Evidence map›Paper›PMID 39605436›Full record

ArticlebioRxiv : the preprint server for biology2024

Identifying Alzheimer's disease-associated genes using PhenoGeneRanker.

Most Tahmina Rahman, Fahad Saeed, Serdar Bozdag, Alzheimer’s Disease Neuroimaging Initiative

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Most Tahmina RahmanDepartment of Computer Science and Engineering, University of North Texas, 1155 Union Circle #311366 Denton, Texas 76203, United States.ORCID 0009-0004-6096-0713
Fahad SaeedKnight Foundation School of Computing and Information Sciences, Florida International University, 11200 SW 8 Street, CASE 354 Miami, Florida 33199, United States.ORCID 0000-0002-3410-9552
Serdar BozdagDepartment of Computer Science and Engineering, University of North Texas, 1155 Union Circle #311366 Denton, Texas 76203, United States.ORCID 0000-0002-4813-4310
Alzheimer’s Disease Neuroimaging Initiative

Funding

Alzheimer's Disease Neuroimaging Initiative - SupplementU01AG024904 · NIA · NORTHERN CALIFORNIA INSTITUTE RES &EDUC · PI WEINER, MICHAEL W · 2004 to 2015
$121.0M
lntegrating multi-omics datasets to infer phenotype-specific driver genes, regulatory interactions and drug responseR35GM133657 · NIGMS · UNIVERSITY OF NORTH TEXAS · PI Serdar Bozdag · 2019 to 2026
$3.1M
NIA NIH HHS U01 AG024904NIGMS NIH HHS R35 GM133657
6 · The paper itself

Abstract

Alzheimer's disease (AD) is a neurogenerative disease that affects millions worldwide with no effective treatment. Several studies have been conducted to decipher to genomic underpinnings of AD. Due to its complex nature, many genes have been found to be associated with AD. Despite these findings, the pathophysiology of the disease is still elusive. To discover new putative AD-associated genes, in this study, we integrated multimodal gene and phenotype datasets of AD using network biology methods to prioritize potential AD-related genes. We constructed a multiplex heterogeneous network composed of patient and gene similarity networks utilizing phenotypic and omics datasets of AD patients from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. We applied PhenoGeneRanker to traverse this network to discover potential AD-associated genes. To assess the impact of each network layer and seed gene, we also run PhenoGeneRanker on different variants of the network and seed genes. Our results showed that top-ranked genes captured several known AD-related genes and were enriched in Gene Ontology (GO) terms related to AD. We also observed that several top-ranked genes that are not in AD-associated gene list had literature supporting their potential relevance to AD.

Indexed as

Alzheimer’s Disease genesAPPgene prioritizationnetwork biologynetwork propagationPhenoGeneRanker

Identifiers

PMID39605436
PMCPMC11601490

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.