• Databases
• Firms
• Labs & Publications
• Links
• Material
• News
• Organisms
  • C. elegans Prepare samples for submission to Kim's Lab
  • S. cerevisiae
  • Mouse

ses

Databases

• Data analysis and molecular databases for Genomic & Proteomic Research
  • cDNA microarray gene expression data and correlative drug activity data.
  • Affymetrix microarray gene expression data.
  • ABC transporter real-time RT-PCR gene expression data.
• Genome Consortium for Active Teaching

  • Yeast

  • E. coli

  • Human

  • Arabidopsis

  • Drosophila

  • Dictyostelium

• Ecole Normale Superieure
• MGAP - MicroArray Explorer - Mouse mammary db [LECB,NCI/FCRDC)]:
  • C57BL/6 Wildtype "Mammary Development"
  • Stat5a K.O. "Mammary Development"
  • bB-inhibin K.O. "Mammary Development"
  • C/EBP-b K.O. "Mammary Development"
  • C57BL/6 Development vs. Developmental Models
  • Tumor Models
  • Poly(A) vs. Total RNA
  • Reproducibility
  • Large sets of hybridizations
  • OLD startup databases (will be deprecated)
• Oncomine: Cancer Microarray Database
• Prostate Expression Database

Data Mining, Processing, Analysis, & Probe Design

• Array Designer - Helps by automating the selections of appropriate oligonucleotide probes or cDNA primer pairs for microarray analysis (Reviewed by S. Lalitha , BioMedNet May 11, 2001 · Issue 102).
• CAGED (Cluster Analysis of Gene Expression Dynamics) is a program for the analysis of temporal profiles of gene expression data. To learn more, please enter here (Marco Ramoni, Harvard).
• List-to-List (L2L; U of Washington).
• MGAP - MicroArray Explorer - an exploratory data analysis facility for cDNA microarrays from mouse mammary tissue and databases from the Mammary Genome Anatomy Project (MGAP). A new enhanced version  is available for download. This Java application works on Windows 95/98/NT, Macintosh, Solaris, Linux, and other Unix and Java enabled computers; Tutorials
  [LECB,NCI/FCRDC)].
• CLEAVER : "The Cleaver (Classification of Expression Array Version 1.0) internet site providing tools for analysis of microarray expression data including  visualization, classification, and clustering. Computations are done on the server side & taking take no longer than five to ten minutes to compute" (Snowdeal.org, 7/1/00); read about it here (Stanford Biomedical Informatics).
• Data analysis and molecular databases for Genomic & Proteomic Research.
  • MatchMiner: Batch-translates among many types of gene and protein identifiers.
  • GoMiner: Leverages the Gene Ontology for biological interpretation of microarrays data, etc.
  • MedMiner: Searches and organizes the PubMed literature on genes and drugs.
  • CIMminer: Produces Clustered Image Maps (CIMs) (i.e., clustered .heat maps.).
  • MIMminer: Electronically navigates Kohn Molecular Interaction Maps.
  • Also: An (opinionated) guide to microarray data analysis.
  • Coming soon: AbMiner: A database resource on available monoclonal antibodies
• Many other Data processing links (Ecole Normale Superieure (B. Martin & P. Marc; Paris, France).

Microarray Data - Protein function & biochemical Network (European Bioinformatics Institute).    

     Human:

• ABC transporter real-time RT-PCR gene expression data.
• Affymetrix microarray gene expression data.
• Brain
• Cancer Microarray Database - Oncomine
• cDNA microarray gene expression data and correlative drug activity data.
• Fibroblast

     Mouse

• C57BL/6 Wildtype "Mammary Development"
• Stat5a K.O. "Mammary Development"
• bB-inhibin K.O. "Mammary Development"
• C/EBP-b K.O. "Mammary Development"
• C57BL/6 Development vs. Developmental Models
• Tumor Models
• Reproducibility

     Nematode

• SAGE
• C. elegans - how to prepare samples for submission to Kim's Lab

     Yeast:

• Wild-type transcriptome
• Cell cycle
• Diauxic shift
• YAP1 surexpression
• TUP1 deletion
• Sporulation
• Gal data
• Heat shock
• Galactose/glucose
• Heat-shock response
• Mating-type
• General transcription factors
• SAGE data
• Gene clustering

Data Standards

• Taking arrays from the lab to the field: trying to make sense of the unknown

• Standards at last!

• MIAME Guidelines ((Nature Genetics 29, 365–371; 2001)

• Checklist of variables that should be included in  every microarray publication

• Submission of microarray data to either of two databases: GEO; ArrayExpress

• Design Issues for cDNA Microarray Experiment
• Data Standard - minimum information about a microarray experiment, MIAME, MGED.

Special Microarray Links

• DNA Microarray Homepage (Patrick Brown lab, Stanford U., USA).

• Gene Chips Home Page (Leming Shi, gene- chips.com).

• Stuart Kim Laboratory  - how to prepare C. elegans RNA samples for submission to Kim's Lab (Stanford U., USA).

• Andreas Matern's list of links (Cornell U., USA).

• ArrayExpress db (European Bioinformatics Institute).

• Nature Site

• Microarray Directory at EMBL-EBI - Susanna Sansone