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Table 10 Top five important pathways sorted by p-value for each gene list

From: Combining entity co-occurrence with specialized word embeddings to measure entity relation in Alzheimer’s disease

Proposed
Pathway nameEntitiesReactions
foundratiop-valueFDR*foundratio
 Nuclear signaling by ERBB43 / 350.0025.37e-050.0123 / 220.002
 Signaling by interleukins7 / 6400.0462.60e-040.0196 / 4910.041
 MECP2 regulates transcription of neuronal ligands3 / 610.0042.74e-040.0193 / 370.003
 Signaling by receptor tyrosine kinases2 / 139.25e-043.41e-040.0192 / 86.68e-04
 NRIF signals cell death from the nucleus6 / 5210.0375.89e-040.02371 / 6330.053
Co-occurrence
 MECP2 regulates transcription of neuronal ligands2 / 139.25e-043.18e-040.0362 / 86.68e-04
 RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs)2 / 170.0015.41e-040.0362 / 200.002
 NRIF signals cell death from the nucleus2 / 180.0016.06e-040.0364 / 75.84e-04
 Amyloid fiber formation3 / 880.0067.15e-040.03616 / 330.003
 Neurodegenerative diseases2 / 300.0020.0020.0562 / 220.002
COALS
 Plasma lipoprotein assembly3 / 300.0024.18e-050.018 / 190.002
 MECP2 regulates transcription of neuronal ligands2 / 139.25e-043.91e-040.0422 / 86.68e-04
 HDL assembly2 / 180.0017.44e-040.0427 / 97.51e-04
 NRIF signals cell death from the nucleus2 / 180.0017.44e-040.0424 / 75.84e-04
 Amyloid fiber formation3 / 880.0069.67e-040.04416 / 330.003
Word2Vec
 Transfer of LPS from LBP carrier to CD141 / 32.13e-040.0050.0752 / 21.67e-04
 NTF3 activates NTRK2 (TRKB) signaling1 / 42.85e-040.0060.0753 / 32.50e-04
 NTF4 activates NTRK2 (TRKB) signaling1 / 42.85e-040.0060.0753 / 32.50e-04
 BDNF activates NTRK2 (TRKB) signaling1 / 42.85e-040.0060.0753 / 32.50e-04
Defective GSS causes glutathione synthetase deficiency (GSS deficiency)1 / 42.85e-040.0060.0751 / 18.34e-05
  1. * False Discovery Rate