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. 2014 Sep 30;15(1):825. doi: 10.1186/1471-2164-15-825

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© Yin et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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A gene co-expression network of rx3 ^-/- regulated genes. (A) In red and green, are the gene nodes down-regulated or up-regulated, respectively, between rx3 ^-/- mutants and siblings. Group 1, 2 and 3 genes from the hierarchical clustering analysis in Figure 5 are represented by colored circles, rectangles or triangles, respectively. Edges connecting different nodes indicate co-expression (correlation coefficient r ≥ 0.95 or ≤ -0.95) between genes, with solid lines for positive correlations and dashed lines for negative correlations. (B) Distribution of the connectivity scores from the permutation depicted as a bar plot. The connectivity score was calculated as the average absolute correlation coefficient of any gene pairs in the selected genes. The permutation test was performed 1000 times on randomly selected genes. The red line is the connectivity score of rx3 ^-/-regulated genes. (C) A dot plot showing that the fold change in expression of deregulated genes between rx3 ^-/- mutants and siblings positively correlates with the number of gene linkages on the co-expression network. A fitted linear model of fold changes to the number of linkages was plotted. Genes with a higher number of connections in the co-expression network have higher fold changes in rx3 ^-/- mutants.