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CentriMo specifications

Information


Unique identifier OMICS_05787
Name CentriMo
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data DNA sequences, DNA/RNA motifs
Operating system Unix/Linux
Computer skills Advanced
Version 4.10.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline FIMO Team <>

Information


Unique identifier OMICS_05787
Name CentriMo
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data DNA sequences, DNA/RNA motifs
Computer skills Basic
Version 4.10.1
Stability Stable
Maintained Yes

Maintainer


  • person_outline FIMO Team <>

Publications for CentriMo

CentriMo in pipelines

 (7)
2018
PMCID: 5825159
PMID: 29432416
DOI: 10.1371/journal.pgen.1007224

[…] rabbit anti-brdu (rockland 600-401-c29), and fitc conjugated goat anti-gfp (abcam ab6662). brdu stain denaturing was performed according to []., sox motif central enrichment was assessed using centrimo v.4.11.2 []. nearest gene annotation was performed using great v.3.0.0. the number of reads within a peak set bed file present in each chip-seq file was calculated using samtools bedcov […]

2018
PMCID: 5868199
PMID: 29581148
DOI: 10.15252/msb.20167435

[…] regions with a significant macs p‐value (fdr < 0.01 and a read count ≥ 10 in at least two of the individual chip samples). enrichment of the smad3 motif (jaspar core ma0513.1) was performed with centrimo (bailey & machanick, ), using the 250‐bp regions around peak summits obtained by running macs on the combined reads from all the samples. peaks were mapped to genes using the chipenrich […]

2017
PMCID: 5340393
PMID: 28267806
DOI: 10.1371/journal.pone.0173421

[…] analysis. the 101 nucleotides centered on the summits detected by macs2 were used for detection of the consensus m6a motif by dreme (version: 4.10.2) []. motif central enrichment was performed by centrimo (version: 4.10.2) [] with 301 nucleotides centered on the summits. to compare the positional distribution of the motif in the peaks, the top three rrm6ach motifs and one false positive […]

2017
PMCID: 5400504
PMID: 28287392
DOI: 10.7554/eLife.22631.041

[…] enrichment of the oct4:sox2 dual motif sequence, in addition to significant enrichments for the highly similar oct2 motif and two de novo oct4 motifs. these motifs are enriched at the peak centre (centrimo analysis), and 60% of peaks contained at least one of these motifs. this is comparable with other studies for transcription factor motifs and binding (valouev et al., 2008, heinz et al., […]

2017
PMCID: 5561104
PMID: 28819152
DOI: 10.1038/s41598-017-08754-9

[…] molecular function terms significantly enriched for both the binomial and the hyper-geometric by a p-value lower than 0.05 were considered., prediction of tf binding motifs was performed using the centrimo algorithm of the meme-chip pipeline v.4.9.1 in default settings. a genomic region of +/−100 bp focused on each binding sites center was considered for this analysis., the normalization […]


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CentriMo in publications

 (65)
PMCID: 5954283
PMID: 29764360
DOI: 10.1186/s12864-018-4459-6

[…] k-mers were obtained by picking out the most important words for enhancer and promoter respectively, in every sentence with positive label. then we performed motif enrichment analysis using centrimo [] to compare these words against known motifs in the hocomoco v9 dataset [], and drew out top enriched motifs with sequence logo []., to consolidate the importance of our work, we compare […]

PMCID: 5896119
PMID: 29642851
DOI: 10.1186/s12862-018-1147-8

[…] information (synteny, timing of wgds) that was not available to notung. those proposed, additional duplications are not discussed in detail within the main document, but may be inspected in detail., centrimo [] was used to perform a local (positional) enrichment analysis of in vivo and in vitro dna- and rna-binding protein (dpb/rbp) motifs from the following databases: ray 2013 restricted […]

PMCID: 5892119
PMID: 29463600
DOI: 10.1128/JB.00779-17

[…] these regions were searched for transcription motifs (bre and tata box) using multiple sequence alignments, visualization with weblogo (default parameters), and motif searching with meme and centrimo (default parameters) (, )., twenty micrograms of total rna and [32p]atp end-labeled century-plus rna markers was loaded onto 5% denaturing urea polyacrylamide gels (sequagel; national […]

PMCID: 5872397
PMID: 29587824
DOI: 10.1186/s13059-018-1420-6

[…] file : table s17. the specificity of each antibody was tested using spike-in controls; validation results are shown in additional file : table s21., motifs were identified using meme-suite/centrimo/homer software at the default settings. matching frequencies to the input sequences (± 300 bp of each highly modified 5hmc or 5fc/5cac site) and significance assessment (e-value) […]

PMCID: 5868199
PMID: 29581148
DOI: 10.15252/msb.20167435

[…] regions with a significant macs p‐value (fdr < 0.01 and a read count ≥ 10 in at least two of the individual chip samples). enrichment of the smad3 motif (jaspar core ma0513.1) was performed with centrimo (bailey & machanick, ), using the 250‐bp regions around peak summits obtained by running macs on the combined reads from all the samples. peaks were mapped to genes using the chipenrich […]


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CentriMo institution(s)
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia

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