Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana.

We chose a highly significant setting ( L = 10 kb, N = 3, and h n ≥ 2; P < 10 −5 ) that both allowed for extending clusters over genes potentially missing from the expression array and assured that a cluster was not solely formed by a single set of duplicated genes (since h n > 1) (Figure 1A and B ).

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We did not find any clusters with both gene homology and significant promoter similarities, although clusters #8 and #13 both contained homologs and were nominally significant in the promoter similarity score analysis.

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