LocExpress – a web server for efficiently estimating expression of novel transcripts

The temporal and spatial-specific expression pattern of a transcript in multiple tissues and cell types can indicate key clues about its function. While several gene atlas available online as pre-computed databases for known gene models, it’s still challenging to obtain expression profiles for previously uncharacterized (i.e. novel) transcripts efficiently.

Now, researchers from Peking University have developed LocExpress, a web server for efficiently estimating expression of novel transcripts across multiple tissues and cell types in human (20 normal tissues/cells types and 14 cell lines) as well as in mouse (24 normal tissues/cell types and nine cell lines). As a wrapper to RNA-Seq quantification algorithm, LocExpress efficiently reduces the time cost by making abundance estimation calls increasingly within the minimum spanning bundle region of input transcripts. For a given novel gene model, such local context-oriented strategy allows LocExpress to estimate its FPKMs in hundreds of samples within minutes on a standard Linux box, making an online web server possible.

The workflow of LocExpress

rna-seq

For an input novel transcript, LocExpress infers MSB for abundance estimation, and obtains FPKM accordingly

Availability – The server is publicly available at http://loc-express.cbi.pku.edu.cn

Hou M, Tian F, Jiang S, Kong L, Yang D, Gao G. (2016) LocExpress: a web server for efficiently estimating expression of novel transcripts. BMC Genomics 17(Suppl 13):1023. [article]

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