TFsHMsMethods.markdown

+21 TFs in 4 cell lines: BHLHE40 CHD1 CHD2 E2F4 ELF1 EP300 ETS1 GABPA JUND MAFK MAX MEF2A MXI1 MYC NRF1 RAD21 SIN3A SMC3 TBP USF1 USF2
+
+In red the one (GABPA)  also Analyzed by Anshul and Sunduz:
+Type	Organism	Mark/Protein	Cell Type
+TF	Human	CTCF	GM12878
+TF	Human	P300	K562
+TF	Human	POL2-4H8	H1-hESC
+TF	Human	POL2-4H8	H1-Neuron
+TF	Human	ZNF274	K562
+TF	Human	GABP	Hela-S3
+TF	Human	GABP	GM12878
+
+8 HMs in 4 cell lines: H3K27ac H3K27me3 H3K36me3 H3K4me1 H3K4me3 H3K79me2 H3K9ac H3K9me3
+
+In red those also Analyzed by Anshul and Sunduz, all from GM12878:
+
+Chromatin	Human	H3K4me3	
+Chromatin	Human	H3K4me1	
+Chromatin	Human	H3K36me3
+Chromatin	Human	H3K27ac	
+Chromatin	Human	H3K27me3	
+Chromatin	Human	H3K9me3	
+
+Peak calling methods: GEM, SPP, MACS2, peakRanger
+DOMod methods: CexoR, csaw, dPeak, MACS2, jMOSAiCS 
+
+Tasks
+1.	Map all genes to the new genome versions, MySQL
+2.	List the gene pairs in MySQL
+3.	List human-mouse orthologous genes
+4.	Knockout/knockdown/overexpression
+5.	Co-binding TF sets: MYC/MAX/MXI1 (OK) and CTCF/ZZZ3 (next time)
+6.	Electronic downsampling
+7.	Replicates – IDR
+8.	Enrichment of DNA binding motifs
+9.	Simulations – from csaw
+10.	Improvement due to controls
+
+