Transcript Slide 1
BeeSpace – USER NEEDS Moushumi Sen Sarma Nov 8th, 2006 BeeSpace should fulfil two kinds of needs (for two kinds of users or the same user at two different stages of research): 1. Stage 1: Pre-experiment exploratory search and hypothesis generation (the beginner) 2. Stage 2: Post-experiment multilevel analysis (the expert) exploration Hypothesis generation Experimentation and testing predictions Results and conclusion Stage 1: What I was doing in 2004 (pre-BeeSpace) 1. 2. 3. 4. 5. Conceptualizing the problem Generation of terms describing the behavior Exploring in literature collections Mental leaps of reasoning Testing ideas with pilot expts What I am doing currently 1. Grappling with a large amount of microarray data 2. Making sense of gene lists and comparing (superficially) 3. Planning more microarray experiments What I would like to be able to do (reach Stage 2) 1. Meta-analyze! 2. Visualize the interactome (Rhodes and Chinnaiyan 2005) 3. Visualize pathways (KEGG http://www.genome.jp/kegg/pathway.html) 4. Visualize networks (Zhou et al 2005) My project needs meta-analysis! The approach- using species differences in the dance language in lieu of mutants to get at the genes Experiment 1 (47 (cDNA) microarrays) Whole brain expression data of foragers and day-olds to establish differences/similarities between 4 different species Experiment 2 (samples collected awaiting (cDNA) microarrays) Expression data on dancers of 4 different species comparing candidate CNS regions Experiment 3 (samples collected awaiting (oligo) microarrays) Activity dependent gene expression of dancers (with known behavioral histories) of A. mellifera comparing candidate CNS regions Experiment 4 (still being planned) Expanding expt 3 to include the Asian species (“mutants”) Experiment 1 Experiment 2 Meta-analysis Experiment 3 Experiment n Co-regulated gene networks Regulatory genes In general, the Robinson lab would vastly benefit for a platform enabling metaanalysis to discover gene networks and regulatory pathways involved in behavioral maturation Stage 1: Exploratory concept based search involves all the units currently being developed 1. 2. 3. 4. Concept navigator Gene summarizer Theme generator Cluster generator More needed 1. Cross domain searchability 2. Genes to concepts to genes navigability 3. Multi-browser- windows system 4. Keep track of searches and graphically show hierarchy, allow selection of leaves or nodes (a modification of Azadeh’s program) An example search process term = circadian Domain switching Fly collection documents documents terms behaviors methods Bee collection Genes Pubmed/mammalian/ other invertebrates function terms behaviors pharmacology? function ? sequence? sequence mutants Genes methods “mutants” ? pharmacology ? Simplified for visual simplicity but gives idea of multiple levels of search Concept Navigator: Features that I liked about V1 and is missing in V2 1. Domain/collection switching 2. A dual window system 3. Terms extracted and displayed and can be selected to form a new theme Dynamic clustering would be a very important addition Gene summarizer: Should allow 1. Search across orthologs with different names 2. Collection switching 3. Should indicate collection etc on top of result page The issue of updating databases and having information on the same is important for the user