Table 1 Genes and pathways found in evidence chains that have an effect in preclinical experiments in the Fmr1 KO mouse model for Ibudilast

From: An experimentally validated approach to automated biological evidence generation in drug discovery using knowledge graphs

Gene

P value

Pathway associated

FDR-adjusted pathway P value

PDE4D

0.0276 ↑

cAMP signalling pathway

1.02 E-4 ↑

PENK

0.0434 ↓

Neuroactive ligand–receptor interaction

0.0123 ↓

FOS

0.0602 ↑(significant logFC = 0.854)

cAMP signalling pathway

1.02 E-4 ↑

AKT1

0.029 ↓

cAMP signalling pathway

1.02 E-4 ↑

MEF2C

0.0287 ↑

cGMP-PKG signalling pathway

0.0184 ↑

NPY2R

0.0094 ↓

Neuroactive ligand–receptor interaction

0.0123 ↓

  1. Columns are Gene; HGNC gene symbol, P value; statistical significance of the gene being differentially expressed based on an estimate of log fold change following drug treatment. Values computed by DESeq2, P values are two-sided. Pathway associated; pathway term describing gene function following analysis by gene set enrichment analysis, FDR-adjusted pathway P value; statistical significance of pathway enrichment score corrected for multiple hypothesis testing using Benjamini–Hochberg procedure.
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