Evidence map›Paper›PMID 33396416›Full record

ArticleGenes2020

Mapping the Transcriptional and Fitness Landscapes of a Pathogenic

Francesca Bushell, John M J Herbert, Thippeswamy H Sannasiddappa, Daniel Warren, A Keith Turner, Francesco Falciani, Peter A Lund

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

Article in Genes, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.5field-weighted citation impact, top 36% 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

4 citing papers in PubMed, 10 citations in OpenAlex.

  1. Review
  2. Article
  3. Article
  4. 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

7 authors at 3 institutions in 1 country.

Francesca BushellSchool of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK.
John M J HerbertInstitute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
Thippeswamy H SannasiddappaSchool of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK.ORCID 0000-0003-1082-3919
Daniel WarrenInstitute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
A Keith TurnerQuadram Institute Biosciences, Rosalind Franklin Road, Norwich Research Park, Norwich NR4 7UQ, UK.
Francesco FalcianiInstitute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
Peter A LundSchool of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK.ORCID 0000-0002-6381-8526
University of Birmingham · GBUniversity of Liverpool · GBNorwich Research Park · GB

Funding

Biotechnology and Biological Sciences Research Council BB/K019171/1Biotechnology and Biological Sciences Research Council BB/K019546/1
6 · The paper itself

Abstract

Several methods are available to probe cellular responses to external stresses at the whole genome level. RNAseq can be used to measure changes in expression of all genes following exposure to stress, but gives no information about the contribution of these genes to an organism's ability to survive the stress. The relative contribution of each non-essential gene in the genome to the fitness of the organism under stress can be obtained using methods that use sequencing to estimate the frequencies of members of a dense transposon library grown under different conditions, for example by transposon-directed insertion sequencing (TraDIS). These two methods thus probe different aspects of the underlying biology of the organism. We were interested to determine the extent to which the data from these two methods converge on related genes and pathways. To do this, we looked at a combination of biologically meaningful stresses. The human gut contains different organic short-chain fatty acids (SCFAs) produced by fermentation of carbon compounds, and

Indexed as

Gene Expression Regulation, BacterialGenetic FitnessTranscription, GeneticAcetic AcidAerobiosisAnaerobiosisButyric AcidCulture MediaDNA Transposable ElementsEscherichia coli ProteinsGene LibraryGenome, BacterialHumansHydrogen-Ion ConcentrationPropionatesUropathogenic Escherichia coliAcetic AcidButyric AcidCulture MediaDNA Transposable ElementsEscherichia coli ProteinsPropionatespropionic acidacid stressgastrointestinal tractorganic acidRNAseqSCFAshort-chain fatty acidTraDISuropathogenic E. coli

Identifiers

PMID33396416
PMCPMC7824302
OpenAlexW3118051334

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.