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. 2019 Mar 26;10:235. doi: 10.3389/fgene.2019.00235

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Copyright © 2019 Verma, Shukla, Pandey, MacLennan and Gupta.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Ingenuity pathway analysis of differentially expressed transcript in TRAMP mice compared with non-transgenic littermates. The stacked bar chart represents the percentage (%) of genes that were upregulated (red), and downregulated (green) and genes not overlapped with TRAMP mouse dataset (white) in each canonical pathway. The numerical value at the top of each bar represents the total number of genes in the canonical pathway. The secondary y-axis (down) shows the –log of P-value calculated by the Benjamini-Hochberg (B-H) method; the B-H method was used to adjust the right-tailed Fisher's exact test P-value, which indicates the significance of each pathway (left panel graph). The right panel graph calculated z-score indicates a pathway with genes exhibiting decreased mRNA levels (blue bars) or under the state of inhibition (light blue bars). The ratio (orange dots connected by a line) indicates the ratio of genes from the dataset that map to the pathway divided by the total number of genes that map to the same pathway.