Evidence map›Paper›PMID 31612944›Full record

ArticleNucleic acids research2020

Transcriptome visualization and data availability at the Saccharomyces Genome Database.

Patrick C Ng, Edith D Wong, Kevin A MacPherson, Suzi Aleksander, Joanna Argasinska, Barbara Dunn, Robert S Nash, Marek S Skrzypek, Felix Gondwe, Sagar Jha and 6 more

Open access · goldAbstract read
In one paragraph

Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
1.4field-weighted citation impact, top 19% 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

14 citing papers in PubMed, 23 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. bioRxiv : the preprint server for biology · 2024
    Article
  7. Article
  8. Article
  9. Article
  10. Prospective bacterial and fungal sources of hyaluronic acid: A review.Computational and structural biotechnology journal · 2022
    Review
  11. Article
  12. Article
  13. Review
  14. Automated generation of gene summaries at the Alliance of Genome Resources.Database : the journal of biological databases and curation · 2020
    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

16 authors at 2 institutions in 1 country.

Patrick C NgDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Edith D WongDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Kevin A MacPhersonOregon Health Sciences University, Portland, OR 97239, USA.
Suzi AleksanderDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Joanna ArgasinskaDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Barbara DunnDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Robert S NashDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Marek S SkrzypekDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Felix GondweDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Sagar JhaDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Kalpana KarraDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Shuai WengDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Stuart MiyasatoDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Matt SimisonDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Stacia R EngelDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
J Michael CherryDepartment of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA.
Palo Alto University · USOregon Health & Science University · US

Funding

Resource ProjectU41HG002273 · NHGRI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI CHERRY, J. MICHAEL, MUNGALL, CHRISTOPHER J · 2012 to 2021
$34.7M
Genomic Resource for the Yeast SaccharomycesU41HG001315 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2011 to 2020
$26.4M
WormBase: a core data resource for C. elegans and other nematodesU41HG002223 · NHGRI · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI KERSEY, PAUL, SCHEDL, TIM · 2013 to 2017
$20.5M
NHGRI NIH HHS U41 HG001315NHGRI NIH HHS U41 HG002223NHGRI NIH HHS U41 HG002273
6 · The paper itself

Abstract

The Saccharomyces Genome Database (SGD; www.yeastgenome.org) maintains the official annotation of all genes in the Saccharomyces cerevisiae reference genome and aims to elucidate the function of these genes and their products by integrating manually curated experimental data. Technological advances have allowed researchers to profile RNA expression and identify transcripts at high resolution. These data can be configured in web-based genome browser applications for display to the general public. Accordingly, SGD has incorporated published transcript isoform data in our instance of JBrowse, a genome visualization platform. This resource will help clarify S. cerevisiae biological processes by furthering studies of transcriptional regulation, untranslated regions, genome engineering, and expression quantification in S. cerevisiae.

Indexed as

Genome, FungalTranscriptomeComputational BiologyDatabases, GeneticGenomicsMolecular Sequence AnnotationOpen Reading FramesProtein IsoformsReference ValuesRNA-SeqSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsUser-Computer InterfaceWeb BrowserProtein IsoformsSaccharomyces cerevisiae Proteins

Identifiers

PMID31612944
PMCPMC7061941
OpenAlexW2980573777

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.