Evidence map›Paper›PMID 36427152›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2023

Mapping Transcription Regulation with Run-on and Sequencing Data Using the Web-Based tfTarget Gateway.

Nating Wang, Zhong Wang, Charles G Danko, Tinyi Chu

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 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, top 67% 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

0 citing papers in PubMed, 0 citations in OpenAlex.

No citing paper in PubMed yet.

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

4 authors at 2 institutions in 2 countries.

Nating WangSchool of Software Technology, Dalian University of Technology, Dalian, China.
Zhong WangSchool of Software Technology, Dalian University of Technology, Dalian, China.
Charles G DankoBaker Institute for Animal Health, Cornell University, Ithaca, NY, USA.
Tinyi ChuBaker Institute for Animal Health, Cornell University, Ithaca, NY, USA. tc532@cornell.edu.
Cornell University · USDalian University of Technology · CN

Funding

Mapping RNA polymerase in tissue samples with ChRO-seq.R01HG009309 · NHGRI · CORNELL UNIVERSITY · PI DANKO, CHARLES GRAHE · 2017 to 2021
$1.9M
NHGRI NIH HHS R01 HG009309
6 · The paper itself

Abstract

Run-on and sequencing assays like GRO-seq, PRO-seq, and ChRO-seq allow for joint profiling of transcription activity of transcriptional regulatory elements (TREs), i.e., promoters and active enhancers, and target genes. Variation in biological conditions, such as treated vs. control, results in changes in the activity of transcription factors (TFs), which induces concerted changes in TREs and target genes. By modeling the differences between two biological conditions, we developed the computational pipeline known as tfTarget that predicts a set of putative TREs and target genes responding to each TF under the biological condition of interest. In this chapter, we demonstrate the use of the new web-based tfTarget in mapping transcription regulation using run-on sequencing data.

Indexed as

Gene Expression RegulationRegulatory Elements, TranscriptionalInternetPromoter Regions, GeneticTranscription FactorsTranscription FactorsChRO-seqEnhancersGene regulationGRO-seqPRO-seq

Identifiers

PMID36427152
OpenAlexW4310079732

What OpenQuestion holds

Textmetadata
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.