The predictive overall accuracy of defensins families based on different <i>N</i>-peptide composition with S size alphabet (N, S).

<p>The predictive overall accuracy of defensins families based on different <i>N</i>-peptide composition with S size alphabet (N, S).</p

The heatmap shows the adjacent correlation of 13 reduced amino acids for five different defensin families.

<p>The heatmap shows the adjacent correlation of 13 reduced amino acids for five different defensin families.</p

Violin plots show the length distribution of five defensin families.

<p>Violin plots show the length distribution of five defensin families.</p

Microarray Analysis of the Gene Expression Profile and Lipid Metabolism in <i>Fat-1</i> Transgenic Cattle

<div><p>Long-chain n-3 polyunsaturated fatty acids (n-3 PUFAs) are beneficial for human health. However, humans and mammals are unable to synthesize n-3 PUFAs because they lack the n-3 desaturase gene <i>fat-1</i> and must therefore obtain this type of fatty acid through their diet. Through the production of <i>fat-1</i> transgenic animals, it is possible to obtain animal products that are rich in n-3 PUFAs, such as meat and milk. The aim of this study was to analyze the gene expression profile and the mechanism of lipid metabolism in <i>fat-1</i> transgenic cattle and to accumulate important basic data that are required to obtain more efficient <i>fat-1</i> transgenic cattle. Transcriptome profiling of <i>fat-1</i> transgenic and wild-type cattle identified differentially expressed genes that are involved in 90 biological pathways, eight pathways of which were related to lipid metabolism processes 36 genes of which were related to lipid metabolism. This analysis also identified 11 significantly enriched genes that were involved in the peroxisome proliferator-activated receptor signaling pathway. These findings were verified by quantitative polymerase chain reaction. The information obtained in this study indicated that the introduction of an exogenous <i>fat-1</i> gene into cattle affects the gene expression profile and the process of lipid metabolism in these animals. These results may provide important insights into how an exogenous <i>fat-1</i> gene synthesizes n-3 PUFAs in transgenic cattle and other mammals.</p></div

The significantly enriched genes in the ‘PPAR signaling pathway’.

<p>Red nodes indicate the significantly up-regulated genes in <i>fat-1</i> transgenic cattle, and the pink nodes indicate the significantly down-regulation genes.</p

Microarray biological process (GO Ontology) classification.

<p>The x-axis indicates the likelihood [−log2(pvalue)] in a category, and the y-axis means the different subcategories of biological process. The GO terms related to lipid metabolism are represented by red boxes.</p

A semi-screenshot to show the top page of the iDPF-PseRAAAC web-server.

<p>A semi-screenshot to show the top page of the iDPF-PseRAAAC web-server.</p

Validation of sixteen microarray differentially expressed genes by RT-qPCR.

<p>The fold-change value is expressed as positive when the genes are highly expressed in transgenic cattle and as negative when the genes are highly expressed in wild-type cattle. The gene names are displayed below the histogram.</p

Comparing the performance of the proposed method with our previous methods.

<p><b>A:</b> indicated the prediction results of defensin family; <b>B:</b> indicated the prediction results of vertebrate defensin subfamily.</p

The significantly up-regulated lipid metabolism-related genes in <i>fat-1</i> transgenic cattle.

<p>The genes marked with an asterisk are the same as the 11 genes from the PPAR signaling pathways by the KEGG enrichment analysis.</p><p>The significantly up-regulated lipid metabolism-related genes in <i>fat-1</i> transgenic cattle.</p