mosGraphFlow: a novel integrative graph AI model mining disease targets from multi-omic data

Publication date: Aug 05, 2024

Multi-omic data can better characterize complex cellular signaling pathways from multiple views compared to individual omic data. However, integrating multi-omic data to rank key disease biomarkers and infer core signaling pathways remains an open problem. Compared to other AI models, graph AI can integrate multi-omic data with large-scale signaling networks and rank biomarkers and signaling interactions using attention mechanisms. In this study, we present a novel graph AI model, mosGraphFlow, and apply it on multi-omic datasets of Alzheimer’s disease (AD). The comparison results show that the proposed model not only achieves the best classification accuracy but also identifies important AD disease biomarkers and signaling interactions. Moreover, the signaling sources are highlighted at specific omic levels to facilitate the understanding of the pathogenesis of AD. The proposed model can also be applied and expanded for other studies using multi-omic data. And the model code are uploaded via GitHub with link: https://github.com/mosGraph/mosGraphFlow

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Concepts Keywords
Environmental Biorxiv
Graphs Cc
Histopathological Display
Lollipop Expression
Graph
Https
International
Multi
Nodes
Omic
Org
Pathway
Pathways
Preprint
Signaling

Semantics

Type Source Name
drug DRUGBANK Tropicamide
gene GENE TNFRSF11A
gene GENE LARGE1
disease MESH Alzheimer’s disease
gene GENE BEST1
disease MESH pathogenesis
drug DRUGBANK Coenzyme M
gene GENE TPI1
gene GENE ARHGEF5
gene GENE HAVCR1
gene GENE TIMELESS
gene GENE SEPTIN4
gene GENE PRPS1
disease MESH dementia
disease MESH cognitive impairment
disease MESH amyloid plaques
disease MESH neurofibrillary tangles
gene GENE MAPT
disease MESH neuroinflammation
gene GENE TTC41P
gene GENE CELP
gene GENE CEL
gene GENE STIP1
gene GENE HOPX
gene GENE ST13
gene GENE IDS
gene GENE KIT
gene GENE GLYAT
gene GENE CRAT
gene GENE CAT
drug DRUGBANK Ilex paraguariensis leaf
gene GENE MAT1A
gene GENE ACAT1
gene GENE MC3R
disease MESH cancers
gene GENE RPS27A
gene GENE UBC
gene GENE BMS1
gene GENE ACACA
gene GENE KCNK3
gene GENE MAX
gene GENE MSE
gene GENE ENO3
gene GENE LINC00273
gene GENE THOP1
drug DRUGBANK Huperzine B
gene GENE ELAVL2
gene GENE BFAR
gene GENE ADRB2
gene GENE NR1H4
gene GENE IK
gene GENE DYRK3
gene GENE GNG8
gene GENE RXFP2
gene GENE PLA2G4F
gene GENE MYLK2
gene GENE MYLK3
gene GENE PLA2G4C
gene GENE CXCL11
gene GENE NGF
gene GENE ADCY7
gene GENE SOCS5
gene GENE PPP3R2
gene GENE PLA2G4D
gene GENE GH1
gene GENE PTGER3
gene GENE GNGT2
gene GENE VIPR2
gene GENE GNB2
gene GENE PYGL
gene GENE ARF6
gene GENE CCNE1
gene GENE CALML3
gene GENE HOMER2
gene GENE CYTH3
gene GENE SOCS6
gene GENE CDK6
gene GENE NOS2
gene GENE NANOS2
gene GENE CAMK2A
gene GENE AKT3
gene GENE ADCY8
gene GENE PLCG2
gene GENE PHKG1
gene GENE PRKAG1
gene GENE CCND3
gene GENE NFATC3
gene GENE RPS6KA2
gene GENE RAP1B
gene GENE GNG4
gene GENE STAT5B
gene GENE NFKBIE
gene GENE NRAS
gene GENE GNAI3
gene GENE CALML5
gene GENE PHKA2
gene GENE CAMK2D
gene GENE ADRA1A
gene GENE ADRA1D
gene GENE RPS6KA6
gene GENE MAPK8
gene GENE ADCY9
gene GENE GNG10
gene GENE CAMK1D
gene GENE MAPKAPK3
gene GENE TAB2
gene GENE VEGFC
gene GENE MAP3K20
gene GENE MAP3K1
gene GENE FGFR4
gene GENE MAP3K8
gene GENE CYTH2
gene GENE GNG5
gene GENE GNG11
gene GENE PPP1R3C
gene GENE ADCY6
gene GENE RASGRP1
gene GENE BPIFA4P
disease MESH virus infection
disease MESH cytomegalovirus infection
drug DRUGBANK Rasagiline
drug DRUGBANK Calcium
drug DRUGBANK Oxytocin
disease MESH Morphine addiction
gene GENE APLN
gene GENE REG1A
drug DRUGBANK L-Tryptophan
gene GENE TYRP1
drug DRUGBANK Gonadorelin
gene GENE GNRH1
gene GENE APLNR
gene GENE PIK3CG
gene GENE PIK3CD
gene GENE PIK3CA
gene GENE PIK3CB
gene GENE AKT1
disease MESH oxidative stress
disease MESH neurological disorders
gene GENE SMAD2
gene GENE RXFP1
gene GENE EIF2AK3
gene GENE NOS1
disease MESH fibrosis
drug DRUGBANK Cyclic Adenosine Monophosphate
gene GENE CAMP
gene GENE CHAMP1
gene GENE PRRT2
gene GENE VEGFA
gene GENE OXT
gene GENE EPHB2
gene GENE MAPK1
gene GENE AHSA1
gene GENE POLDIP2
gene GENE GRAP2
gene GENE MAPK14
gene GENE CRK
gene GENE AIMP2
gene GENE COX5A
gene GENE CPOX
gene GENE COX8A
gene GENE ISYNA1
disease MESH brain inflammation
gene GENE MAPK3
disease MESH death
gene GENE CASP3
drug DRUGBANK Ketamine
disease MESH pathological processes
gene GENE CLOCK
gene GENE BMAL1
gene GENE TNFSF14
gene GENE TBATA

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