Evidence map›Paper›PMID 26415229›Full record

ArticleOncotarget2015

A genome wide transcriptional model of the complex response to pre-TCR signalling during thymocyte differentiation.

Hemant Sahni, Susan Ross, Alessandro Barbarulo, Anisha Solanki, Ching-In Lau, Anna Furmanski, José Ignacio Saldaña, Masahiro Ono, Mike Hubank, Martino Barenco and 1 more

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

Article in Oncotarget, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed, 1 pooled it
1.5field-weighted citation impact, top 18% 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

13 citing papers in PubMed, 1 synthesis or guideline pooled it, 20 citations in OpenAlex.

  1. Modeling Immunity In Vitro: Slices, Chips, and Engineered Tissues.Annual review of biomedical engineering · 2021
    Pooled it
  2. Review
  3. Article
  4. T cells in health and disease.Signal transduction and targeted therapy · 2023
    Review
  5. Review
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Hedgehog Signalling in the Embryonic Mouse Thymus.Journal of developmental biology · 2016
    Article
  13. 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

11 authors at 1 institution in 1 country.

Hemant SahniInstitute of Child Health, University College London, London WC1N 1EH, UK.
Susan RossInstitute of Child Health, University College London, London WC1N 1EH, UK.
Alessandro BarbaruloInstitute of Child Health, University College London, London WC1N 1EH, UK.
Anisha SolankiInstitute of Child Health, University College London, London WC1N 1EH, UK.
Ching-In LauInstitute of Child Health, University College London, London WC1N 1EH, UK.
Anna FurmanskiInstitute of Child Health, University College London, London WC1N 1EH, UK.
José Ignacio SaldañaInstitute of Child Health, University College London, London WC1N 1EH, UK.
Masahiro OnoInstitute of Child Health, University College London, London WC1N 1EH, UK.
Mike HubankInstitute of Child Health, University College London, London WC1N 1EH, UK.
Martino BarencoInstitute of Child Health, University College London, London WC1N 1EH, UK.
Tessa CromptonInstitute of Child Health, University College London, London WC1N 1EH, UK.
University College London · GB

Funding

Biotechnology and Biological Sciences Research CouncilMedical Research CouncilWellcome Trust
6 · The paper itself

Abstract

Developing thymocytes require pre-TCR signalling to differentiate from CD4-CD8- double negative to CD4+CD8+ double positive cell. Here we followed the transcriptional response to pre-TCR signalling in a synchronised population of differentiating double negative thymocytes. This time series analysis revealed a complex transcriptional response, in which thousands of genes were up and down-regulated before changes in cell surface phenotype were detected. Genome-wide measurement of RNA degradation of individual genes showed great heterogeneity in the rate of degradation between different genes. We therefore used time course expression and degradation data and a genome wide transcriptional modelling (GWTM) strategy to model the transcriptional response of genes up-regulated on pre-TCR signal transduction. This analysis revealed five major temporally distinct transcriptional activities that up regulate transcription through time, whereas down-regulation of expression occurred in three waves. Our model thus placed known regulators in a temporal perspective, and in addition identified novel candidate regulators of thymocyte differentiation.

Indexed as

Cell DifferentiationModels, GeneticTranscription, GeneticAnimalsCells, CulturedCluster AnalysisGene Expression ProfilingGene Expression Regulation, DevelopmentalGenetic MarkersGenome-Wide Association StudyGenotypeHomeodomain ProteinsMice, Inbred C57BLMice, KnockoutOligonucleotide Array Sequence AnalysisPhenotypeGenetic MarkersHomeodomain ProteinsProtein PrecursorsRAG-1 proteinReceptors, Antigen, T-CellRNATranscription FactorsDPfoetal thymic organ culturesgenome wide transcriptional modellingImmune responseImmunityImmunology Sectionpre-TCRthymus

Identifiers

PMID26415229
PMCPMC4745683
OpenAlexW2163599242

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.