BMC Genomics 2009, 10(Suppl 2):S4 http://www.biomedcentral.com/1471-2164/10/S2/S4 List of abbreviations used MIC: minimum inhibitory concentration; CTC: chlortet- racycline; AMX: amoxicillin; ENR: enrofloxacin; BHI: brain heart infusion; COG: Clusters of Orthologous Groups; DE: differentially expressed; recA: recombinase A; gyrB: DNA gyrase B. Competing interests The authors declare that they have no competing interests. Authors' contributions BN cultured Pm70, did RNA isolations, data analysis and network modeling and wrote the draft of the manuscript. LAS carried out the qPCR validations and contributed to the methods and results of this aspect in the manuscript. ML and SCB conceived and coordinated this study and helped draft the manuscript. All authors read and approved the final manuscript. Additional material Additional file 1 Significant changes identified in P. multocida gene expression with AMX, CTC and ENR. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-S2-S4-S1.xls] Additional file 2 Supplemental table 2. Significant changes identified in P. multocida gene expression common to more than one antibiotic. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-S2-S4-S2.doc] Additional file 3 Supplemental figures. Interaction networks. The network diagrams show changes in gene expression in response to sub-MIC. Red and green indicate significant increase and decrease in expression respectively. Genes whose expression did not change (pink) and genes in the network from other bacteria (gray) are also included. Supplemental figure 1. fnr reg- ulated genes with CTC administration. Supplemental figure 2. Interac- tion network with genes involved in SOS response with AMX administration. Supplemental figure 3. Interaction network with genes involved in SOS response with CTC administration. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-S2-S4-S3.ppt] Additional file 4 Supplemental table 3. Quantitative RT-PCR probes and primers. The sequences of primers used for qPCR validations of selected gene expression changes in microarray. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-S2-S4-S4.doc] Acknowledgements This project was partially supported by a grant from the National Science Foundation (EPS-0556308-06040293) and a competitive grant from Missis- sippi State University Life Sciences and Biotechnology Institute (LSBI). We acknowledge Dr. Vivek Kapur for P. multocida Pm70 strain and Dr. Carolyn Boyle for statistical analysis of microarray datasets. This article has been published as part of BMC Genomics Volume 10 Supple- ment 2, 2009: Proceedings of the Avian Genomics Conference and Gene Ontology Annotation Workshop. The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2164/10?issue=S2 References 1. Pasteur L: De l'att'enuation du virus du chol'era des poules. C R Acad Sci 1880, 91:673-680. 2. Pasteur L: Sur les virus-vaccins du chol'era des poules et du charbon. C R Trav Congr Int Dir Agronom session de Versailles 1881:161-162. 3. Ellison ML, Champlin FR: Outer membrane permeability for nonpolar antimicrobial agents underlies extreme suscepti- bility of Pasteurella multocida to the hydrophobic biocide tri- closan. Vet Microbiol 2007, 124(3–4):310-318. 4. Harper M, Boyce JD, Adler B: Pasteurella multocida pathogene- sis: 125 years after Pasteur. FEMS Microbiol Lett 2006, 265(1):1-10. 5. Talan DA, Citron DM, Abrahamian FM, Moran GJ, Goldstein EJ: Bac- teriologic analysis of infected dog and cat bites. Emergency Medicine Animal Bite Infection Study Group. N Engl J Med 1999, 340(2):85-92. 6. May BJ, Zhang Q, Li LL, Paustian ML, Whittam TS, Kapur V: Com- plete genomic sequence of Pasteurella multocida, Pm70. Proc Natl Acad Sci USA 2001, 98(6):3460-3465. 7. Boyce JD, Wilkie I, Harper M, Paustian ML, Kapur V, Adler B: Genomic scale analysis of Pasteurella multocida gene expres- sion during growth within the natural chicken host. Infect Immun 2002, 70(12):6871-6879. 8. Paustian ML, May BJ, Cao D, Boley D, Kapur V: Transcriptional response of Pasteurella multocida to defined iron sources. J Bacteriol 2002, 184(23):6714-6720. 9. Paustian ML, May BJ, Kapur V: Transcriptional response of Pas- teurella multocida to nutrient limitation. J Bacteriol 2002, 184(13):3734-3739. 10. Nanduri B, Lawrence ML, Boyle CR, Ramkumar M, Burgess SC: Effects of subminimum inhibitory concentrations of antibiot- ics on the Pasteurella multocida proteome. J Proteome Res 2006, 5(3):572-580. 11. Nanduri B, Lawrence ML, Peddinti DS, Burgess SC: Effects of Sub- minimum Inhibitory Concentrations of Antibiotics on the Pasteurella multocida Proteome: A Systems Approach. Comp Funct Genomics 2008:254836. 12. Melnikow E, Schoenfeld C, Spehr V, Warrass R, Gunkel N, Duszenko M, Selzer PM, Ullrich HJ: A compendium of antibiotic-induced transcription profiles reveals broad regulation of Pasteurella multocida virulence genes. Vet Microbiol 2008. 13. Weston AD, Hood L: Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res 2004, 3(2):179-196. 14. Kaldalu N, Mei R, Lewis K: Killing by ampicillin and ofloxacin induces overlapping changes in Escherichia coli transcription profile. Antimicrobial agents and chemotherapy 2004, 48(3):890-896. 15. Walsh C: Antibiotics: actions, origins, resistance. ASM press; 2003. 16. Yonath A, Bashan A: Ribosomal crystallography: initiation, pep- tide bond formation, and amino acid polymerization are hampered by antibiotics. Annu Rev Microbiol 2004, 58:233-251. 17. Freiberg C, Fischer HP, Brunner NA: Discovering the mechanism of action of novel antibacterial agents through transcrip- tional profiling of conditional mutants. Antimicrobial agents and chemotherapy 2005, 49(2):749-759. 18. Hutter B, Schaab C, Albrecht S, Borgmann M, Brunner NA, Freiberg C, Ziegelbauer K, Rock CO, Ivanov I, Loferer H: Prediction of mechanisms of action of antibacterial compounds by gene Page 9 of 10 (page number not for citation purposes)