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MPIIComputationalEpigenetics / Dive

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Use case: TFs analysis #128

Closed felipealbrecht closed 4 years ago

felipealbrecht commented 6 years ago

Pou5f1 Sox2 Nanog

felipealbrecht commented 5 years ago

Pou5f1, Sox2, Nanog are crucial factors for the pluripotency of ES cells.

felipealbrecht commented 5 years ago

Experiment SRX1053369

felipealbrecht commented 5 years ago

colocalization

felipealbrecht commented 5 years ago

Sox2: SRX512370 Nanog: SRX702041

felipealbrecht commented 5 years ago

Overlapping by CSS Strong Enhancers , BioSources H1-hESC and HUVEC cell. It is possible to see that these TFs are present in more abundances in the Strong Enhancers of the ESC cell line. GM12878 is derived from lymphoblast cells

Same for "Enh" state: Induced pluripotent stem cell skeletal muscle tisue stromal

felipealbrecht commented 5 years ago

Extend 2.5K to both directions Gene Ontology - check the genes

felipealbrecht commented 5 years ago

TFs as background EP300 universal activating in enhancers - background SRX027482

felipealbrecht commented 5 years ago

https://dive.mpi-inf.mpg.de/#/load_query?qid=q7694160&gid=g1&cid=q7694243&cid=q7694211

also load the EP300 (see above) dataset.

Find the regions that does not overlap and enrich these regions

felipealbrecht commented 5 years ago

The three previous factors are crucial for pluripotency

EZH2 and SUZ12 are transcriptor repressors the data

Compare these in the Pluripotent and differentiated cells.

felipealbrecht commented 5 years ago

In ES: The 3 factors are activated In oposite surpresed

in differentiated cells the kind of repressor proteins EZH2 and SUZ12 are binding new the genes in ES cells, because these genes are suppressed in differentiated cells

Find an example.

felipealbrecht commented 5 years ago

Plots with 6 datasets: 3 ESC 2 Repressors 1 EP300