matrix-clustering study cases

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

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

References

• Kulakovskiy IV et al. (2015) HOCOMOCO : expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res., 10.1093/nar/gkv1249.
• Mathelier A et al. (2015) JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Res., 10.1093/nar/gkv1176.
• Mahony S & Benos PV. (2007) STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res. 35, W253–8.

Study case 4

Clustering of taxon motif collections