Evidence map›Paper›PMID 27933038›Full record

ArticleFrontiers in microbiology2016

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation.

José P Faria, James J Davis, Janaka N Edirisinghe, Ronald C Taylor, Pamela Weisenhorn, Robert D Olson, Rick L Stevens, Miguel Rocha, Isabel Rocha, Aaron A Best and 5 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in microbiology, 2016. 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
1.0field-weighted citation impact, top 21% 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, 9 citations in OpenAlex.

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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

15 authors at 6 institutions in 2 countries.

José P FariaComputation Institute, University of ChicagoChicago, IL, USA; Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne, IL, USA; Centre of Biological Engineering, University of Minho, Campus de GualtarBraga, Portugal; Mathematics and Computer Science Division, Argonne National LaboratoryArgonne, IL, USA.
James J DavisComputation Institute, University of ChicagoChicago, IL, USA; Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne, IL, USA.
Janaka N EdirisingheComputation Institute, University of ChicagoChicago, IL, USA; Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne, IL, USA.
Ronald C TaylorComputational Biology and Bioinformatics Group, Pacific Northwest National Laboratory (U.S. Dept. of Energy) Richland, WA, USA.
Pamela WeisenhornMathematics and Computer Science Division, Argonne National Laboratory Argonne, IL, USA.
Robert D OlsonComputation Institute, University of ChicagoChicago, IL, USA; Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne, IL, USA.
Rick L StevensComputation Institute, University of ChicagoChicago, IL, USA; Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne, IL, USA; Department of Computer Science, Ryerson Physical Laboratory, University of ChicagoChicago, IL, USA.
Miguel RochaCentre of Biological Engineering, University of Minho, Campus de Gualtar Braga, Portugal.
Isabel RochaCentre of Biological Engineering, University of Minho, Campus de Gualtar Braga, Portugal.
Aaron A BestBiology Department, Hope College Holland, MI, USA.
Matthew DeJonghComputer Science Department, Hope College Holland, MI, USA.
Nathan L TintleDepartment of Mathematics, Statistics and Computer Science, Dordt College Sioux Center, IA, USA.
Bruce ParrelloComputing, Environment and Life Sciences, Argonne National LaboratoryArgonne, IL, USA; Fellowship for Interpretation of GenomesBurr Ridge, IL, USA.
Ross OverbeekComputation Institute, University of ChicagoChicago, IL, USA; Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne, IL, USA; Fellowship for Interpretation of GenomesBurr Ridge, IL, USA.
Christopher S HenryComputation Institute, University of ChicagoChicago, IL, USA; Mathematics and Computer Science Division, Argonne National LaboratoryArgonne, IL, USA.
Argonne National Laboratory · USHope College · USUniversity of Minho · PTDordt University · USPacific Northwest National Laboratory · USUniversity of Chicago · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Understanding gene function and regulation is essential for the interpretation, prediction, and ultimate design of cell responses to changes in the environment. An important step toward meeting the challenge of understanding gene function and regulation is the identification of sets of genes that are always co-expressed. These gene sets,

Indexed as

atomic regulonCLRclusteringEscherichia coligene expression analysishierarchical clusteringk-means clusteringtranscriptomic data

Identifiers

PMID27933038
PMCPMC5121216
OpenAlexW2548072407

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.