Evidence map›Paper›PMID 25792550›Full record

ArticleBioinformatics (Oxford, England)2015

iTagPlot: an accurate computation and interactive drawing tool for tag density plot.

Sung-Hwan Kim, Onyeka Ezenwoye, Hwan-Gue Cho, Keith D Robertson, Jeong-Hyeon Choi

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

5 authors.

Sung-Hwan KimSchool of Computer Science and Engineering, Pusan National University, Busan, South Korea.
Onyeka EzenwoyeHull College of Business, Georgia Regents University, Augusta, GA, USA.
Hwan-Gue ChoSchool of Computer Science and Engineering, Pusan National University, Busan, South Korea.
Keith D RobertsonDepartment of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
Jeong-Hyeon ChoiCancer Center and Department of Biostatistics and Epidemiology, Medical College of Georgia, Georgia Regents University, Augusta, GA, USA.

Funding

RNA epigenetic regulation of cancer metabolismR01CA190429 · NCI · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI HAN-FEI DING · 2014 to 2026
$3.7M
Developmental pathways, environmental agents, and epigenetics in liver diseaseR01AA019976 · NIAAA · MAYO CLINIC ROCHESTER · PI LIU, CHEN, ROBERTSON, KEITH D · 2011 to 2015
$3.0M
A GENOME-WIDE METHYLATION STUDY ON ESSENTIAL HYPERTENSIONR01HL104125 · NHLBI · AUGUSTA UNIVERSITY · PI WANG, XIAOLING · 2011 to 2015
$2.9M
Epigenetic regulation of T-cell dysfunction in chronic lymphocytic leukemiaR21CA185833 · NCI · AUGUSTA UNIVERSITY · PI SHI, HUIDONG · 2014 to 2015
$362k
NCI NIH HHS CA185833NCI NIH HHS CA190429NCI NIH HHS R21 CA185833NHLBI NIH HHS HL104125NIAAA NIH HHS AA019976NIAAA NIH HHS R01 AA019976
6 · The paper itself

Abstract

motivationTag density plots are very important to intuitively reveal biological phenomena from capture-based sequencing data by visualizing the normalized read depth in a region.

resultsWe have developed iTagPlot to compute tag density across functional features in parallel using multicores and a grid engine and to interactively explore it in a graphical user interface. It allows us to stratify features by defining groups based on biological function and measurement, summary statistics and unsupervised clustering. AVAILABILITY AND IMPLEMENTATION: http://sourceforge.net/projects/itagplot/.

Indexed as

Sequence Tagged SitesSoftwareCell LineCluster AnalysisComputer GraphicsCpG IslandsDNA MethylationGene ExpressionHigh-Throughput Nucleotide SequencingHumans

Identifiers

PMID25792550
PMCPMC4495303

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.