yes. Find enriched known or de novo motifs; map motifs to genomic locations

Yes. Find de novo motifs; map motifs to genomic locations

Not available

Other tools

Liftover both BED/WIGGLE files; low level operations on text manipulation and format conversion through Galaxy

Many useful scripts for format conversions, to calculate overlaps and so on

Not available

Genome browser visualization

Redirect to mirrored UCSC genome browser on Cistrome, or external genome browsers supported by Galaxy

Local installed genome browser on Windows operating system

Not available