PMID- 20436461
OWN - NLM
STAT- MEDLINE
DCOM- 20100830
LR  - 20230131
IS  - 1546-1696 (Electronic)
IS  - 1087-0156 (Print)
IS  - 1087-0156 (Linking)
VI  - 28
IP  - 5
DP  - 2010 May
TI  - GREAT improves functional interpretation of cis-regulatory regions.
PG  - 495-501
LID - 10.1038/nbt.1630 [doi]
AB  - We developed the Genomic Regions Enrichment of Annotations Tool (GREAT) to 
      analyze the functional significance of cis-regulatory regions identified by 
      localized measurements of DNA binding events across an entire genome. Whereas 
      previous methods took into account only binding proximal to genes, GREAT is able 
      to properly incorporate distal binding sites and control for false positives 
      using a binomial test over the input genomic regions. GREAT incorporates 
      annotations from 20 ontologies and is available as a web application. Applying 
      GREAT to data sets from chromatin immunoprecipitation coupled with massively 
      parallel sequencing (ChIP-seq) of multiple transcription-associated factors, 
      including SRF, NRSF, GABP, Stat3 and p300 in different developmental contexts, we 
      recover many functions of these factors that are missed by existing gene-based 
      tools, and we generate testable hypotheses. The utility of GREAT is not limited 
      to ChIP-seq, as it could also be applied to open chromatin, localized epigenomic 
      markers and similar functional data sets, as well as comparative genomics sets.
FAU - McLean, Cory Y
AU  - McLean CY
AD  - Department of Computer Science, Stanford University, Stanford, California, USA.
FAU - Bristor, Dave
AU  - Bristor D
FAU - Hiller, Michael
AU  - Hiller M
FAU - Clarke, Shoa L
AU  - Clarke SL
FAU - Schaar, Bruce T
AU  - Schaar BT
FAU - Lowe, Craig B
AU  - Lowe CB
FAU - Wenger, Aaron M
AU  - Wenger AM
FAU - Bejerano, Gill
AU  - Bejerano G
LA  - eng
GR  - R01 HD059862/HD/NICHD NIH HHS/United States
GR  - 1R01HD059862/HD/NICHD NIH HHS/United States
GR  - HHMI/Howard Hughes Medical Institute/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20100502
PL  - United States
TA  - Nat Biotechnol
JT  - Nature biotechnology
JID - 9604648
RN  - 0 (Serum Response Factor)
RN  - EC 2.3.1.48 (E1A-Associated p300 Protein)
RN  - EC 2.3.1.48 (Ep300 protein, mouse)
SB  - IM
MH  - Animals
MH  - Chromatin Immunoprecipitation
MH  - Data Mining/*methods
MH  - Databases, Genetic
MH  - E1A-Associated p300 Protein
MH  - *Genome
MH  - Genomics/*methods
MH  - Humans
MH  - Jurkat Cells
MH  - Mice
MH  - Protein Binding
MH  - *Regulatory Elements, Transcriptional
MH  - Serum Response Factor
MH  - *Software
PMC - PMC4840234
MID - NIHMS768381
EDAT- 2010/05/04 06:00
MHDA- 2010/08/31 06:00
PMCR- 2016/04/22
CRDT- 2010/05/04 06:00
PHST- 2010/05/04 06:00 [entrez]
PHST- 2010/05/04 06:00 [pubmed]
PHST- 2010/08/31 06:00 [medline]
PHST- 2016/04/22 00:00 [pmc-release]
AID - nbt.1630 [pii]
AID - 10.1038/nbt.1630 [doi]
PST - ppublish
SO  - Nat Biotechnol. 2010 May;28(5):495-501. doi: 10.1038/nbt.1630. Epub 2010 May 2.