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Table 3 Results of the experimental verification of predicted modules

From: An integrative computational approach to effectively guide experimental identification of regulatory elements in promoters

Predicted cis-regulatory modules Fragments used to test the respective moduleb
Experimental round I Experimental round II
1 Meme1a + TSS 301_1 (+), 48_1 (+) 134_1 (−), 156_4 (−), 212_2 (−)
2 NagC + BRCZ4 + TSS 272_1 (−) 134_1 (−), 134_2 (−), 212_2 (−)
3 (FNR + NagC) OR (FNR + NagC + TSS) 48_2 (−), 156_1 (−), 272_1 (−) 156_4 (−), 134_1 (−), 134_2 (−)
4 (TGIF + FNR + NagC) OR (TGIF + FNR + NagC + TSS) 301_1 (+), 48_1 (+) 134_3 (+), 212_1 (+)
5 Meme1a + HNF1 301_1 (+), 48_1 (+) 134_1 (−), 134_2
6 Meme1a + FNR + NagC 301_1 (+), 48_1 (+) 134_1 (−), 134_2 (−), 156_4 (−)
7 MEF2 + TGIF 301_2 (−)  
8 BRCZ4 + HNF1 271_1 (−) 134_1 (−), 134_2 (−)
9 (RcsAB + MDScan3) OR (RcsAB + MDScan2) 48_2 (−) 134_1 (−), 134_2 (−)
10 (DME1 + RcsAB + Poly-(A)8 + TSS) 301_1 (+) 156_4 (−)
11 MEF2 + Meme4 156_2 (−), 272_2 (−), 48_2 (−)  
  1. a Motif identical to tusp[6].
  2. b Fragments showing specific expression (+) support the respective regulatory module, fragments showing no- or unspecific expression (−) reject respective modules. After two experimental rounds module 4 is proved to be functional.