BMC Genomics 2008, 9:627 http://www.biomedcentral.com/1471-2164/9/627 A. N2 Antimycin A + Air N2 + Antimycin A TFMs 0 0.040.080.130.190.250.380.501.02.03.0 A+Air0 0.040.080.130.190.250.380.501.02.03.0 N2+A0 0.040.080.130.190.250.380.501.02.03.0 MIPS Function B. Antimycin A + Air CA-O21 TSMFCCMBBs N2 0 0.040.080.130.190.250.380.501.02.03.0 N2+ADAmNMAinIosPyaSnctihFd.ub&niorcsetypinolitcnha.ti/oMnetab. CA-O22 PAAbfC1 RRPE rRNA transcription / Synth. DNA synth. & rep. / Process. rRNA transcription / Synth. Protein Synth. / Ribo. biogen. Metab. of energy reserves C-cmpd. & carbo. metab. C-cmpd. & carbo. metab. Energy Energy Glycolysis & gluconeogen. Mitochondrion Respiration Amino acid metab. / Biosynth. Oxidation of fatty acids Metabolism C-cmpd. & carbo. metab. Metabolism Metab. of energy reserves Stress response Cell rescue, def. & virulence Stress response Cell rescue, def. & virulence Amino acid biosynth. / Metab. Metabolism Amino acid biosynth. DNA synth. & rep. rRNA transcription / Synth. DNA synth. & rep. Abf1 rRNA transcription / Process. CA-O23 PAC Pyrimidine ribonucleo. metab. RRPE PRribootesionmseynbthioegseisnesis IEonneicrghyo/mMeistoo.s/taRseissp. Mito. / Ribo. biogenesis Energy / Respiration Amino acid metabolism Protein folding & stabiliz. C-cmpd. & carbo. metab. Proteolytic degradation C-cmpd. & carbo. metab. Metab. of energy reserves C-cmpd. & carbo. metab. Metabolism AGmlyicnoolyascisid&mgelutacboonleisomgen. CA-O24 Msn2/4 CA-O25 Msn2/4 CA-O26 Gcn4 CA-N24 3’-Puf3 Put3 CA-N25 AT Rep’s CA-N26 Swi6 CA-N27 Rox1 CA-N28 Msn2/4 C. N2 + Antimycin A TFMs N2 0 0.040.080.130.190.250.380.501.02.03.0 A+Air MIPS Function CA-N21 Gcn4 Pyrimidine metab. CA-N22 Put3 Hap1 Lipid, FA & isopren. synth. Respiration CA-N23 Put3 Mitochondrion C-cmpd. & carbo. metab. Extracell. / Secretion proteins CA-N29 Upc2 Aft2 Stress response Cell rescue, def. & virulence CA-N210 Rph1 Yap5 <-8x 1x >8x CN21 SMCCBB CN22 PARAbRfCP1E CN23 PRARCPE CN24 PRARCPE CN25 Hap1 CN26 3’-Puf3 CN27 Ume6 CN28 Msn2/4 CN29 Msn2/4 CN210 STRE CN211 Rox1 CN212 RUpocx21 CN213 RUpocx21 TFmrieganuntsrcienri3apitrh(eBa),t amnadpsuabnsdeqsutaetnisttaicnaalecroombipoasrisisoinntshoefpgreenseesnctheaotfsiagnntiifmicyacnitnlyAre(sCp)onded to anaerobiosis (A), antimycin A treat- Transcript heat maps and statistical comparisons of genes that significantly responded to anaerobiosis (A), antimycin A treatment in air (B), and subsequent anaerobiosis in the presence of antimycin A (C). The temporal profiles of genes whose transcript levels responded significantly (P ≤ 0.01) to each treatment were clustered separately using Kohonen's SOM algorithm with 1D string topology and standard correlation as the distance metric. Appropriate K values for gene network discovery were determined by evaluating CS and FCS using a range of K values (2 – 30) (see "Materials and Methods"). Figure 3A compares the response of all genes that significantly responded to anaerobiosis (N2, far left) to their response to antimycin A treatment in air (middle panel) and to subsequent anaerobiosis in the presence of antimycin A (right panel). Note that only those genes denoted by a black bar responded significantly to the indicated treatment (A + Air = antimy- cin A under aerobiosis, N2 + A = antimycin A under anaerobiosis, and N2 = anaerobiosis). The blue text is an abridged list of transcription factor motifs (TFMs, left) and MIPS functional categories (MIPS Function, right) that were significantly (P ≤ 0.01) overrepresented in each gene cluster. Panel B shows the clustering results for all genes that significantly responded to antimy- cin A treatment in air while panel C shows that for those significantly responded to anaerobiosis in the presence of antimycin A. The time scale is the number of generations after the indicated treatment. Page 6 of 14 (page number not for citation purposes)