BMC Genomics 2008, 9:627 http://www.biomedcentral.com/1471-2164/9/627 FACiogtmruerpaeatmr2iseonnt oinf agiernaensdthsautbsceoqmupernitseanthaeraocbuitoes,istransient phase of the anaerobic response with those that respond to antimycin Comparison of genes that comprise the acute, transient phase of the anaerobic response with those that respond to antimycin A treatment in air and subsequent anaerobiosis. Genes that responded within the first 0.25 generations of anaerobiosis were classified as acutely responding (acute N ) whereas those that responded after this period 2 were classified as chronically responding (chronic N2) (see Figure 1A for phase dynamics). Genes that comprise each of these classes are compared to those that responded to the antimycin A treatments (light gray for air and darker gray for N2). The area of the circles is scaled to the number of genes (ORFs), and the percentage of genes found in each phase is indicated in the parentheses. air (Antimycin A + air, middle) and to a shift to anaerobi- Figure 3B shows the clustered expression profiles and osis after pre-treatment with antimycin A (N2 + antimycin A, right). Note that only those genes that are indicated by the black bars to the left of each heat map responded sig- nificantly (P ≤ 0.01) in the presence of inhibitor. Finally, recovered gene networks for the 901 genes that responded significantly to antimycin A treatment in air ( C A-O2 1 – 6) and Figure 3C the same for the 669 genes that responded to the subsequent shift to anaerobiosis ( C A-N2 1 – 10). Page 5 of 14 (page number not for citation purposes)