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ENCODE ChIP-Seq Significance Tool specifications


Unique identifier OMICS_19555
Name ENCODE ChIP-Seq Significance Tool
Interface Web user interface
Restrictions to use None
Input data A gene list.
Programming languages Javascript
Database management system MySQL
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Atul Butte

Publication for ENCODE ChIP-Seq Significance Tool

ENCODE ChIP-Seq Significance Tool citations


Gene expression analysis in asthma using a targeted multiplex array

PMCID: 5725935
PMID: 29228930
DOI: 10.1186/s12890-017-0545-9

[…] tics and non-asthmatic respectively. All were significantly correlated but in opposite directions (p < 0.05, Fig. ).All eight pairs of differentially co-expressed genes (Table ) were entered into the ENCODE ChIP-SEQ significance tool. All but one of the genes (IDO1) from the pairs was regulated by the transcriptional repressor CCCTC-binding factor or CTCF. Since only 47% of the candidate genes hav […]


Biotinidase deficiency: Genotype biochemical phenotype association in Brazilian patients

PLoS One
PMCID: 5428951
PMID: 28498829
DOI: 10.1371/journal.pone.0177503

[…] ver, and C/EBPdelta and Sp1 present in the pancreas. The transcription factors Sp1 and C/EBPdelta were included in the list of transcription factors identified in the 5’ region of the BTD gene by the ENCODE ChIP-Seq Significance Tool. […]


Histone deacetylase inhibitors provoke a tumor supportive phenotype in pancreatic cancer associated fibroblasts

PMCID: 5386671
PMID: 27894105
DOI: 10.18632/oncotarget.13572

[…] d via the Student's t-test. Values of ≤0.05 were considered statistically significant. Statistical analyses were performed using Prism 6 Software (GraphPad). Transcription binding significance of the ENCODE ChIP-Seq Significance Tool results are calculated by a hypergeometric test with a multiple hypothesis correction []. […]


snpGeneSets: An R Package for Genome Wide Study Annotation

PMCID: 5144977
PMID: 27807048
DOI: 10.1534/g3.116.034694

[…] , and histone modification regions, will further enhance post-GWS annotation and analysis. Cscan (), HaploReg (), and RegulomeDB () identify epigenetic factors related to a list of SNPs or genes. The ENCODE ChIP-Seq Significance Tool identifies the transcription factors enriched in genes based on public ENCODE data (). snpGeneSets can be used with these packages and tools to provide a comprehensiv […]


Widespread parainflammation in human cancer

Genome Biol
PMCID: 4937599
PMID: 27386949
DOI: 10.1186/s13059-016-0995-z

[…] genes with expression levels highly correlated with the PI score (R > 0.5) in the carcinoma cell lines (Additional file ). We then performed transcription factor binding enrichment analysis using the ENCODE ChIP-Seq Significance Tool [] (Additional file : Table S4). The analysis again affirmed our claim that PI has a distinct pattern of inflammation, where the top enriched transcription factors we […]


From System Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach

PLoS One
PMCID: 4642966
PMID: 26562430
DOI: 10.1371/journal.pone.0142147

[…] hodologically similar but go a step further and, by additionally exploiting curated data on kinase-substrate relationships, suggest signaling pathways highlighted by input lists of altered genes [,]. ENCODE ChIP-Seq Significance Tool is a web-based interface which allows users to mine a back-end comprised of mouse and human TF binding site data generated as part of the ENCODE series of experiments […]


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ENCODE ChIP-Seq Significance Tool institution(s)
Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
ENCODE ChIP-Seq Significance Tool funding source(s)
Supported in part by March of Dimes Prematurity Research Center at Stanford University School of Medicine.

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