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Department of Biomedical Informatics Biomedical Data Visualization Kun Huang Department of Biomedical Informatics OSUCCC Biomedical Informatics Shared.

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Presentation on theme: "Department of Biomedical Informatics Biomedical Data Visualization Kun Huang Department of Biomedical Informatics OSUCCC Biomedical Informatics Shared."— Presentation transcript:

1 Department of Biomedical Informatics Biomedical Data Visualization Kun Huang Department of Biomedical Informatics OSUCCC Biomedical Informatics Shared Resource The Ohio State University 2011

2 Department of Biomedical Informatics 2 Outline Introduction Scientific visualization vs graphics Data transformation Common issues in visualization Color mapping / transfer functions Coordinate systems Networks Visual analytics

3 Department of Biomedical Informatics 3 Example 1 http://www.youtube.com/watch?v=firxS8BEhTk&feature=related Example 2

4 Department of Biomedical Informatics 4

5 Department of Biomedical Informatics Typical workflow Primary analysis Secondary analysis Tertiary analysis Image acquisition and bead processing Quality metrics Color calls Base calls Sequence alignment Sequence stats Consensus calling Create QC files Tag counting Application-specific analysis Re-sequencing De novo sequencing ChIP-seq Whole transcriptome DNA methylation … Next Generation Sequencing Primary analysisSecondary analysisTertiary analysis Image acquisition and bead processing Quality metrics Color calls Base calls Sequence alignment Sequence stats Consensus calling Create QC files Tag counting Application-specific analysis Re-sequencing De novo sequencing ChIP-seq Whole transcriptome DNA methylation …

6 Department of Biomedical Informatics Chromatin Immunoprecipitation Sequencing (previously PCR or microarray - ChIP-chip) Mapping sequence tags to reference genome ChIP-seq Shah, Nature Methods (6), 2009 Sequences Histograms 1-D signal Locations

7 Department of Biomedical Informatics 7 Outline Introduction Scientific visualization vs graphics Data transformation Common issues in visualization Color mapping / transfer functions Coordinate systems Networks Visual analytics

8 Department of Biomedical Informatics UCSC Genome Browser ChIP-seq

9 Department of Biomedical Informatics UCSC Genome Browser Integrative Genome Viewer ChIP-seq

10 Department of Biomedical Informatics Landscapes of H3K4me2 (left) and Pol II (right) binding profiles ChIP-seq

11 Department of Biomedical Informatics Representation 1050030100 2028742 53111040 1100020051 Gene 110 Gene 2500 Gene 330 Gene 4100 Gene 520 Gene 628 Gene 77 …… Gene 1105060… Gene 2500400800… Gene 3303835… Gene 4100107120… Gene 5205070… Gene 6284233… Gene 77158… ……………

12 Department of Biomedical Informatics 12

13 Department of Biomedical Informatics 13

14 Department of Biomedical Informatics 14 Mountain map visualization. gCLUTO's mountain visualization. Each mountain represents a cluster, where position, height, width and slope depend on cluster characteristics such as the genes grouped, the number of genes and their homogeneity. Santamaría et al. BMC Bioinformatics 2008 9:247 doi:10.1186/1471-2105-9-247

15 Department of Biomedical Informatics Genome viewer ChIP-seq

16 Department of Biomedical Informatics Circos http://circos.ca/intro/published_images/

17 Department of Biomedical Informatics MizBee - A Multiscale Synteny Browser

18 Department of Biomedical Informatics http://vis.lbl.gov/Events/SC07/Drosophila/Parallel-Coordinates-Scatterplot-Embryo-Interaction.png http://vis.lbl.gov/Events/SC07/Drosophila/

19 Department of Biomedical Informatics Embedding Pairwise distance is known Can we find a coordinate system in which the Euclidean distances between points are the same as the known distances? Embedding theorems Whitney Nash Multiple dimensional scaling (MDS)

20 Department of Biomedical Informatics Two views of the map of the protein structure space Hou J et al. PNAS 2005;102:3651-3656 ©2005 by National Academy of Sciences

21 Department of Biomedical Informatics http://www.ayasdi.com/index.php/iris/gallery/ Topological Mapping

22 Department of Biomedical Informatics 22 IPA – Interactive Pathways

23 Department of Biomedical Informatics GenMapp

24 Department of Biomedical Informatics Network Layouts Sipes et al, Toxicol Sci. 2011 Nov;124(1):109-27. Epub 2011 Aug 26.

25 Department of Biomedical Informatics Force-based or force-directed algorithms Spectral layout Tree layout Orthogonal layout … Demo using NodeXL Force layout http://en.wikipedia.org/wiki/Force-based_layout

26 Department of Biomedical Informatics CytoScape

27 Department of Biomedical Informatics Computational methods (e.g., machine learning, pattern recognition) are limited in terms of recognizing patterns. Human cognitive system is highly effective in identifying patterns, integration of different knowledge sources and interpretation (“Blink” and “Think”). Demo – Hanalyzer (http://www.youtube.com/watch?v=jAegU3aZbWI)http://www.youtube.com/watch?v=jAegU3aZbWI Not just nice pictures – visual analytics

28 Department of Biomedical Informatics Summary ArtScience Engineering Visualization

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