SMD Annotating Batch Files

As of Jan 22, 2010, Debby & I (BM) have decided on the following list of potential terms for the key word in the c-4 annotation column for SMD.

• The most important thing is KEY word! Pick the term that BEST suits the sample.
• Annotations are for each sample in an experiment set. The term chosen may vary accordingly in the set, but each sample will be given a term.

the problem is that we developed this ontology for c-4 assuming the samples were two-channel experiments. However, the microarrays for E. coli are single-channel. So the terms below annotate the experiment set again, not the sample.

terms I have been using: cis-1,2-dichloroethylene (cis-DCE) & no treatment control; Biofilm & Planktonic;

SMD c-4 terms

Potential c-4 terms	Example or brief explanation
Biofilm vs planktonic
Biofilm + chemical	Put the actual chemical name in.
Chemical	Again, put the chemical name here.
Control	ie. if sample is replicate1 vs replicate2 of same strain
Ultraviolet (UV) light
Wild type vs mutant
Wild type vs complemented null mutant
Wild type vs overexpression
Null mutant vs complemented null mutant
Strain comparison	ie. E. coli K-12 MG1655 compared to E. coli B REL606
Stationary phase	This includes starvation.
Heat shock
Cold shock
Minimal medium + carbon source	replace carbon source with the actual one (ie. glucose, glycerol, acetate, etc.) use this term ONLY if this is the point!! ie. mutant vs wild type if it fits better than this.
Growth curve	Following expression changes as a function of cell density.
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