Evidence map›Paper›PMID 28185554›Full record

ArticleBMC genomics2016

Evolution of transcriptional networks in yeast: alternative teams of transcriptional factors for different species.

Adriana Muñoz, Daniella Santos Muñoz, Aleksey Zimin, James A Yorke

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

Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
1.2field-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

6 citing papers in PubMed, 8 citations in OpenAlex.

  1. Article
  2. Article
  3. Review
  4. The rewiring of transcription circuits in evolution.Current opinion in genetics & development · 2017
    Review
  5. Review
  6. Review
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 1 institution in 2 countries.

Adriana MuñozInstitute for Physical Science and Technology, University of Maryland, College Park, Maryland, 20742, USA. adri.embo@gmail.com.
Daniella Santos MuñozInstitute for Physical Science and Technology, University of Maryland, College Park, Maryland, 20742, USA.
Aleksey ZiminInstitute for Physical Science and Technology, University of Maryland, College Park, Maryland, 20742, USA.
James A YorkeInstitute for Physical Science and Technology, University of Maryland, College Park, Maryland, 20742, USA.
University of Maryland, College Park · US

Funding

Reliable Assembler for Whole Genome Shotgun Data.R01HG002945 · NHGRI · UNIV OF MARYLAND, COLLEGE PARK · PI YORKE, JAMES A · 2003 to 2013
$2.1M
NHGRI NIH HHS R01 HG002945
6 · The paper itself

Abstract

backgroundThe diversity in eukaryotic life reflects a diversity in regulatory pathways. Nocedal and Johnson argue that the rewiring of gene regulatory networks is a major force for the diversity of life, that changes in regulation can create new species.

resultsWe have created a method (based on our new "ping-pong algorithm) for detecting more complicated rewirings, where several transcription factors can substitute for one or more transcription factors in the regulation of a family of co-regulated genes. An example is illustrative. A rewiring has been reported by Hogues et al. that RAP1 in Saccharomyces cerevisiae substitutes for TBF1/CBF1 in Candida albicans for ribosomal RP genes. There one transcription factor substitutes for another on some collection of genes. Such a substitution is referred to as a "rewiring". We agree with this finding of rewiring as far as it goes but the situation is more complicated. Many transcription factors can regulate a gene and our algorithm finds that in this example a "team" (or collection) of three transcription factors including RAP1 substitutes for TBF1 for 19 genes. The switch occurs for a branch of the phylogenetic tree containing 10 species (including Saccharomyces cerevisiae), while the remaining 13 species (Candida albicans) are regulated by TBF1.

conclusionsTo gain insight into more general evolutionary mechanisms, we have created a mathematical algorithm that finds such general switching events and we prove that it converges. Of course any such computational discovery should be validated in the biological tests. For each branch of the phylogenetic tree and each gene module, our algorithm finds a sub-group of co-regulated genes and a team of transcription factors that substitutes for another team of transcription factors. In most cases the signal will be small but in some cases we find a strong signal of switching. We report our findings for 23 Ascomycota fungi species.

Indexed as

AlgorithmsEvolution, MolecularCandida albicansGene Regulatory NetworksPhylogenySaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsShelterin ComplexTelomere-Binding ProteinsTranscription FactorsTranscription, GeneticRAP1 protein, S cerevisiaeSaccharomyces cerevisiae ProteinsShelterin ComplexTelomere-Binding ProteinsTranscription FactorsAscomycotaEvolutionRegulationRewiringTranscriptional networksTranscription factorYeast

Identifiers

PMID28185554
PMCPMC5123246
OpenAlexW2551913931

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.