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Sungear Multifactor Visualization

Sungear Multifactor Visualization. Joint work with Rodrigo Guti é rrez, Manny Katari, Brad Paley, Chris Poultney, and Gloria Coruzzi. Typical Genomic Questions.

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Sungear Multifactor Visualization

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  1. Sungear Multifactor Visualization Joint work with Rodrigo Gutiérrez, Manny Katari, Brad Paley, Chris Poultney, and Gloria Coruzzi

  2. Typical Genomic Questions • Multiple experiments (multiple time points, multiple conditions), many Go categories, or other features of genes: want to know when certain Go categories are highly represented. • Many species, want to know which genes have presence in many species and perhaps which GO categories

  3. Computational Desires • Simple, responsive interface • Visualize lots of data • Many ways to query • Many different data representations

  4. Sungear Design • Generalizes Venn diagrams to more than three • Visual outline is an ellipse having anchors on borders and vessels in the interior. • Each vessel points to associated anchors. • Linked views to hierarchies, lists, and graphs, so can simultaneously update data depending on user queries (selection events).

  5. Sungear Principle • “Sungear is stupid” • Doesn’t care which kind of data it is representing, though there is built-in support for genes (because of links to GO and to cytoscape). • Basic Sungear representation could be used to describe anything from yachting gear to demographics.

  6. Stage No. Description(main stage of embryogenesis) Hours after flowering Sample harvested AtGE No. 1 up to four cells 12 - 24 - (Weigel) 2 early globular to mid globular 24 - 48 - 3 mid globular to early heart 48 - 66 siliques containing seeds ATGE_76 4 early heart to late heart 66 - 84 siliques containing seeds ATGE_77 5 late heart to mid torpedo 84 - 90 siliques containing seeds ATGE_78 6 mid torpedo to late torpedo 90 - 96 isolated seeds ATGE_79 7 late torpedo to early walking-stick 96 - 108 isolated seeds ATGE_81 8 walking-stick to early curled cotyledons 108 - 120 isolated seeds ATGE_82 9 curled cotyledons to early green cotyledons 120 - 144 isolated seeds ATGE_83 10 green cotyledons 144 - 192 isolated seeds ATGE_84 Seed Development Stages(an example)

  7. Demos • Growth stages showing when genes are transcribed (N-reg AtGenExpSeedDev) • Blast comparison of Arabidopsis against most fully sequenced organisms. • Nitrogen, carbon, light, organ showing regulation -- relative expression (cnlo) • Interspecies comparisons that might show which kinds of genes are missing in gymnosperms, for example (Vicogenta)

  8. Genes that respond to N in leaves and C in roots form the largest group (cnlo)

  9. PII and other genes involved in N-metabolism are among these 566

  10. HYPOTHESIS: Most of the regulated genes are involved in metabolism.

  11. … this is not the case for other processes

  12. Genes that are regulated by N & L together

  13. Gene networks of NL-responsive genes

  14. Conclusion • If you have lots of data about some common entity (genes, people, goods, whatever) and several factors or experiments whose interaction you want to visualize, Sungear is for you. • Still under development but works.

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