Evidence map›Paper›PMID 37066361›Full record

ArticlebioRxiv : the preprint server for biology2023

Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions.

Mateusz Chiliński, Jakub Lipiński, Abhishek Agarwal, Yijun Ruan, Dariusz Plewczynski

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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, 1 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors at 3 institutions in 3 countries.

Mateusz ChilińskiLaboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw 00-662, Poland.
Jakub LipińskiCellular Genomics, Warsaw, Poland.
Abhishek AgarwalLaboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.
Yijun RuanThe Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA.
Dariusz PlewczynskiLaboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw 00-662, Poland.
Warsaw University of Technology · PLJackson Laboratory · USUniversity of Warsaw · PL

Funding

Nucleome Positioning System for Spatiotemporal Genome Organization and RegulationU54DK107967 · NIDDK · JACKSON LABORATORY · PI WEI, CHIA-LIN · 2015 to 2019
$3.6M
NIDDK NIH HHS U54 DK107967
6 · The paper itself

Abstract

There have been multiple attempts to predict the expression of the genes based on the sequence, epigenetics, and various other factors. To improve those predictions, we have decided to investigate adding protein-specific 3D interactions that play a major role in the compensation of the chromatin structure in the cell nucleus. To achieve this, we have used the architecture of one of the state-of-the-art algorithms, ExPecto (J. Zhou et al., 2018), and investigated the changes in the model metrics upon adding the spatially relevant data. We have used ChIA-PET interactions that are mediated by cohesin (24 cell lines), CTCF (4 cell lines), and RNAPOL2 (4 cell lines). As the output of the study, we have developed the Spatial Gene Expression (SpEx) algorithm that shows statistically significant improvements in most cell lines.

Identifiers

PMID37066361
PMCPMC10104055
OpenAlexW4362662553

What OpenQuestion holds

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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.