October tasks and questions

Phase1: tasks and questions

Gene regulation:
How are tissue specific and broadly expressed genes encoded?

• Tissue specific motifs? Tissue specific TFBS cluster combinations?

How are highly expressed and weakly expressed genes encoded? (single molecule gives us this)

• Copy number? TFBS clusters? Promoter shape/length?

What factors are necessary to induce expression of a particular gene?

• Insulin, Hemoglobin

Transcription factors:
Agreed upon set of TFs – must be finalised in this meeting!!! – and curated to TFBS cluster
Which TFs can we predict the motif for?
What is the tissue specificity of transcription factors?
How connected are sample specific as opposed to broadly expressed transcription factors? Are they leaves or hubs?

Motifs:
A figure to present the motifs analyses?

• Integration of multiple methods?
• Integrated figure with TF expression?
• Known motifs and ab-initio treated separately?
  
  

Networks:
How many unique combinations of transcription factors are expressed in human cells? What can we say about combinatorial regulation?
Does promoter complexity make the network/gene expression more robust to perturbations?
Can we say cell line networks are more unique than primary cell networks? (ie. each cell line is a unique entity)

Cellular identity and evolution:
Distributions of gene utilization in man (comparatively how many genes actually expressed in each state? Measure of transcript complexity – how diverse is the mix?)
What can we say about multicellularity?
Tissue specificity of genes evolved since multicellularity?
Best figure to demonstrate tissue/cell specificity?

Other:
A set of ‘snippet’ insights from satellites (Main paper will make a call out to the satellite)