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Software and Services: GeneTraffic

GeneTraffic

Getting Started

Calendar

Training

FAQs

We are pleased to announce that GeneTraffic by Iobian will soon be available to BimCore Microarray subscribers. We have licensed a 5 concurrent user agreement which means that subcribers can have quick and easy access to state of the art hybridization analysis software via the Web. Since the package is server based there is no need for an installation of software packages on your personal computer. The client-interface/server-database design of the GeneTraffic package gives you the power to exchange data with remote collaborators and create local date repositories

HeatMap Visualization

3D Clustering

GeneTraffic allows you to manage large data sets and store your data and results in a relational database. Data can be qualified and validated prior to biological analysis. The software provides extensive gene annotation search tools coupled with the ability to query on intensity or expression level features. Advanced clustering algorithims allow you to analyze spot and gene tables in great detail. The ability to perform simultaneous hierarchical and K-means clustering allows you to assess how well the two clustering methods correlate. All clusters and lists can be stored and archived with the rest of your project data.

INTRODUCTION

Training Movies And Documentation

Requirements for use

Query Data And Create Data Sets	Data Standardization And Visualization
• Search GeneChip Data Based On - Experimental and Base Line Signal - Absolute Call and Probe Set ID - Correlate Raw Probe Intensities to Absolute Call • Search TwoColor MicroArray Data On - Raw Intensities, Reference and Evaluated - Flag Status Including User Defined Status - Sample ID and Gene ID - Number of Valid Spots per Gene • For Both GeneChip data and Two Color MicroArray Data: - Cross Index Gene Function to Evaluated or Reference Intensities - Regulate log2 ratios and fold change to biological function - Query Gene ID, Gene Description, and Gene Annotation	• Simultaneous K-means (median) and Hierarchical clustering • Cluster Genes and Experiments Together or Independently • Apply Gene Weights • Distance metrics - Pearson Correlation, absolute and/or centered - Euclidean, Mahattam, Maximum • 3D Cluster Visualization Options • Clustering Methods - Average, Single or Complete - Kmeans and Kmedians • Upload Externally Created Cluster Files • Easily Export Clusters For Publications • Search Clusters For Genes Or With Gene Lists
Data Upload And Archiving	Data Standardization And Visualization (cont)
• Integrated Descriptors for MIAME Standards • Store raw data and 16 bit Tiff Images for spotted arrays • Upload CEL, CDF, EXP and RPT Files for GeneChip data arrays • Import and house gene annotations • Flag spots on absolute or relative intensity ratios • Retain flags from image analysis • Define customized flags specific to your needs • Upload customized array layout files • Preloaded chip definition files	• 2 color data normlization with - LOWNESS, intensity, ratio, housekeeping and contorl genes - Full and Sub-grid normalization • GeneChip data standardization - Single or Multiple files for basline definition - Alternative Probe Level Analysis - RMA, Robust Multi-Chip Average - MBEI Method of Li & Wong • Visualize spots or probe sets for genes of interest • Multiple Scatter plot visualization and export options • User defined colors, axis and symbols for scatter plots