RSAT matrix-clustering study cases

Supporting material - Castro-Mondragon JA

Study case 1

Clustering of motifs discovered in Lhx3 ChIP-seq peaks using RSAT peak-motifs

Input data: Sequences and motifs

Motif collection	File	Motif discovery results	Sequences
Lhx3_8h	Motifs (transfac format)	RSAT peak-motifs results	Fasta file
Lhx3_12h	Motifs (transfac format)	RSAT peak-motifs results	Fasta file
Lhx3_24h	Motifs (transfac format)	RSAT peak-motifs results	Fasta file
Lhx3_48h	Motifs (transfac format)	RSAT peak-motifs results	Fasta file
Negative control	Motifs (transfac format)	RSAT peak-motifs results	Fasta file
Sample motifs	Motifs (transfac format)

Clustering results

Clustering Results	Motif comparison metric	Agglomeration rule	Thresholds
Lhx3 + Neg control + Reference motifs	Ncor	Average	cor >= 0.6; Ncor >= 0.4; w >= 5
Lhx3 + Neg control + Reference motifs	Ncor	Average	cor >= 0.65; Ncor >= 0.45; w >= 5

The complete set of results can be reproduced using the following snakemake file: workflow

Reference: Velasco S et al. 2017. A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells. Cell Stem Cell 20 (2): 205–217.e8. doi:10.1016/j.stem.2016.11.006.