Analysis EnvironmentsAnalysis Environments For Functional GenomicsFor Functional Genomics
Bruce R. SchatzInstitute for Genomic Biology
University of Illinois at [email protected]
www.beespace.uiuc.edu
Bioinformatics SummitUIUC Computer Science
March 6, 2006
What are Analysis EnvironmentsWhat are Analysis Environments
Functional Analysis Find the underlying Mechanisms Of Genes, Behaviors, Diseases
Comparative Analysis Top-down data mining (vs Bottom-up) Multiple Sources especially literature
Building Analysis EnvironmentsBuilding Analysis Environments
Manual by Humans Interaction user navigation Classification collection indexing
Automatic by Computers Federation search bridges Integration results links
BeeSpace FIBR ProjectBeeSpace FIBR Project
BeeSpace project is NSF FIBR flagshipFrontiers Integrative Biological Research, $5M for 5 years at University of Illinois
Analyzing Nature and Nurture in Societal Roles using honey bee as model
(Functional Analysis of Social Behavior)
Genomic technologies in wet lab and dry lab BeeBee [Biology] gene expressions SpaceSpace [Informatics] concept navigations
CONCEPT SWITCHINGCONCEPT SWITCHING
“Concept” versus “Term” set of “semantically” equivalent terms
Concept switching region to region (set to set) match
term
Semantic region
Concept SpaceConcept Space
Prototype SystemPrototype System
Overall Architecture and Interface -- Todd Littell
Language Parsing and Entity Recognition – Jing Jiang Normalization and Theme Clustering – Qiaozhu Mei
Concept Navigation and Switching – Azadeh Shakery Document Clustering and Partitioning – Brant Chee
Annotation Pipeline and Classification – Xin He Entity Summarization and Integration – Xu Ling
Support 5 CS PhD students under ChengXiang Zhai!
BeeSpace Prototype CollectionsBeeSpace Prototype Collections Organism
Bee: Apis mellifera Fly: Fly Ecology, Evolution and Behavior Bird: Bird Communication
Development Behaviorial Maturation Development: Development of insects Communication: Communication by insects
Behavior Agonistic: Agonistic and Territorial Behaviors Forage: Behavior of Resource Acquisition Nest: Home Maintenance and Defense Social: Behavior of Social Integration in Insects
Towards the InterspaceTowards the Interspace
The Analysis Environment technology is GENERAL!
BirdSpace? BeeSpace?PigSpace? CowSpace? BehaviorSpace? BrainSpace?SoySpace? CropSpace?
BioSpace… Interspace
Computer Science ProblemsComputer Science Problems
Automatic Entity Summarization Generate structured summaries from collection
Interactive Semantic Indexing Relating concepts within dynamic collections
Multiple Synchronized Views Comparing themes from different collections
Gene SummarizationGene SummarizationD. melanogaster gene foraging , abbreviated as for , is reported here . It has also been known in FlyBase as BcDNA:GM08338, CG10033 and l(2)06860. It encodes a product with cGMP-dependent protein kinase activity (EC:2.7.1.-) involved in protein amino acid phosphorylation which is a component of the cellular_component unknown . It has been sequenced and its amino acid sequence contains an eukaryotic protein kinase , a protein kinase C-terminal domain , a tyrosine kinase catalytic domain , a serine/Threonine protein kinase family active site , a cAMP-dependent protein kinase and a cGMP-dependent protein kinase . It has been mapped by recombination to 2-10 and cytologically to 24A2--4 . It interacts genetically with Csr . There are 27 recorded alleles : 1 in vitro construct (not available from the public stock centers), 25 classical mutants ( 3 available from the public stock centers) and 1 wild-type. Mutations have been isolated which affect the larval nerve terminal and are behavioral, pupal recessive lethal, hyperactive, larval neurophysiology defective and larval neuroanatomy defective. for is discussed in 80 references (excluding sequence accessions), dated between 1988 and 2003. These include at least 6 studies of mutant phenotypes , 2 studies of wild-type function , 3 studies of natural polymorphisms and 7 molecular studies . Among findings on for function, for activity levels influence adult olfactory trap response to a food medium attractant. Among findings on for polymorphisms, the frequency of for R and for s strains in three natural populations are studied to determine the contribution of the local parasitoid community to the differences in for R and for s frequencies.
Functional PhrasesFunctional Phrases<gene> encodes <chemical> Sokolowski and colleagues demonstrated in Drosophila melanogaster that the foraging gene (for) encodes a cGMP dependent protein kinase (PKG). The dg2 gene encodes a cyclic guanosine monophosphate (cGMP)- dependent protein kinase (PKG). <chemical> affects/causes <behavior> Thus, PKG levels affected food-search behavior. cGMP treatment elevated PKG activity and caused foraging behavior. <gene> regulates <behavior> Amfor, an ortholog of the Drosophila for gene, is involved in the regulation of age at onset of foraging in honey bees. This idea is supported by results for malvolio (mvl), which encodes a manganese transporter and is involved in regulating Drosophila feeding and age at onset of foraging in honey bees.
Well Characterized GeneWell Characterized Gene
Poorly Characterized GenePoorly Characterized Gene
Interactive Semantic IndexingInteractive Semantic Indexing Build Concept Space for Functional Analysis
-Partition Literature into Community Collections-Extract and Index Concepts within Collections-Compute Relation Graph of Mutual Information-Cluster Related Concepts for User Navigation
Graph Generation is non-linear unless local??? Supplement PMI with LSH (Locality Sensitive Hashing)
Conceptual Navigation in BeeSpaceConceptual Navigation in BeeSpace
NeuroscienceLiterature
MolecularBiology
Literature
BeeLiterature
Flybase,WormBase
BeeGenome
Brain RegionLocalization
Brain GeneExpression
Profiles
BehavioralBiologist
MolecularBiologist
Neuro-scientist
System ArchitectureSystem Architecture
