This article is part of the supplement: The 2007 International Conference on Bioinformatics & Computational Biology (BIOCOMP'07)
Characterization of the Shewanella oneidensis Fur gene: roles in iron and acid tolerance response
1 Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
2 School of Computing, Clemson University, Clemson, SC 29634, USA
3 Institute for Environmental Genomics, and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
BMC Genomics 2008, 9(Suppl 1):S11 doi:10.1186/1471-2164-9-S1-S11Published: 20 March 2008
Additional file 1:
(A) Sequences of quantitative RT-PCR (qPCR) primers used in this study; (B) Comparison of expression measurements by microarray and qPCR assays. Values > 1 and values < 1 indicate up- and down-regulation, respectively. Pearson correlation coefficient of 0.92 was obtained by comparing microarray data with qRCR data.
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Additional file 2:
(A) The gene co-expression network derived from the microarray data of the fur mutant. Each node represents a gene and the width of line represents the correlation coefficient of two linked genes. Blue and gray lines indicate positive and negative correlation coefficients, respectively. Colors were assigned to nodes according to their functional categories per conventions used by TIGR (http://www.tigr.org webcite): red represents the major functional category of each module, as indicated by text; pink represents transcriptional regulator; white represents unknown genes and black nodes are genes whose association to other genes are not understood. The italic bold numbers are the cutoffs used to isolate modules. (B) Functional predictions from the gene co-expression network in (A).
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