Computational protocol: Differential expression of genes related to gain and intake in the liver of beef cattle

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Protocol publication

[…] Differentially expressed genes were analyzed with the Protein Analysis Through Evolutionary Relationships (PANTHER) statistical over-representation test for Bos taurus with the default parameters, except the Bonferroni correction for multiple testing was not used. The over-represented GO-Slim biological processes and molecular functions are summarized in Tables  and . PANTHER Version 10.0, released May 15, 2015 was used in the analysis [, ]. Ingenuity® Pathway Analysis (IPA®) by Qiagen was also used for differential expression analysis to identify genes over-represented in canonical pathways. The top five pathways with the lowest P value (P < 0.05) were reported by the system. […]

Pipeline specifications

Software tools PANTHER, IPA
Application Protein sequence analysis
Organisms Bos taurus