Function Express

November 30, 2007

Function Express: Architecture

Integrated DB

(Oracle 9i)

LocalDB (MySQL)

Chip DataGene AnnotationsAnalysis

Chip DataVirtual Experiment Data

LocalDB (MySQL)

Individual

Laboratory

Bioinformatics Core

MGA MAC

Compute Nodes

Function Express: Log in & Auto Update

Function Express: Experiment Menu

Creating and Opening Virtual Experiments

Function Express: Overview

Importing Data and Security Features

Security Movie

Manipulating Categories

Function Express: Viewers

Plotting Microarray Data

Function Express: Viewers

Clinical Data

Probeset Data

Probeset Comments Category Comments

Category History

BioCarta Pathway browser

Gene Inspector

Browsing Gene Annotations

Manipulating and Importing Analysis ResultsMovies

Function Express: Analyzing Data

SAMPCA

Weighted Voting

• SVM

• Consensus Clustering

• Comparative Marker Selection

Function Express: Analyzing Data

• Are co-expressed genes co-regulated?

• What regulatory networks are operating/perturbed in your experimental paradigm?

• What pathways/processes emerge from a set of ‘interesting’ genes?– Promoter Analysis Pipeline

– Gene Network Viewer

– IPA

Function Express: What to do after analysis?

PromoterAnalysisPipeline

GeneNetworkViewer

Acknowledgments

Promoter PipelineGary Stormo

On-site PersonnelLi-Wei ChangHrishikesh DeshmukhBurr FontaineCaerie HouchinsGeorge JosephSunita KoulRekha MeyerMukesh SharmaJoanne Zhao

Software Project ManagerSrikanth Adiga

Off-shore PersonnelAnuj TiwariJaydeep ChovatiaRahul JainMadhumita ShrikandeMadhurima BhattacharjeeAshwini Patil