A diagrammatic representation of our methodology.

<p><b>(A)</b> Cis-regulatory element information is collected from PLACE database. <b>(B)</b> Promoter sequence data is collected from Rice Genome Annotation Project database. <b>(C)</b> RepeatMasker masks all the repeated regions in the promoter sequences. <b>(D)</b> Signal Scan tool scans the promoter sequences to estimate the occurrences and positions of the CREs. <b>(E)</b> A cartoon diagram shows the location of individual CREs in the promoter regions. <b>(F, G)</b> Selection of input gene-sets (differentially up-regulated genes) and background (rest of the genome). <b>(H)</b><i>COR</i> values are estimated for all possible CRE pairs. <b>(I)</b> First filtering step: <i>COR</i> > 1.5 values are chosen. <b>(J)</b> Second filtering step: only the CRE pairs present in ≥ 3 promoters are selected for further analyses. <b>(K)</b> Third filtering step: significance of a <i>COR</i> value in the input gene-set is compared against the background by a Z-statistics (<i>p</i> < 0.05 is chosen). <b>(L)</b> Matrix representation of CRE pairs with statistically significant co-occurrence. <b>(M)</b> This matrix is transformed into an edge-weighted network (nodes represent individual CREs, edge weights represent the <i>COR</i> values). <b>(N)</b> Network analysis reveals the unique cliques of CREs.