ENCODE ChIP-Seq Significance Tool protocols

View ENCODE ChIP-Seq Significance Tool computational protocol

ENCODE ChIP-Seq Significance Tool statistics

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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 in pipeline

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

[…] the vicinity of hdac2 binding in cafs ()., we further broadly queried common transcription factors that regulate a panel of pro-inflammatory genes upregulated after hdaci treatment in cafs using the encode chip-seq significance tool []. this tool identifies transcription factors that commonly regulate sets of genes by searching publically available chip-seq data sets from the encode project. […]

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ENCODE ChIP-Seq Significance Tool in publications

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

[…] 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 […]

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

[…] 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 []., hdac - histone deacetylase, hdaci – histone deacetylase inhibitor, pdac – […]

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

[…] 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 […]

PMCID: 4551916
PMID: 26117541
DOI: 10.1093/nar/gkv642

[…] one value per each bin. plots were generated using the ggplot2., to identify enrichment of tf motifs around the 5 kb tss regions of genes bound by ncor1 (nt gene list) and the indicated subsets, the encode chip-seq significance tool (http://encodeqt.simple-encode.org/) was used to mine for significant enrichment within the genes of tfs listed in the encode chip-seq data derived in k562 cells. […]

PMCID: 4167139
PMID: 25187168
DOI: 10.1186/s40478-014-0093-y

[…] option to assess the enrichment for these custom gene sets in the complete list of discovery meta-analysis genes with their corresponding meta-effect sizes, regardless of significance., we used the encode chip-seq significance tool [] to identify transcription factors enriched in the up-regulated and down-regulated components of the cnm. we used the following parameters: organism, human (hg19); […]

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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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