L519:  Lab Session 8 (10/28/05)

Today's Topics

• Public Microarray Databases (SMD, ArrayExpress, GEO)
• Cluster (Eisen Lab)
• TreeView (Eisen Lab)
• Mini-Group Project#2 Presentation

---

¤ Public Microarray Databases

•  Stanford Microarray Database (http://genome-www5.stanford.edu/index.shtml)
• Microarray research database for Stanford investigators and their collaborators.
• Making freely available all of its source code and providing full public access to data published by SMD users.
• Features of SMD
• Data management
• Storage, archiving, and data viewing tools.
• Raw and normalized data
• Integration with analysis tools and external information
• Clustering, partitioning and output of data for other use
• Provides linkages with SGD and GO
• Publication of data
• Provide data, images, analysis and connections with biological resources (SGD)
• Easy data retrieval interface
• Data Access through 'Public Login'
• Explorer the SMD.
• Retrieve any microarray data.
• SMD Tools Helps (http://genome-www5.stanford.edu/help/smd_tools.shtml)
• Other Public Microarray Databases              
• ArrayExpress (http://www.ebi.ac.uk/arrayexpress/)
• GEO - Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/)
• Other gene expression related databases (NAR)
• Some resources for Microarray Data Analysis
• A comprehensive guid to DNA Microarray Data Analysis (PDF)
• Microarrays.org
• MGED - Microarray Gene Expression Data Society
• Bibliography on Microarray Data Analysis (~1,270 papers)
   

¤ Cluster (Eisen Lab)

• The Cluster has been developed by the Eisen Lab (UC Berkeley and Lawrence Berkeley National Lab (LBNL)).
• It perform a variety of types of cluster analysis and other types of processing on large microarray datasets.
• Current available clustering methods include hierarchical clustering, self-organizing maps (SOMs), k-means clustering, and principal component analysis.
• Available for download (Windows)
• Cluster 3.0 developed by Michiel de Hoon of the University of Tokyo (Mac OS X, Linux, and Unix)
• Test data obtained from SMD (Yeast H2O2 0.32mM Time Series)
• Manual for Cluster and TreeView

¤ TreeView (Eisen Lab)

• Graphically browse results of clustering and other analyses from Cluster.
• Supports tree-based and image based browsing of hierarchical trees.
• Multiple output formats for generation of images for publications
• Available for download (Windows)
• Java Treeview - Open source extensible viewer

               

¤ Mini-group Project#2 Presentation

• http://darwin.informatics.indiana.edu/cgi-bin/col/courses/L519/Eval/Proj2/EvalProj2.cgi

 

---

Last Modified : October 27, 2005

Maintained by : Junguk Hur ()