Evidence map›Paper›PMID 35705328›Full record

ArticleGenome research2022

Dynamic regulatory module networks for inference of cell type-specific transcriptional networks.

Alireza Fotuhi Siahpirani, Sara Knaack, Deborah Chasman, Morten Seirup, Rupa Sridharan, Ron Stewart, James Thomson, Sushmita Roy

Open access · hybridAbstract read
In one paragraph

Article in Genome research, 2022. 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
–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

4 citing papers in PubMed, 6 citations in OpenAlex.

  1. Review
  2. Article
  3. 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

8 authors at 3 institutions in 1 country.

Alireza Fotuhi Siahpirani *Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, USA.
Sara Knaack *Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, USA.ORCID http://orcid.org/0000-0002-1178-2517
Deborah Chasman *Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, USA.
Morten SeirupMorgridge Institute for Research, Madison, Wisconsin 53715, USA.
Rupa SridharanWisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, USA.
Ron StewartMorgridge Institute for Research, Madison, Wisconsin 53715, USA.
James ThomsonMorgridge Institute for Research, Madison, Wisconsin 53715, USA.
Sushmita RoyWisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, USA.
University of Wisconsin–Madison · USUniversity of Wisconsin System · USMorgridge Institute for Research · US

Funding

R01 Renewal: Collaboration of chromatin remodeling and signaling pathways in pluripotencyR01GM113033 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI SRIDHARAN, RUPA · 2015 to 2023
$2.9M
Computational Inference of Regulatory Network Dynamics on Cell LineagesR01GM117339 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI ROY, SUSHMITA · 2016 to 2020
$1.5M
NIGMS NIH HHS R01 GM113033NIGMS NIH HHS R01 GM117339
6 · The paper itself

Abstract

Changes in transcriptional regulatory networks can significantly alter cell fate. To gain insight into transcriptional dynamics, several studies have profiled bulk multi-omic data sets with parallel transcriptomic and epigenomic measurements at different stages of a developmental process. However, integrating these data to infer cell type-specific regulatory networks is a major challenge. We present dynamic regulatory module networks (DRMNs), a novel approach to infer cell type-specific

Indexed as

Gene Regulatory NetworksGenomeChromatinGenomicsTranscriptomeChromatin

Identifiers

PMID35705328
PMCPMC9341506
OpenAlexW4282974527

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.