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Title: Quantitative Visualization of ChIP-chip Data by Using Linked Views

Abstract

Most analyses of ChIP-chip in vivo DNA binding have focused on qualitative descriptions of whether genomic regions are bound or not. There is increasing evidence, however, that factors bind in a highly overlapping manner to the same genomic regions and that it is quantitative differences in occupancy on these commonly bound regions that are the critical determinants of the different biological specificity of factors. As a result, it is critical to have a tool to facilitate the quantitative visualization of differences between transcription factors and the genomic regions they bind to understand each factor's unique roles in the network. We have developed a framework which combines several visualizations via brushing-and-linking to allow the user to interactively analyze and explore in vivo DNA binding data of multiple transcription factors. We describe these visualization types and also provide a discussion of biological examples in this paper.

Authors:
; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
Computational Research Division; Life Sciences Division
OSTI Identifier:
1012475
Report Number(s):
LBNL-4491E
TRN: US201110%%110
DOE Contract Number:
DE-AC02-05CH11231
Resource Type:
Conference
Resource Relation:
Conference: Workshop on Integrative Data Analysis in Systems Biology (IDASB10)
Country of Publication:
United States
Language:
English
Subject:
97; BIOLOGY; DATA ANALYSIS; DNA; IN VIVO; SPECIFICITY; TRANSCRIPTION FACTORS

Citation Formats

Huang, Min-Yu, Weber, Gunther, Li, Xiao-Yong, Biggin, Mark, and Hamann, Bernd. Quantitative Visualization of ChIP-chip Data by Using Linked Views. United States: N. p., 2010. Web.
Huang, Min-Yu, Weber, Gunther, Li, Xiao-Yong, Biggin, Mark, & Hamann, Bernd. Quantitative Visualization of ChIP-chip Data by Using Linked Views. United States.
Huang, Min-Yu, Weber, Gunther, Li, Xiao-Yong, Biggin, Mark, and Hamann, Bernd. Fri . "Quantitative Visualization of ChIP-chip Data by Using Linked Views". United States. doi:. https://www.osti.gov/servlets/purl/1012475.
@article{osti_1012475,
title = {Quantitative Visualization of ChIP-chip Data by Using Linked Views},
author = {Huang, Min-Yu and Weber, Gunther and Li, Xiao-Yong and Biggin, Mark and Hamann, Bernd},
abstractNote = {Most analyses of ChIP-chip in vivo DNA binding have focused on qualitative descriptions of whether genomic regions are bound or not. There is increasing evidence, however, that factors bind in a highly overlapping manner to the same genomic regions and that it is quantitative differences in occupancy on these commonly bound regions that are the critical determinants of the different biological specificity of factors. As a result, it is critical to have a tool to facilitate the quantitative visualization of differences between transcription factors and the genomic regions they bind to understand each factor's unique roles in the network. We have developed a framework which combines several visualizations via brushing-and-linking to allow the user to interactively analyze and explore in vivo DNA binding data of multiple transcription factors. We describe these visualization types and also provide a discussion of biological examples in this paper.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Fri Nov 05 00:00:00 EDT 2010},
month = {Fri Nov 05 00:00:00 EDT 2010}
}

Conference:
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