Evidence map›Paper›PMID 30097049›Full record

ArticleGenome biology2018

ChromTime: modeling spatio-temporal dynamics of chromatin marks.

Petko Fiziev, Jason Ernst

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Article
  5. Review
  6. Review
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

2 authors.

Petko FizievBioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.
Jason ErnstBioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA. jason.ernst@ucla.edu.ORCID 0000-0003-4026-7853

Funding

"Ribonomics" of Gene Regulation to predict Innate Immune ResponsesU01HG007912 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI BLACK, DOUGLAS L, HOFFMANN, ALEXANDER · 2015 to 2017
$5.8M
Deciphering the Relationship between Substance Use and Psychiatric Disorders from Whole Genome Sequencing DataDP1DA044371 · NIDA · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ERNST, JASON · 2017 to 2021
$2.3M
Epigenomic control of RNA splicingR01ES024995 · NIEHS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI HOFFMANN, ALEXANDER, XING, YI · 2014 to 2015
$616k
NHGRI NIH HHS U01 HG007912NIDA NIH HHS DP1 DA044371NIEHS NIH HHS R01 ES024995
6 · The paper itself

Abstract

To model spatial changes of chromatin mark peaks over time we develop and apply ChromTime, a computational method that predicts peaks to be either expanding, contracting, or holding steady between time points. Predicted expanding and contracting peaks can mark regulatory regions associated with transcription factor binding and gene expression changes. Spatial dynamics of peaks provide information about gene expression changes beyond localized signal density changes. ChromTime detects asymmetric expansions and contractions, which for some marks associate with the direction of transcription. ChromTime facilitates the analysis of time course chromatin data in a range of biological systems.

Indexed as

SoftwareChromatinDatabases, GeneticDeoxyribonuclease IGene Expression RegulationHistonesMethylationModels, GeneticProtein BindingReproducibility of ResultsTime FactorsTranscription FactorsTranscription, GeneticChromatinDeoxyribonuclease IHistonesTranscription FactorsChromatin marksEpigenomicsHistone modificationsSpatial dynamicsTime course

Identifiers

PMID30097049
PMCPMC6085762

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.