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



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.



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 .
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China.
Mei
M
Hou
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China.|Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, People's Republic of China.
Feng
F
Tian
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China.
Shuai
S
Jiang
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China.
Lei
L
Kong
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China.
Dechang
D
Yang
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China. gaog@mail.cbi.pku.edu.cn.
Ge
G
Gao
D000465:Algorithms; D000818:Animals; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D051379:Mice; D012984:Software; D014158:Transcription, Genetic; D059467:Transcriptome; D014584:User-Computer Interface; D064878:Web Browser; D057188:Workflow
Expression estimation; RNA-Seq; Transcriptome; Web server