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The analysis of microarray results using a traditional 2-fold change in gene expression cutoff and a 10% false-discovery rate revealed a well-developed APR in catfish, with particularly high upregulation (>50-fold) of genes involved in iron homeostasis (i.e. intelectin, hemopexin, haptoglobin, ferritin, and transferrin).
Analysis of microarray results was done using SAM.
We thank Simply FlorCruz for the technical assistance and Xiaoyue Zhao for bioinformatics analysis of microarray results.
PM participated in analysis of microarray results.
Details on experimental setup, lab work and statistical analysis of microarray results are described in [ 21].
SL performed the statistical normalization analysis of microarray results and large scale mapping of eQTL.
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Tissue collected from the precentral gyrus of the cerebral cortex was placed in RNALater according to vendor instructions and was used for the microarray analysis and validation of microarray results.
JL performed the pathway analysis, experimental confirmation of microarray results and wrote the paper.
From this analysis, 100% validation of microarray results was observed (Table 1).
The expression levels of the twelve genes generated by qRT-PCR were consistent with the microarray analysis, demonstrating the reliability and accuracy of microarray results (Additional file 14: Figure S8a-8 l).
Pathway analysis of the microarray results predicted a network of genes involved in neuropeptide or neurotransmitter signaling.
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