matrix-clustering study cases

Supplementary material - Castro-Mondragon JA, Thieffry D, Thomas-Chollier M, van Helden J. submitted


Study case 1

Clustering of motifs discovered in Oct4 ChIP-seq peaks using RSAT peak-motifs, MEME-ChIP and HOMER

Input motifs: RSAT peak-motifs , MEME-ChIP , HOMER

matrix-clustering results: Clustering of Oct4 dataset

Comparison with motif clustering tools

Clustering Input Tool website
MATLIGN results Motifs (consensus format) MATLIGN
STAMP results Motifs (transfac format) STAMP
m2match results Motifs (transfac format) m2match (registration required)
Gmacs results Motifs (tab format) GMACS (command-line tool)

Reference: Chen X, et al. 2008. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133(6): 1106-1117.


Study case 2

Clustering of motifs discovered in 12 TF ChIP-seq peaks of mouse ES cells

Input motifs: cMyc , Ctcf , Esrrb , E2f1 , Klf4 , Nanog , nMyc , Oct4 , Sox2 , Stat3 , Tcfcp211 , Zfx

matrix-clustering results: Clustering of 12 TF datasets

Reference: Chen X, et al. 2008. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133(6): 1106-1117.


Study case 3

Clustering of complete motif databases

Collection Results Input
Jaspar insect [matrix-clustering]
[STAMP]
Insect motifs
Jaspar vertebrate [matrix-clustering]
[STAMP]
Vertebrate motifs
Hocomoco human [matrix-clustering]
[STAMP]
Human motifs
Hocomoco mouse [matrix-clustering]
[STAMP]
Mouse motifs

References


Study case 4

Clustering of taxon motif collections

Taxon Results Input Non-redundant
Insects Clustering of Insect motif collections [Cisbp]
[Dmmpmm]
[DrosophilaTF]
[FlyFactorSurvey]
[Idmmpmm]
[Jaspar]
[OnTheFly]
Non-redundant motifs
Plants Clustering of Plant motif collections [ArabidopsisPBM]
[Athamap]
[Cisbp]
[Cistrome]
[Jaspar]
Non-redundant motifs
Vertebrates Clustering of Vertebrate motif collections [Cisbp]
[ENCODE]
[Epigram]
[Fantom5_novel]
[Hocomoco_human]
[HOMER]
[Hocomoco_mouse]
[hPDI]
[HumanTF]
[HumantTF_dimers]
[Jaspar]
[Uniprobe]
Non-redundant motifs