Evidence map›Paper›PMID 36941541›Full record

ArticleBMC bioinformatics2023

Snapshot: a package for clustering and visualizing epigenetic history during cell differentiation.

Guanjue Xiang, Belinda Giardine, Lin An, Chen Sun, Cheryl A Keller, Elisabeth F Heuston, Stacie M Anderson, Martha Kirby, David Bodine, Yu Zhang and 1 more

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

Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
2.2field-weighted citation impact, top 13% 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

4 citing papers in PubMed, 15 citations in OpenAlex.

  1. Whole genome sequencing of neurotoxin-producingFrontiers in public health · 2025
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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

11 authors at 2 institutions in 1 country.

Guanjue XiangThe Bioinformatics and Genomics Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA. guanjuexiang@gmail.com.
Belinda GiardineDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Lin AnThe Bioinformatics and Genomics Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
Chen SunDepartment of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, USA.
Cheryl A KellerDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Elisabeth F HeustonNHGRI Hematopoiesis Section, GMBB, Bethesda, MD, USA.
Stacie M AndersonNHGRI Flow Cytometry Core, Bethesda, MD, USA.
Martha KirbyNHGRI Flow Cytometry Core, Bethesda, MD, USA.
David BodineNHGRI Hematopoiesis Section, GMBB, Bethesda, MD, USA.
Yu ZhangDepartment of Statistics, The Pennsylvania State University, University Park, PA, USA.
Ross C HardisonDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA. rch8@psu.edu.ORCID http://orcid.org/0000-0003-4084-7516
Pennsylvania State University · USNational Human Genome Research Institute · US

Funding

VISION: ValIdated Systematic IntegratiON of epigenomic dataR24DK106766 · NIDDK · PENNSYLVANIA STATE UNIVERSITY, THE · PI BLOBEL, GERD A, BODINE, DAVID M. · 2016 to 2020
$6.2M
A 2D segmentation method for jointly characterizing epigenetic dynamics in multiple cell linesR01GM121613 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI MAHONY, SHAUN AENGUS · 2017 to 2019
$1.0M
NHGRI NIH HHS Internal fundsNIDDK NIH HHS R24 DK106766NIGMS NIH HHS R01 GM121613NIH HHS DK106766NIH HHS GM121613
6 · The paper itself

Abstract

backgroundEpigenetic modification of chromatin plays a pivotal role in regulating gene expression during cell differentiation. The scale and complexity of epigenetic data pose significant challenges for biologists to identify the regulatory events controlling cell differentiation.

resultsTo reduce the complexity, we developed a package, called Snapshot, for clustering and visualizing candidate cis-regulatory elements (cCREs) based on their epigenetic signals during cell differentiation. This package first introduces a binarized indexing strategy for clustering the cCREs. It then provides a series of easily interpretable figures for visualizing the signal and epigenetic state patterns of the cCREs clusters during the cell differentiation. It can also use different hierarchies of cell types to highlight the epigenetic history specific to any particular cell lineage. We demonstrate the utility of Snapshot using data from a consortium project for ValIdated Systematic IntegratiON (VISION) of epigenomic data in hematopoiesis.

conclusionThe package Snapshot can identify all distinct clusters of genomic locations with unique epigenetic signal patterns during cell differentiation. It outperforms other methods in terms of interpreting and reproducing the identified cCREs clusters. The package of Snapshot is available at GitHub: https://github.com/guanjue/Snapshot .

Indexed as

ChromatinEpigenomicsCell DifferentiationCluster AnalysisEpigenesis, GeneticChromatincCRE Clustering and VisualizationcCRE indexingCell differentiationEpigenetic state visualization

Identifiers

PMID36941541
PMCPMC10026520
OpenAlexW4328049593

What OpenQuestion holds

Textfull text, public
LicenceCC BY
measurements read27
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.