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
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