Cistrome protocols

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Cistrome specifications

Information


Unique identifier OMICS_02173
Name Cistrome
Interface Web user interface
Restrictions to use None
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • Seqpos

Maintainer


  • person_outline Yaron Turpaz <>

Publication for Cistrome

Cistrome in pipelines

 (18)
2017
PMCID: 5282477
PMID: 28139699
DOI: 10.1038/srep41598

[…] or znf764 association to their top 10 binding sites found in the chip-seq in reconstituted chip assays. the closest genes to the identified binding peaks were determined with the peak2gene tool of cistrome (http://cistrome.org/ap/), using the criteria that their transcription start sites (tsss) are located within 30 kbs upstream or downstream of the respective binding peak. rna-seq data […]

2017
PMCID: 5314486
PMID: 28209164
DOI: 10.1186/s13059-017-1159-5

[…] were computed using computematrix in deeptools []. the heatmapper in deeptools was used to create heatmaps of each chip. ceas (version 1.0.0) and aggregate profile analyses were performed in galaxy/cistrome []. the h3k27me3 targeted distal regions were obtained by considering only the regions further than 5 kb upstream or downstream of gene bodies. active enhancers were defined as enriched […]

2017
PMCID: 5385585
PMID: 28387316
DOI: 10.1038/ncomms14922

[…] and then rescaled to a larger of total number of uniquely alignable sequences in two data sets. histone modification profiles were then generated with the ‘heatmap' function or the sitepro module in cistrome analysis pipeline (http://cistrome.org/). wiggle files were also visualized in the integrative genomics viewer (robinson et al., 2011)., to correlate chip-seq and gene set enrichment, peaks […]

2017
PMCID: 5515408
PMID: 28719624
DOI: 10.1371/journal.pone.0180147

[…] genome (hg19) using bowtie for illumina. unmapped reads were removed and the sam files were converted to bam files. the bam files were transferred to a galaxy server dedicated to chip-seq analysis, cistrome (http://cistrome.org) []. myc peaks were called using the macs software version 2. only significant peaks with p values below 1e-08 were recognized. macs peaks were ranked by fold enrichment […]

2017
PMCID: 5937281
PMID: 28869966
DOI: 10.1038/nature23881

[…] chip-seq data were aligned to mouse genome mm9 using bowtie with n = 1 and m =3 as parameter. normalized bigwig files were obtained using deeptools. bioinformatics analyses were performed via the cistrome platform or bioconductor. promoter reads were counted from -2000 to +2000 relative to the transcription start site and normalized to reads per million (rpm). following public data sets […]


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Cistrome in publications

 (319)
PMCID: 5945652
PMID: 29749381
DOI: 10.1038/s41598-018-25921-8

[…] one week after the third passage for four biological replicate experiments, and gene expression was measured using affymetrix mouse genome 430 2.0 microarrays. processing of this data using the cistrome platform revealed 1208 genes (7.3% of those assayed, based on entrez ids) having altered expression with false discovery rate (fdr) <0.10 (supplementary data file 1). analysis using […]

PMCID: 5954277
PMID: 29764390
DOI: 10.1186/s12864-018-4469-4

[…] and sequence logos of each cstf on all other conditions can be retrieved from our online database (http://wcchang.itps.ncku.edu.tw/cstfanalysis/). the motif-motif similarity between cstfs and plant cistrome database were estimated by using the tomtom program [, ]., the microarray expressions data including 276 samples for six hormones treatments were downloaded from ricexpro []. a list of rice […]

PMCID: 5935921
PMID: 29728068
DOI: 10.1186/s12864-018-4691-0

[…] motif enrichment (ame) was used. functional annotation was performed with motif comparison tool tomtom against databases of transcription factor binding sites, jaspar core 2016 plants [] and plant cistrome database []., additional file 1: additional file 2: additional file 3: additional file 4: additional file 5: additional file 6: additional file 7: additional file 8: additional file 9: […]

PMCID: 5932758
PMID: 29720215
DOI: 10.1186/s13058-018-0963-5

[…] activity in sh-unc5a cells, suggesting ligand-independent activity of erα which typically involves growth factor receptor–erα crosstalk []. egfr is forefront in this crosstalk as it can alter erα cistrome and erα-regulated gene expression []. second, sh-unc5a cells showed luminal/basal hybrid phenotype, and egfr activation is common in cells with basal phenotype []. third, a recent study […]

PMCID: 5906632
PMID: 29670118
DOI: 10.1038/s41467-018-03904-7

[…] regions in both libraries were correlated using mergepeaks script of homer. after that, the unique and common regions were subjected to 'ceas: enrichment on chromosome and annotation' in the cistrome pipeline analysis to perform the hypergeometric test shown in fig. . the promoter was considered up to 3k bases upstream to the tss of the genes., next-generation sequencing data […]


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Cistrome institution(s)
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA

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