Table 1 |
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Overview comparison of functionalities of Cistrome, CisGenome and SeqMINER |
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Cistrome |
CisGenome 2 |
SeqMINER 1.2.1 |
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Data preprocessing |
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ChIP-chip preprocessing |
Yes. Affymetrix or NimbleGen platform |
Yes. Affymetrix or other platform through conversions |
Not available |
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ChIP-seq preprocessing |
Yes |
Yes. No support for SAM/BAM |
Not available |
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General peak calling |
Yes. Through wiggle file for signals |
No direct solution |
Not available |
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Cross-platform analysis |
Yes. Across different ChIP-chip platforms, or across different ChIP-seq libraries |
Not available |
Not available |
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Expression analysis |
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From normalization, differential expression, to gene ontology |
Yes. Affymetrix or NimbleGen platform |
Not available |
Not available |
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Integrative analysis |
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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 |
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Correlation between samples |
Yes. Whole genome or peak centered Pearson correlation; Venn diagram |
Not available |
Yes. Pearson correlation at enriched regions |
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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 |
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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 |
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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 |
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Liu et al. Genome Biology 2011 12:R83 doi:10.1186/gb-2011-12-8-r83 |
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