use-cases.txt

Use cases for Network Portal
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==How are these genes related?
==How are these genes regulated?
1) enter a set of genes into search box
2) get back matching genes, biclusters, functions & species
3) view network showing - gene membership, shared regulation, motifs
4) drill down into individual genes, motifs, regulators, biclusters

==Given a set of genes, what functions do they have?

==Given a regular, what does it regulate?
1) enter a regulator into search box
2) get back matching genes, biclusters, functions & species
3) click on regulator - get it's regulated genes (for each network?)
4) just show regulated biclusters?

==Given a regulator, what functions does it regulate?

==Given a function, what genes / regulons perform that function?
1) search for a function
2) 

==find all possible motifs for a regulator?

Questions
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How do we want to narrow by species?
Do we want to compute functional enrichment for a set of biclusters? Or just one bicluster at a time?
Is it a goal to assign functions to unannotated genes or correct annotated functions?

Can we build promoter architectures from regular (non-ensemble) cMonkey? How should we explore by motif?