1 / 16

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.

kordell
Télécharger la présentation

Sungear Multifactor Visualization

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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.

More Related