DNA Microarrays, Transcriptomics and Gene Expression Analysis
Microarrays - NCBI Science Primer
DNA Microarray Fact Sheet at National Human Genome Research Institute (NIH)
Gene Expression Omnibus (GEO) at NCBI - a gene expression and molecular abundance repository and a curated resource for gene expression data browsing, query and retrieval
Array Express and other resources at EBI for transcriptomics and related data
CIBEX - a gene expression database system at DDBJ (DNA Data Bank of Japan)
Stanford MicroArray Database - SMD stores raw and normalized data from microarray experiments, and provides data retrieval, analysis and visualization interfaces
L2L (at the U. of Washington) - a database of published microarray gene expression data and a software tool for comparing that published data to a user's own microarray results
Gene Set Enrichement Analysis (GSEA) at the Broad Institute, includes the Molecular Signatures Database (MSigDB)
R project - a language and free software environment for statistical computing and graphics
Bioconductor - an open source and open development software project for the analysis and comprehension of genomic data
MIAME (Minimum Information About a Microarray Experiment) - a standard for reporting microarray experiment data
MIBBI - Minimum Information for Biological and Biomedical Investigations project at sourceforge.net
ArrayTrack - an integrated solution for managing, analyzing, and interpreting microarray gene expression data at FDA
Microarray Quality Control Project (MAQC) at FDA - provides quality control tools to the microarray community and to develop guidelines for microarray data analysis
microarrays.org - a public source for microarray protocols and software, built and maintained by the DeRisi Lab at UCSF
GNF SymAtlas - database of gene function and structure at the Genomics Institute of the Novartis Research Foundation
Connectivity Map at MIT/Harvard Broad Institute - links gene patterns associated with disease to corresponding patterns produced by drug candidates and a variety of genetic manipulations
Transcriptomics at Nature Omics Gateway
BMC Microarrays Gateway - open access, peer-reviewed articles related to microarrays and gene expression analysis
Nature Reviews web focus on microarrays (2004)
MGED Society - an organization of biologists, computer scientists, and data analysts that aims to facilitate the sharing of data generated using the microarray and other functional genomics technologies for a variety of applications including expression profiling
Pharmacogenomics and Toxicogenomics
Pharmacogenomics - NCBI Science Primer
PharmGKB - Pharmacogenomics Knowledge Base at Stanford University - contains curated information about the relationships among drugs, diseases and genes, including their variations and gene products
FDA Critical Path Initiative - an effort to modernize the sciences through which FDA-regulated products are developed, evaluated, and manufactured
Pharmacogenomics at Nature Omics Gateway
Comparative Toxicogenomics Database (CTD) - curated information on relationships between chemicals, genes and diseases
Gene Ontology and Biological Pathways
Gene Ontology (GO) - a controlled vocabulary to describe gene and gene product attributes in any organism
KEGG: Kyoto Encyclopedia of Genes and Genomes - a database of biological systems that integrates genomic, chemical and systemic functional information
Reactome - a curated knowledge base of biological pathways
Clinical trials
ClinicalTrials.gov at NIH - a registry of federally and privately supported clinical trials conducted in the United States and around the world
Food and Drug Administration (FDA, USA)
European Medicines Agency (EMEA, EU)
21 CFR - Title 21 of the Code of Federal Regulations - governs food and drugs in the USA (chapter I concerns the FDA)
21 CFR Part 11 - FDA guidelines on electronic records and electronic signatures in the USA. (text, resources.)