Table 2

Filters - InSilico web application

Filter

Function


Dataset source

Separates unpublished sample collections (such as obtained by grouping samples; My safe) from public-repository-derived content (Public). User-contributed datasets are only visible to the owner and his/her collaborators (see the 'A collaborative platform' section in the text). The Public filter can be expanded to select from the available public repositories. The InSilico filter contains InSilico DB compiled datasets. The Community filter contains datasets shared by InSilico DB users

Curation

Separates Manually curated datasets from To curate datasets. Manually curated clinical annotations have been structured and manually curated using the InSilico DB curation interface (see the 'Clinical annotations and biocuration' section in the text)

Platforms

Platforms are divided into two groups: gene expression microarray and next-generation sequencing. These groups can be expanded to select specific platforms

Data pre-processing

The data pre-processing filters are divided in microarray and next-generation sequencing groups. When raw data are available, InSilico DB pre-processes datasets using state-of-the-art algorithms, for example, fRMA for Affymetrix arrays, and Tophat-Cufflinks for RNA-Seq (see the 'Genomic dataset pre-processing pipelines' section in the text). The Original filter contains data as originally normalized submitted by the authors

Measurement type

The measurement type filters are divided into microarray (RNA) and next-generation sequencing (RNA-Seq, exome sequencing) groups


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

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