Table 3

Comparing InSilico DB with other databases

InSilico DB functionality


GEO comparison

Expression Atlas

Data sources

Public repositories

Support main platforms of GEO, SRA and notable public datasets

All platforms supported, limited to submissions

Support for Array-Express


New datasets created by subsetting and combining datasets



Commonalizing biocuration effort through collaborative platform


User-defined tabular structured text

Free text

Ontologies & free text


Multiple, user-contributed, batch submissions from biocuration projects, and in-house biocurator

In-house biocuration

In-house biocuration


Enrich curation with analysis results

Data management

Processing raw data with latest algorithms, for example, fRMA for microarrays, TopHat+Cufflinks for RNA-Seq

Datasets can be shared at progressive levels, including groups, and published to the InSilico DB public repository

Data export

Raw data

Raw data are available for download

Raw data are available for download

Through ArrayExpress links

Output Format

Multiple ready-to-use analysis-tool-compatible format (GenePattern, R/Bioconductor and IGV compatible)

GEO-defined SOFT and text formats

Programmatic access

InSilico Db R/Bioconductor package

Through third-party GEOquery R/Bioconductor package

SRA, Short Read Archive.

Coletta et al. Genome Biology 2012 13:R104   doi:10.1186/gb-2012-13-11-r104

Open Data