Microarray Links 2005

The following is an excellent book on Microarray analysis:

Data Analysis Tools for DNA Microarrays
by Sorin Draghici

The following  papers are key for selecting significant genes.

Draghici S. - Statistical intelligence: effective analysis of high-density microarray data ,  Drug Discovery Today, in press..
Draghici S., Kulaeva O., Petrov A.,  Hoff B., Kuklin A., Shams S., Tainsky M. - Computational methods for the selection of differentially regulated genes in cell immortalization, submitted to Genome Research, 2002.
Draghici S., Kuklin A., Hoff B. Shams S. - Experimental Design, Analysis of Variance and Slide Quality Assessment in Gene Expression Arrays , Current Opinion in Drug Discovery & Development, vol. 4, no. 3, 2001.

Quackenbush, J. (2002). Microarray data normalization and transformation. Nat Genet 32 Suppl, 496-501.

Park, T., Yi, S. G., Kang, S. H., Lee, S., Lee, Y. S., and Simon, R. (2003). Evaluation of normalization methods for microarray data. BMC Bioinformatics 4, 33.

Cheadle, C., Vawter, M. P., Freed, W. J., and Becker, K. G. (2003). Analysis of microarray data using z score transformation. J Mol Diagn 5, 73-81.

These are useful microarray links.



SED, a normalization free method for DNA microarray data analysis
method for analyzing microarrays without normalization
Acuity Microarray Analysis, Visualization, and Database software
PC based microarray software, client server model, $4000 one time fee for 1 user at a time
AMADA software
Free Windows software package for gene array analysis - Excel like -includes cluster and principal component analyses
Analysis of Microarray Data Using Z Score Transformation
paper advocating use of Z scores for cross comparison of data sets
visual basic program for image analysis of microarrays- available from c_patriotis@fccc.edu - also se article in Oct 2001 biotechniques
BASE 1.0.6
Linux based database software for microarrays - free
BioArray - a tool to analyze macroarray images
another free software package for quantitating images (Davidson lab)
Bioinformatics -- Abstracts: Olshen and Jain 18 (7): 961
permuation based methods for validating microarray data
BioPathways consortium
Homepage of the biobpathways consortium with mailing lists and documents
Church Lab WWW Server
Gerorg Church microarry databases
comparing testing methods
Grant and Stoekert paper comparing the ability of various methods to detect significant changes among small replicates
Comparison of DNA labelling methods compared
This article compares 5 methods for labelling cDNAs for microarrays and finds appreciable differences between them. T7 polymerase labelling was found to be the best and antibody methods the worst.
CyberT - web based gene analysis
web based microarray analysis - bayesian approach
Cytoscape: Analyzing and Visualizing Biological Network Data
free java based pathay analysis of microarray data developed by leading centers
DNA-Chip Analyzer (dChip) Beta-test Version User's Agreement
software for gene array analysis that incoporates the GO ontology
eBMJ -- Statistics at Square One: Appendix Table B
t test ditribution table to .001
Evaluation and optimization of procedures for target labeling and hybridization
paper comparing 4 different cDNA labelling methods, concludes that genisphere is the bast
Experimental design, analysis of variance and slide quality assessment in gene e
Another good Drahici article on selecting significant genes
FatiGO Data mining with Gene Ontology
allows GO annotatin comparisions between gene lists
Gary Churchill's Statistical Genetics page
Churchill group's statistical analysis of gene arrays - excellent ANOVA analysis with special emphasis on the 2 dye problem
Gene expression databases and analysis tools
NCGR table of gene array databases and analysis tools (annotated - good)
Gene Expression Omnibus Home
This is the NCBI repository for archiving gene array data of all types
online tool for building and analyzing pathways with genetic and microarray data - excellent and intuitive
GenePublisher 1.01 Server
web site that performs automated analysis of microarray data
client server based microarray analysis program. Server runs on linux dual processor. Client must be windows.
Genisphere Home Page - 3DNA hybridization probes for Gene Expression Microarrays
maker of microarray hybridization kits and services including 4 channel detection
GenMAPP - Home Page
GenMapp is a PC based program for integrating microarray data with functional and pathway data - reported to be outstanding
Genome Biology | Full text | A high performance test of differential gene expres
statistical model for identifying true positive genes in affymetirx arrays
tool for analyzing microarray results by GO ontology
Grace Bio Labs
This company makes coverslips that are said to be good for glass slide microarrays.
Image Analysis Workshop
gene array analysis workshop at Harvard
Is Lowess a pancea?
paper that points out deficencies in the LOWESS method of microarray normalization
Java Ontology Browser by Steffen Schulze-Kremer
microarry ontology browser
longhorn array database
this is a free implementation of the stanford microarray database on Linux using postgre SQL
MarC-V Infromation and Download
free excel spreadsheet for analysis of microarrays- doesn't do clustering and has limited mac functionality but may be good for intial analysis
Melanie 3 - 2D Gel Analysis Software
This is software for analysis of 2 D gels with some mass spec features
methods for detecting differential expression
A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
MGED - International Meetings on Microarray Gene Expression Databases Group
homepage of microarray annotation working group
MicroArray explorer
beta version of java based microarray analysis program from NIH (free)
Microarray Protocols
Pat Brown's microarray protocols including T7 amplification procedure
microarray simulator tool
This is a tool for evaluating microarray analysis methods (published in Cancer Biol Ther. 2003 Jul-Aug;2(4):383-91.)
Microarrays at Ontario Cancer Institute: Home page
inexpensive glass slide cDNA arrays and protocols from Toronto
microarrays.org - mailing list
Web driven database server software for microarray. Also a database repository currently without data.
neural tumors
Golub paper using gene arrays to classify tumors by type and response - good method example
NHGRI Microarray Project: Image Analysis
step by step image analysis for microarrays
automated system for translating expression data into funtional profiles
PAM - prediction analysis for microarrays
new version of free excel addin for microarray analysis
paper on normalization of microarray data
method for normalizing microarray data based on the assumption that most genes don't change between treatment groups
Plaid models for dna microarray data
Homepage for PLAID genearray software from stanford supposedly unique functionality
PNAS -- Lee et al. 97 (18): 9834
paper with maximum likelihood approach to determining significance in microarrays by replication - similar to Jay's analysis
Prism Guide to Interpreting Statistical Tests
online guide to statistical tests from graph pad (good on t tests)
Resampling Stats
software package for excell and other programs that produces bootstrapped and resampled dataset for analysis
RNA expression analysis using a 30 base pair resolution Escherichia coli genome
George Church paper on using oligos to detect E. coli gene expression - extensive discussion with data of sensitivity and error measurement
Rosetta Biosoftware Resolver
Rosetta's commercial gene array software - unknown cost
SAGE Home Page
homepage for analysis of gene expression by SAGE
Science -- Ren et al. 290 (5500): 2306 Data Supplement - Supplemental Data
New data error analysis of triplicates from Rick Young lab
Significance Analysis of Microarrays
excel addin for SAM significance analysis of microarrays from Chu group -determines false positive rates
Silicon Genetics Products: GeneSpring: The industry leader
Genespring commercial data analysis package - subscription based
SISA allows you to do statistical analysis directly on the Internet.
simple online stat calculator with explanations
SMD Microarray Resources : Software & Tools
Stanford links to microarray analysis software
SOURCE Batch Search
Stanford source metaserach, extracts selected information from databases about groups of genes
Stanford MicroArray Forum
The Stanford Microarray Forum is a good searchable bulletin board for discussion of all things microarray.
Statistical intelligence: effective analysis of high-density microarray data
Outstanding article on selecting significant genes from gene arrays
Submicro Array Detection Troubleshooting Guide
excellent microarray troubleshooting guide -oriented to genisphere but has general aplicability
Supplemental Data, Hughes et al.
This supplement describes reproducibility and error handling of gene arrays.
The Genomics and Bioinformatics Group
John Weinstein lab page with GOminer and Matchminer
The Pathways for the Genes
tool for mapping microarray data to gene pathways
Vector algebra in the analysis of genome-wide expression data.
Vector type analysis of gene array data- I'm not sure if this is the best paper on this subject, but it's probaby the easiest to understand
another link to the SAM error analysis package
Web resources on Gene Expression and DNA Microarray Technologies
EBI microarray links page
Welcome to BioDiscovery, Inc.
Home page for genesight and imagene analysis programs. Good Stats.
Whitehead genomics Publications
Publications with links to datasets from MIT genome center including myc and RhoC papers
Online system for gene array analysis $7500 subscription fee
linux or unix software for automatic spot detection and quantitation of micrarrays - Biotechniques June 2002
z score Calculator
calculating probabilities from z scores