Evidence map›Paper›PMID 35053314›Full record

ArticleCells2022

Correcting Differential Gene Expression Analysis for Cyto-Architectural Alterations in Substantia Nigra of Parkinson's Disease Patients Reveals Known and Potential Novel Disease-Associated Genes and Pathways.

Federico Ferraro, Christina Fevga, Vincenzo Bonifati, Wim Mandemakers, Ahmed Mahfouz, Marcel Reinders

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cells, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.1field-weighted citation impact, top 57% of its field
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

1 citing paper in PubMed, 1 citations in OpenAlex.

  1. Review
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

6 authors at 2 institutions in 1 country.

Federico FerraroErasmus MC, Department of Clinical Genetics, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.ORCID 0000-0003-1365-2529
Christina FevgaErasmus MC, Department of Clinical Genetics, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.ORCID 0000-0001-8267-564X
Vincenzo BonifatiErasmus MC, Department of Clinical Genetics, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.
Wim MandemakersErasmus MC, Department of Clinical Genetics, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands.ORCID 0000-0003-2673-5972
Ahmed MahfouzDelft Bioinformatics Labaratory, Delft University of Technology, 2628 XE Delft, The Netherlands.
Marcel ReindersDelft Bioinformatics Labaratory, Delft University of Technology, 2628 XE Delft, The Netherlands.ORCID 0000-0002-1148-1562
Erasmus MC · NLLeiden University Medical Center · NL

Funding

Alzheimer Nederland WE.03-2019-07Stichting ParkinsonFonds 110825Stichting ParkinsonFonds 110875
6 · The paper itself

Abstract

Several studies have analyzed gene expression profiles in the substantia nigra to better understand the pathological mechanisms causing Parkinson's disease (PD). However, the concordance between the identified gene signatures in these individual studies was generally low. This might have been caused by a change in cell type composition as loss of dopaminergic neurons in the substantia nigra pars compacta is a hallmark of PD. Through an extensive meta-analysis of nine previously published microarray studies, we demonstrated that a big proportion of the detected differentially expressed genes was indeed caused by cyto-architectural alterations due to the heterogeneity in the neurodegenerative stage and/or technical artefacts. After correcting for cell composition, we identified a common signature that deregulated the previously unreported ammonium transport, as well as known biological processes such as bioenergetic pathways, response to proteotoxic stress, and immune response. By integrating with protein interaction data, we shortlisted a set of key genes, such as

Indexed as

Gene Expression ProfilingGenetic Predisposition to DiseaseAgedAged, 80 and overDown-RegulationEndothelial CellsFemaleHumansLinear ModelsMaleNeuronsParkinson DiseaseProtein Interaction MapsRisk FactorsSignal TransductionSubstantia Nigracyto-architectureinteractome analysismeta-analysisParkinson’s diseasetranscriptome analysis

Identifiers

PMID35053314
PMCPMC8774027
OpenAlexW4205685969

What OpenQuestion holds

Textmetadata
LicenceCC BY
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 OpenQuestion graph.