Evidence map›Paper›PMID 36814847›Full record

ArticleCell reports methods2023

MINE is a method for detecting spatial density of regulatory chromatin interactions based on a multi-modal network.

Haiyan Gong, Minghong Li, Mengdie Ji, Xiaotong Zhang, Zan Yuan, Sichen Zhang, Yi Yang, Chun Li, Yang Chen

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

Article in Cell reports methods, 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
0.8field-weighted citation impact, top 28% 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, 5 citations in OpenAlex.

  1. Article
  2. Article
  3. [Advances in methods and applications of single-cell Hi-C data analysis].Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi · 2023
    Article
  4. 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

9 authors at 2 institutions in 1 country.

Haiyan GongBeijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China.
Minghong LiBeijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China.
Mengdie JiState Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China.
Xiaotong ZhangBeijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China.
Zan YuanState Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China.
Sichen ZhangBeijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China.
Yi YangBeijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China.
Chun LiSchool of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China.
Yang ChenState Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China.
University of Science and Technology Beijing · CNChinese Academy of Medical Sciences & Peking Union Medical College · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Chromatin interactions play essential roles in chromatin conformation and gene expression. However, few tools exist to analyze the spatial density of regulatory chromatin interactions (SD-RCI). Here, we present the multi-modal network (MINE) toolkit, including MINE-Loop, MINE-Density, and MINE-Viewer. The MINE-Loop network aims to enhance the detection of RCIs, MINE-Density quantifies the SD--RCI, and MINE-Viewer facilitates 3D visualization of the density of chromatin interactions and participating regulatory factors (e.g., transcription factors). We applied MINE to investigate the relationship between the SD-RCI and chromatin volume change in HeLa cells before and after liquid-liquid phase separation. Changes in SD-RCI before and after treating the HeLa cells with 1,6-hexanediol suggest that changes in chromatin organization was related to the degree of activation or repression of genes. Together, the MINE toolkit enables quantitative studies on different aspects of chromatin conformation and regulatory activity.

Indexed as

ChromatinChromosomesHeLa CellsHumansTranscription FactorsChromatinTranscription Factors3D visualizationHi-Cmulti-modal networkregulatory chromatin interactionsspatial density

Identifiers

PMID36814847
PMCPMC9939382
OpenAlexW4315779664

What OpenQuestion 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 OpenQuestion graph.