Evidence map›Paper›PMID 39179972›Full record

ArticleBMC genomics2024

A novel method for cell deconvolution using DNA methylation in PCA space.

Huan Xu, Ge Zhang, Jing Chen

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Article
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

3 authors.

Huan XuDivision of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Ge ZhangDivision of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Jing ChenDepartment of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. jing.chen2@cchmc.org.

Funding

Integrating genomic studies of gestational duration and birth weight to understand maternal and fetal causes of adverse pregnancy outcomes and links with later diseasesR01HD101669 · NICHD · CINCINNATI CHILDRENS HOSP MED CTR · PI FREATHY, RACHEL, JACOBSSON, BO · 2021 to 2024
$2.1M
Burroughs Wellcome Fund 10172896Eunice Kennedy Shriver National Institute of Child Health and Human Development R01HD101669NICHD NIH HHS R01 HD101669
6 · The paper itself

Abstract

backgroundIn this study, we present a novel method for reference-based cell deconvolution using data from DNA methylation arrays. Different from existing methods like IDOL-Ext, which operate on probe-level data, our approach represents features in the principal component analysis (PCA) space for cell type deconvolution.

resultsOur method's accuracy in estimating cell compositions is validated across various public datasets, including blood samples from glioma patients. It demonstrates precision comparable to IDOL-Ext, with R

conclusionsOur study confirms the efficacy of cell type deconvolution in PCA space. The results indicate wide-ranging applicability and potential for adaptation to other forms of genomic data.

Indexed as

DNA MethylationGliomaPrincipal Component AnalysisHumansBioinformaticsCell deconvolutionDNA methylationPrincipal component analysis

Identifiers

PMID39179972
PMCPMC11344294

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Registered trials

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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.