3D-GNOME: an integrated web service for structural modeling of the 3D genome

Przemyslaw Szalaj , Przemysław Piotr Michalski , Przemysław Wróblewski , Zhonghui Tang , Michał Kadlof , Giovanni Mazzocco , Yijun Ruan , Dariusz Plewczyński

Abstract

Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/.

Author Przemyslaw Szalaj - [Uniwersytet w Bialymstoku]
Przemyslaw Szalaj,,
-
- Uniwersytet w Bialymstoku
, Przemysław Piotr Michalski (FP / SSID)
Przemysław Piotr Michalski,,
- Solid State Ionics Division
, Przemysław Wróblewski - [Uniwersytet w Bialymstoku]
Przemysław Wróblewski,,
-
- Uniwersytet w Bialymstoku
, Zhonghui Tang - [Uniwersytet w Bialymstoku]
Zhonghui Tang,,
-
- Uniwersytet w Bialymstoku
, Michał Kadlof (FMIS / DIPS)
Michał Kadlof,,
- Department of Information Processing Systems
, Giovanni Mazzocco - [Uniwersytet w Bialymstoku]
Giovanni Mazzocco,,
-
- Uniwersytet w Bialymstoku
, Yijun Ruan - [Uniwersytet w Bialymstoku]
Yijun Ruan,,
-
- Uniwersytet w Bialymstoku
, Dariusz Plewczyński (FMIS / DIPS)
Dariusz Plewczyński,,
- Department of Information Processing Systems
Journal seriesNucleic Acids Research, ISSN 0305-1048, e-ISSN 1362-4962
Issue year2016
Vol44
PagesW288-W293
ASJC Classification1311 Genetics
DOIDOI:10.1093/nar/gkw437
Languageen angielski
Score (nominal)40
Score sourcejournalList
ScoreMinisterial score = 40.0, 09-06-2020, ArticleFromJournal
Ministerial score (2013-2016) = 40.0, 09-06-2020, ArticleFromJournal
Publication indicators Scopus Citations = 17; WoS Citations = 12; Scopus SNIP (Source Normalised Impact per Paper): 2016 = 2.657; WoS Impact Factor: 2016 = 10.162 (2) - 2016=9.338 (5)
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