Pathway analysis of Ppt1 deficiency

The IPA software (Ingenuity systems) contains a library of biological pathways published in the literature that are ranked by the significance of the association between the dataset and the canonical pathway. This significance is defined by two parameters: (a) the ratio of the number of proteins from the input dataset that are pertaining to a particular pathway divided by the total number of genes ascribed by the Ingenuity Knowledge Database to that canonical pathway and (b) a P value calculated using Fischer’s test that determines whether the probability of association between component proteins in the input dataset and the canonical pathway are due to chance. Prediction activation scores (z score) are a statistical measure of the match between an expected relationship direction and the observed protein expression within the input dataset. A positive z score indicates activation while a negative z score indicate inhibitiony^{16 (link),18 (link),68 (link)}. A 1.2 fold-change (20%) threshold filter was applied in IPA to the datasets for 3 month cortex, 3 month spinal cord and 7 month spinal cord (Ppt1^−/− vs. wildtype respectively), analyzed and observed interactions were selected for this analysis.

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Nelvagal H.R., Hurtado M.L., Eaton S.L., Kline R.A., Lamont D.J., Sands M.S., Wishart T.M, & Cooper J.D. (2020). Comparative proteomic profiling reveals mechanisms for early spinal cord vulnerability in CLN1 disease. Scientific Reports, 10, 15157.

Publication 2020

IPA software

Biological Cortex Genes Library Ppt1 Protein Spinal cord

Corresponding Organization :

Other organizations : Washington University in St. Louis, Roslin Institute, University of Edinburgh, University of Dundee, King's College London

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Variable analysis

independent variables

Ppt1-/- knockout genotype (compared to wildtype)

dependent variables

Ratio of the number of proteins from the input dataset that are pertaining to a particular pathway divided by the total number of genes ascribed by the Ingenuity Knowledge Database to that canonical pathway
P value calculated using Fischer's test that determines whether the probability of association between component proteins in the input dataset and the canonical pathway are due to chance
Prediction activation scores (z score) - a statistical measure of the match between an expected relationship direction and the observed protein expression within the input dataset

control variables

Wildtype (control) group

controls

Positive control: Not specified
Negative control: Wildtype group

Annotations

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