Dataset Information

LocExpress: a web server for efficiently estimating expression of novel transcripts.

ABSTRACT:

Background

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 get expression profile for previously uncharacterized (i.e. novel) transcripts efficiently.

Results

Here we 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.

Conclusions

To the best of our knowledge, LocExpress is the only web server to provide nearly real-time expression estimation for novel transcripts in common tissues and cell types. The server is publicly available at http://loc-express.cbi.pku.edu.cn .

SUBMITTER: Hou M

PROVIDER: S-EPMC5260097 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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Publications

LocExpress: a web server for efficiently estimating expression of novel transcripts.

Hou Mei M Tian Feng F Jiang Shuai S Kong Lei L Yang Dechang D Gao Ge G

BMC genomics 20161222 Suppl 13

<h4>Background</h4>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 get expression profile for previously uncharacterized (i.e. novel) transcripts efficiently.<h4>Results</h4>Here we developed LocExpress, a web server for efficiently estimating expression of novel transcripts across m ...[more]

PMID: 28155723

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Dataset Information

LocExpress: a web server for efficiently estimating expression of novel transcripts.

Background

Results

Conclusions

Publications

LocExpress: a web server for efficiently estimating expression of novel transcripts.

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