Evidence map›Paper›PMID 24511080›Full record

ArticleBioinformatics (Oxford, England)2014

HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization.

Jonas Paulsen, Geir Kjetil Sandve, Sveinung Gundersen, Tonje G Lien, Kai Trengereid, Eivind Hovig

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.

0numbers the graph read from it
0cells of the map it votes in
21citing papers in PubMed
–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

21 citing papers in PubMed.

  1. Article
  2. Mapping the 3D genome architecture.Computational and structural biotechnology journal · 2025
    Review
  3. Article
  4. Article
  5. Article
  6. Article
  7. Review
  8. Article
  9. Article
  10. Utilizing networks for differential analysis of chromatin interactions.Journal of bioinformatics and computational biology · 2017
    Article
  11. Article
  12. Review
  13. Article
  14. Review
  15. Article
  16. Article
  17. Article
  18. Bioinformatics Analysis of Estrogen-Responsive Genes.Methods in molecular biology (Clifton, N.J.) · 2016
    Article
  19. Article
  20. 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

6 authors.

Jonas PaulsenInstitute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway.
Geir Kjetil SandveInstitute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway.
Sveinung GundersenInstitute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway.
Tonje G LienInstitute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway.
Kai TrengereidInstitute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway.
Eivind HovigInstitute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, NorwayInstitute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, NorwayInstitute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

unlabelledRecently developed methods that couple next-generation sequencing with chromosome conformation capture-based techniques, such as Hi-C and ChIA-PET, allow for characterization of genome-wide chromatin 3D structure. Understanding the organization of chromatin in three dimensions is a crucial next step in the unraveling of global gene regulation, and methods for analyzing such data are needed. We have developed HiBrowse, a user-friendly web-tool consisting of a range of hypothesis-based and descriptive statistics, using realistic assumptions in null-models. AVAILABILITY AND IMPLEMENTATION: HiBrowse is supported by all major browsers, and is freely available at http://hyperbrowser.uio.no/3d. Software is implemented in Python, and source code is available for download by following instructions on the main site.

Indexed as

SoftwareChromatinData Interpretation, StatisticalGenomeGenomicsHigh-Throughput Nucleotide SequencingChromatin

Identifiers

PMID24511080
PMCPMC4029040

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.