NDLI: Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views

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EIC Editorial

Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications

A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats

A Framework for Multiple Kernel Support Vector Regression and Its Applications to siRNA Efficacy Prediction

Network-Based Inference of Cancer Progression from Microarray Data

Generalized Gene Adjacencies, Graph Bandwidth, and Clusters in Yeast Evolution

The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches

Designing Patterns and Profiles for Faster HMM Search

Fuzzy-Adaptive-Subspace-Iteration-Based Two-Way Clustering of Microarray Data

Gene Clustering via Integrated Markov Models Combining Individual and Pairwise Features

Semantics of Multimodal Network Models

Statistical Alignment with a Sequence Evolution Model Allowing Rate Heterogeneity along the Sequence

Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views

Conditioning-Based Modeling of Contextual Genomic Regulation

Multimodal Networks: Structure and Operations

Optimal Aggregation of Binary Classifiers for Multiclass Cancer Diagnosis Using Gene Expression Profiles

Parallel Clustering Algorithm for Large Data Sets with Applications in Bioinformatics

Prediction of Cancer Class with Majority Voting Genetic Programming Classifier Using Gene Expression Data

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Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views

Content Provider	ACM Digital Library
Author	Biggin, Mark D. Hamann, Bernd Luengo hendriks, Cris L. Hagen, Hans Knowles, David W. Weber, Gunther H. Malik, Jitendra Fowlkes, Charless C. Rubel, Oliver Huang, Min-Yu Depace, Angela H. Keranen, Soile V. E.
Abstract	During animal development, complex patterns of gene expression provide positional information within the embryo. To better understand the underlying gene regulatory networks, the Berkeley Drosophila Transcription Network Project (BDTNP) has developed methods that support quantitative computational analysis of three-dimensional (3D) gene expression in early Drosophila embryos at cellular resolution. We introduce PointCloudXplore (PCX), an interactive visualization tool that supports visual exploration of relationships between different genes' expression using a combination of established visualization techniques. Two aspects of gene expression are of particular interest: 1) gene expression patterns defined by the spatial locations of cells expressing a gene and 2) relationships between the expression levels of multiple genes. PCX provides users with two corresponding classes of data views: 1) Physical Views based on the spatial relationships of cells in the embryo and 2) Abstract Views that discard spatial information and plot expression levels of multiple genes with respect to each other. Cell Selectors highlight data associated with subsets of embryo cells within a View. Using linking, these selected cells can be viewed in multiple representations. We describe PCX as a 3D gene expression visualization tool and provide examples of how it has been used by BDTNP biologists to generate new hypotheses.
Starting Page	296
Ending Page	309
Page Count	14
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2007.70249
Volume Number	6
Issue Number	2
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2009-04-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Interactive data exploration, three-dimensional gene expression, spatial expression patterns, information visualization, visualization, physical views, multiple linked views, brushing, scatter plots.
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views

Visual exploration of three-dimensional gene expression using physical views and linked abstract views (2009)

Visual Exploration of Three-dimensional Gene Expression Using Physical Views and Linked Abstract Views. Accepted for Publication in (2007)

Visual Exploration of Three-dimensional Gene Expression Using Physical Views and Linked Abstract Views

Visual Exploration of Three-dimensional Gene Expression Using Physical Views and Linked Abstract Views

Visual exploration of three-dimensional gene expression using physical views and linked abstract views (2009)

Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data

Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data

EyeC: Coordinated Views for Interactive Visual Exploration of Eye-Tracking Data

Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views

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