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