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Changes between Version 2 and Version 3 of SOPs/integrateExpressionIP

v2	v3
1	1	== Introduction ==
2	2
3		Given a ChIP-seq experiment for a transcription factor (TF) of interest and a microarray experiment comparing WT samples to KO or RNAi for the same TF, the goal of this analysis is to find out if the genes potentially regulated by the TF are changing in expression and if there is an enrichment of genes differentially expressed (DE) within the genes bound by the TF and vice versa.
	3	Given a ChIP-seq experiment for a transcription factor (TF) of interest and a microarray or RNA-Seq experiment comparing WT samples to KO or RNAi for the same TF, the goal of this analysis is to find out if the genes potentially regulated by the TF are changing in expression and if there is an enrichment of genes differentially expressed (DE) within the genes bound by the TF and vice versa.
4	4
5	5	We will be using the term “genes bound” or “genes potentially regulated by the TF” to refer to genes that are within a certain distance from a ChIP-Seq peak. This is defined by the user. Some examples of criteria to define “genes bound” by the TF would be: 1) The region from 2kb upstream to 500 pb downstream of the TSS overlaps with a peak. 2) The gene body or the 10Kb upstream or 10 Kb downstream of the gene overlap with a peak.