Evidence map›Paper›PMID 27153610›Full record

ArticleBioinformatics (Oxford, England)2016

CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.

E C Schofield, T Carver, P Achuthan, P Freire-Pritchett, M Spivakov, J A Todd, O S Burren

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 9 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
46citing papers in PubMed, 9 pooled it
–field-weighted citation impact
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

46 citing papers in PubMed, 9 syntheses or guidelines pooled it.

  1. Pooled it
  2. Multi-ancestry genome-wide association study of asthma exacerbations.Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology · 2022
    Pooled it
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  7. Genome-wide meta-analysis reveals shared newAnnals of the rheumatic diseases · 2019
    Pooled it
  8. Mechanistic Characterization ofFrontiers in immunology · 2019
    Pooled it
  9. Pooled it
  10. Article
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  12. Review
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  17. A Secure and Reusable Software Architecture for Supporting Online Data Harmonization.Proceedings : ... IEEE International Conference on Big Data. IEEE International Conference on Big Data · 2021
    Article
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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

7 authors.

E C SchofieldJDRF/Wellcome Trust Diabetes and Inflammation Laboratory, NIHR Cambridge Biomedical Research Centre, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
T CarverJDRF/Wellcome Trust Diabetes and Inflammation Laboratory, NIHR Cambridge Biomedical Research Centre, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
P AchuthanJDRF/Wellcome Trust Diabetes and Inflammation Laboratory, NIHR Cambridge Biomedical Research Centre, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
P Freire-PritchettNuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, UK.
M SpivakovNuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, UK.
J A ToddJDRF/Wellcome Trust Diabetes and Inflammation Laboratory, NIHR Cambridge Biomedical Research Centre, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
O S BurrenJDRF/Wellcome Trust Diabetes and Inflammation Laboratory, NIHR Cambridge Biomedical Research Centre, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.

Funding

Wellcome Trust 091157Wellcome Trust 100140
6 · The paper itself

Abstract

unlabelledPromoter capture Hi-C (PCHi-C) allows the genome-wide interrogation of physical interactions between distal DNA regulatory elements and gene promoters in multiple tissue contexts. Visual integration of the resultant chromosome interaction maps with other sources of genomic annotations can provide insight into underlying regulatory mechanisms. We have developed Capture HiC Plotter (CHiCP), a web-based tool that allows interactive exploration of PCHi-C interaction maps and integration with both public and user-defined genomic datasets. AVAILABILITY AND IMPLEMENTATION: CHiCP is freely accessible from www.chicp.org and supports most major HTML5 compliant web browsers. Full source code and installation instructions are available from http://github.com/D-I-L/django-chicp CONTACT: ob219@cam.ac.uk.

Indexed as

InternetPromoter Regions, GeneticRegulatory Elements, TranscriptionalSoftwareChromosomesComputer GraphicsGenomeGenomics

Identifiers

PMID27153610
PMCPMC4978926

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.