gravatar for Bogdan

3 hours ago by

Palo Alto, CA, USA

Dear all,

'd like to have you suggestions please about the adequate "controls" when performing genome-wide analysis. For example, let's consider 1000 UP_REGULATED genes with increased PROTEIN X and HISTONE MARK Y (on the gene promoters or enhancers):

in order to show that PROTEIN X is related to HISTONE MARK Y for 1000 UP-regulated genes, what "controls" would you use for comparison :

-- 1000 RANDOM GENES

-- 1000 UP-REG GENES with NO PROTEIN X, NO HISTONE MARK Y

-- 1000 UP-REG GENES with PROTEIN X, and NO HISTONE MARK Y

-- 1000 UP-REG GENES with NO PROTEIN X, and with HISTONE MARK Y

-- 1000 NOT-UP-REG GENES with NO PROTEIN X, NO HISTONE MARK Y

-- 1000 NOT-UP-REG GENES with PROTEIN X, and NO HISTONE MARK Y

-- 1000 NOT-UP-REG GENES with NO PROTEIN X, and with HISTONE MARK Y

-- anything else ?

thanks a lot,

-- bogdan

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3 hours ago
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Bogdan950



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