Imperial College London
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ProfessorBorisLenhard

Faculty of Medicine, Institute of Clinical Sciences

Professor of Computational Biology
 
 
 
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Contact

 

+44 (0)20 7594 0911b.lenhard Website

 
 
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Assistant

 

Mr Alastair Douglas Ivor Williams +44 (0)20 3313 4318

 
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Location

 

6.12CLMS BuildingHammersmith Campus

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Summary

 

Publications

Citation

BibTex format

@article{Mathelier:2015:nar/gkv1176,
author = {Mathelier, A and Fornes, O and Arenillas, DJ and Chen, CY and Denay, G and Lee, J and Shi, W and Shyr, C and Tan, G and Worsley-Hunt, R and Zhang, AW and Parcy, F and Lenhard, B and Sandelin, A and Wasserman, WW},
doi = {nar/gkv1176},
journal = {Nucleic Acids Research},
pages = {D110--D115},
title = {JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.},
url = {http://dx.doi.org/10.1093/nar/gkv1176},
volume = {44},
year = {2015}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release.
AU  - Mathelier,A
AU  - Fornes,O
AU  - Arenillas,DJ
AU  - Chen,CY
AU  - Denay,G
AU  - Lee,J
AU  - Shi,W
AU  - Shyr,C
AU  - Tan,G
AU  - Worsley-Hunt,R
AU  - Zhang,AW
AU  - Parcy,F
AU  - Lenhard,B
AU  - Sandelin,A
AU  - Wasserman,WW
DO  - nar/gkv1176
EP  - 115
PY  - 2015///
SN  - 1362-4962
SP  - 110
TI  - JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.
T2  - Nucleic Acids Research
UR  - http://dx.doi.org/10.1093/nar/gkv1176
UR  - http://hdl.handle.net/10044/1/27783
VL  - 44
ER  -
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