Ingenity Pathway Analysis (IPA), as a commercialized bio-information analysis software, has been widely adopted in the industry due to the accuracy and authority of its results. Every year, there are dozens of papers published in authoritative magazines such as Nature, Cell, Science, PNAS, etc. using IPA.
IPA algorithm is a statistical test based on Fisher’s exact test to predict whether a molecule belongs to this pathway/transcription/process. In the interpretation of path results, in addition to the P-value of Fisher’s exact test, we can also evaluate from the Z-score indicator. Z-score considers the directional effect of one molecule acting on another molecule or the effect of molecular change multiple in the data set on biological processes.
The specific names of each molecular enrichment pathway and the important indicators mentioned above can be given through IPA analysis
At the same time, a histogram can be used to show the significance and active state of each pathway.
Annotation: As shown in the figure, the height of the histogram shows the significance of this pathway – Log10 (p-value). The higher the column, the higher the significance. Orange indicates that the pathway is predicted to be active, blue indicates that the pathway is predicted to be inhibited, gray indicates that the pathway cannot be predicted by scoring temporarily, and white indicates that it is not predicted to be active or inhibited.
In addition, you can use bubble charts to display the data in the above tables.
Annotation: As shown in the figure, the size of bubbles indicates the number of molecules enriched in each path, the color of bubbles indicates the significance of the path, and the horizontal axis Ratio indicates the proportion of molecules enriched in the path.