Evidence map›Paper›PMID 33136153›Full record

ArticleBioinformatics (Oxford, England)2021

HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data.

Dhawal Jain, Chong Chu, Burak Han Alver, Soohyun Lee, Eunjung Alice Lee, Peter J Park

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2021. 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
–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

4 citing papers in PubMed.

  1. The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024
    Review
  2. Regulation and function of transposable elements in cancer genomes.Cellular and molecular life sciences : CMLS · 2024
    Review
  3. Review
  4. 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.

Dhawal JainDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Chong ChuDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Burak Han AlverDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.ORCID 0000-0002-5019-7652
Soohyun LeeDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Eunjung Alice LeeDivision of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
Peter J ParkDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.ORCID 0000-0001-9378-960X

Funding

4D Nucleome Network Data Coordination and Integration CenterU01CA200059 · NCI · HARVARD MEDICAL SCHOOL · PI PARK, PETER J · 2015 to 2024
$24.4M
1/2-Somatic mosaicism and autism spectrum disorderU01MH106883 · NIMH · BOSTON CHILDREN'S HOSPITAL · PI PARK, PETER J, WALSH, CHRISTOPHER A. · 2015 to 2019
$9.2M
NCI NIH HHS U01 CA200059NIMH NIH HHS U01 MH106883
6 · The paper itself

Abstract

Hi-C is a common technique for assessing 3D chromatin conformation. Recent studies have shown that long-range interaction information in Hi-C data can be used to generate chromosome-length genome assemblies and identify large-scale structural variations. Here, we demonstrate the use of Hi-C data in detecting mobile transposable element (TE) insertions genome-wide. Our pipeline Hi-C-based TE analyzer (HiTea) capitalizes on clipped Hi-C reads and is aided by a high proportion of discordant read pairs in Hi-C data to detect insertions of three major families of active human TEs. Despite the uneven genome coverage in Hi-C data, HiTea is competitive with the existing callers based on whole-genome sequencing (WGS) data and can supplement the WGS-based characterization of the TE-insertion landscape. We employ the pipeline to identify TE-insertions from human cell-line Hi-C samples. AVAILABILITY AND IMPLEMENTATION: HiTea is available at https://github.com/parklab/HiTea and as a Docker image. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

ChromatinDNA Transposable ElementsChromosomesHumansMolecular ConformationWhole Genome SequencingChromatinDNA Transposable Elements

Identifiers

PMID33136153
PMCPMC8599941

What OpenQuestion holds

Textmetadata
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.