Evidence map›Paper›PMID 24068387›Full record

ArticleDevelopment genes and evolution2013

Functional analysis of limb enhancers in the developing fin.

Betty M Booker, Karl K Murphy, Nadav Ahituv

Open access · greenAbstract read
In one paragraph

Article in Development genes and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.3field-weighted citation impact, top 39% 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

5 citing papers in PubMed, 7 citations in OpenAlex.

  1. Review
  2. Article
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  5. 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

3 authors at 1 institution in 1 country.

Betty M BookerDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
Karl K Murphy
Nadav Ahituv
University of California, San Francisco · US

Funding

PHARMACOGENETICS OF MEMBRANE TRANSPORTERSU01GM061390 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GIACOMINI, KATHLEEN M · 2000 to 2009
$29.2M
Research BaseP30DK063720 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GERMAN, MICHAEL S · 2003 to 2019
$21.8M
UCSF IRACDA Scholars ProgramK12GM081266 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Raymond M. Esquerra, HOLLY A. INGRAHAM · 2007 to 2026
$19.4M
Pharmacogenomics of Membrane TransportersU19GM061390 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KWOK, PUI-YAN · 2010 to 2014
$16.3M
Characterization of regulatory elements leading to human limb malformationsR01HD059862 · NICHD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV, BEJERANO, GILL · 2009 to 2013
$2.2M
Massively parallel, in vivo functional testing of regulatory elementsR01HG006768 · NHGRI · UNIVERSITY OF WASHINGTON · PI AHITUV, NADAV, SHENDURE, JAY ASHOK · 2012 to 2014
$1.8M
Computational & Functional Annotation of the Zebrafish Genome Regulatory ToolboxR01HG005058 · NHGRI · STANFORD UNIVERSITY · PI AHITUV, NADAV, BEJERANO, GILL · 2009 to 2012
$1.6M
Identification & functional characterization of SIM1 obesity-associated variantsR01DK090382 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV, VAISSE, CHRISTIAN · 2012 to 2015
$1.3M
Characterization of neuronal gene regulatory elements associated with epilepsyR01NS079231 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV · 2012 to 2015
$1.2M
NHGRI NIH HHS 1R01HG006768NHGRI NIH HHS R01 HG005058NHGRI NIH HHS R01HG005058NHGRI NIH HHS R01 HG006768NICHD NIH HHS R01 HD059862NICHD NIH HHS R01HD059862NIDDK NIH HHS 1R01DK090382NIDDK NIH HHS P30 DK063720NIDDK NIH HHS R01 DK090382NIGMS NIH HHS 2K12GM081266NIGMS NIH HHS GM61390NIGMS NIH HHS K12 GM081266NIGMS NIH HHS U01 GM061390NIGMS NIH HHS U19 GM061390NINDS NIH HHS 1R01NS079231NINDS NIH HHS R01 NS079231
6 · The paper itself

Abstract

Despite diverging ∼365 million years ago, tetrapod limbs and pectoral fins express similar genes that could be regulated by shared regulatory elements. In this study, we set out to analyze the ability of enhancers to maintain tissue specificity in these two divergent structures. We tested 22 human sequences that were previously reported as mouse limb enhancers for their enhancer activity in zebrafish (Danio rerio). Using a zebrafish enhancer assay, we found that 10/22 (45 %) were positive for pectoral fin activity. Analysis of the various criteria that correlated with positive fin activity found that both spatial limb activity and evolutionary conservation are not good predictors of fin enhancer activity. These results suggest that zebrafish enhancer assays may be limited in detecting human limb enhancers, and this limitation does not improve by the use of limb spatial expression or evolutionary conservation.

Indexed as

Biological EvolutionGene Expression Regulation, DevelopmentalAnimal FinsAnimalsZebrafish

Identifiers

PMID24068387
PMCPMC3869458
OpenAlexW1970907164

What OpenQuestion holds

Textmetadata
LicenceTDM
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.