peak-motifs study cases

Supplementary material - Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J. 2012. RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res 40(4): e31. Pubmed 22156162


Chen_2008

Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J et al. 2008. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133(6): 1106-1117.

Sequences

data/sequences/Chen_2008/

Known motifs

data/known_motifs/ref_motifs_Chen_2008/

Single dataset analysis

Stat3vsGFP_MACS_fdr0.02_splitted_peaks_sorted
Sox2vsGFP_MACS_fdr0.02_splitted_peaks_sorted
NanogvsGFP_MACS_fdr0.02_splitted_peaks_sorted
Oct4vsGFP_MACS_fdr0.02_splitted_peaks_sorted
c-MycvsGFP_MACS_fdr0.02_splitted_peaks_sorted
n-MycvsGFP_MACS_fdr0.02_splitted_peaks_sorted
Klf4vsGFP_MACS_fdr0.02_splitted_peaks_sorted
CtcfvsGFP_MACS_fdr0.02_splitted_peaks_sorted
ZfxvsGFP_MACS_fdr0.02_splitted_peaks_sorted
Tcfcp2l1vsGFP_MACS_fdr0.02_splitted_peaks_sorted
E2f1vsGFP_MACS_fdr0.02_splitted_peaks_sorted
EsrrbvsGFP_MACS_fdr0.02_splitted_peaks_sorted

Differential analysis (test versus control)

NanogvsGFP_MACS_fdr0.02_splitted_peaks_sorted_vs_Oct4vsGFP_MACS_fdr0.02_splitted_peaks_sorted
NanogvsGFP_MACS_fdr0.02_splitted_peaks_sorted_vs_Sox2vsGFP_MACS_fdr0.02_splitted_peaks_sorted
Oct4vsGFP_MACS_fdr0.02_splitted_peaks_sorted_vs_Sox2vsGFP_MACS_fdr0.02_splitted_peaks_sorted
Sox2vsGFP_MACS_fdr0.02_splitted_peaks_sorted_vs_Oct4vsGFP_MACS_fdr0.02_splitted_peaks_sorted
c-MycvsGFP_MACS_fdr0.02_splitted_peaks_sorted_vs_n-MycvsGFP_MACS_fdr0.02_splitted_peaks_sorted
n-MycvsGFP_MACS_fdr0.02_splitted_peaks_sorted_vs_c-MycvsGFP_MACS_fdr0.02_splitted_peaks_sorted


Lin_2010

Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, Sigvardsson M, Hagman J, Espinoza CA, Dutkowski J et al. 2010. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol 11(7): 635-643.

Sequences

data/sequences/Lin_2010/

Known motifs

data/known_motifs/ref_motifs_Lin_2010/

Single dataset analysis

GSM546525_Sample9.RAG1KO-FOXO1
GSM546524_Sample8.RAG1KO-EBF
GSM546517_Sample1.EBFKO-E2A
GSM546523_Sample7.RAG1KO-E2A
GSM537996_Sample14.RAG1KO-PU.1
GSM537995_Sample13.EBFKO-PU.1
GSM546526_Sample10.RAG1KO-CTCF

Differential analysis (test versus control)



Heinz_2010

Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. 2010. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38(4): 576-589.

Sequences

data/sequences/Heinz_2010/

Known motifs

data/known_motifs/ref_motifs_Heinz_2010/

Single dataset analysis

GSM546530_Sample14.RAG1KO-H3K27me3
GSM546531_Sample15.RAG1KO-H3ac
GSM546527_Sample11.RAG1KO-H3K4me1

Differential analysis (test versus control)



Blow_2010

Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F et al. 2010. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet 42(9): 806-810.

Sequences

data/sequences/Blow_2010/

Known motifs

data/known_motifs/ref_motifs_Blow_2010/

Single dataset analysis

GSM348065_midbrain_p300_peaks
GSM348066_limb_p300_peaks
GSM348064_forebrain_p300_peaks
GSM559653_midbrain_p300_peaks
GSM559652_heart_p300_peaks

Differential analysis (test versus control)

GSM348064_forebrain_p300_peaks_vs_GSM348065_midbrain_p300_peaks
GSM348064_forebrain_p300_peaks_vs_not_forebrain_p300_peaks
GSM348065_midbrain_p300_peaks_vs_GSM348064_forebrain_p300_peaks
GSM348065_midbrain_p300_peaks_vs_not_midbrain_p300_peaks
GSM348066_limb_p300_peaks_vs_GSM559652_heart_p300_peaks
GSM348066_limb_p300_peaks_vs_not_limb_p300_peaks
GSM559652_heart_p300_peaks_vs_GSM348064_forebrain_p300_peaks
GSM559652_heart_p300_peaks_vs_GSM348065_midbrain_p300_peaks
GSM559652_heart_p300_peaks_vs_GSM348066_limb_p300_peaks
GSM559652_heart_p300_peaks_vs_GSM559653_midbrain_p300_peaks
GSM559652_heart_p300_peaks_vs_not_heart_p300_peaks
GSM559653_midbrain_p300_peaks_vs_GSM348065_midbrain_p300_peaks
GSM559653_midbrain_p300_peaks_vs_not_midbrain_p300_peaks