Related Information

The following is a list of our favorite links related to genomics and microarray.

University of Kansas Genomics-Related Research Facilities
University of Kansas Genomics-Related Departments and Centers

Comprehensive Genomics & Bioinformatics Portals
Databases
Genomics Data Analysis Tools
Genomics-Related Discussion Groups
Journals
Organizations

University of Kansas Genomics-Related Research Facilities

• Bioinformatics Core Facility
• DNA Sequencing Laboratory
• High Throughput Screening Laboratory
• Kansas Center for Advanced Scientific Computing
• Microscopy and Analytical Imaging Laboratory
• Molecular Structures Group
• Transgenic Mouse Facility
• Tissue Culture and Hybridoma Laboratory
• Bioinformatics Facility (Medical Center)
• Microarray Facility (Medical Center)
• Transgenic and Gene-targeting Institutional Facility (Medical Center)

University of Kansas Genomics-Related Departments and Centers

• Center for Bioinformatics
• Chemistry, Department of
• Electrical Engineering and Computer Science, Department of
• Higuchi Biosciences Center (HBC)
• Information and Telecommunication Technology Center (ITTC)
• Kansas Mental Retardation and Developmental Disability Research Center (MRDDRC)
• Medicinal Chemistry, Department of
• Molecular Biosciences, Department of
• Pharmaceutical Chemistry, Department of
• Pharmacology and Toxicology, Department of

Comprehensive Genomics & Bioinformatics Portals

• BMC Bioinformatics & Genomics Gateway: latest open access research from over 140 journals; new evaluation listings from Faculty of 1000 Biology; news from The Scientist
• BMC Microarrays Gateway
• BMC Systems Biology Gateway

Databases

Comprehensive sequence databases

• Entrez (NCBI): search almost all gene or protein-oriented biomedical information from here, including records on gene or protein sequences and expression patterns (GEO expression pattern). A good one-stop-searching site.
• The EMBL Nucleotide Sequence Database (also known as EMBL-Bank): Europe's primary nucleotide sequence resource.
• DNA Data Bank of Japan (DDBJ): another major nucleotide database from Japan.

Microarray databases

• Gene Expression Omnibus (GEO): an NCBI database for high-throughput gene expression data, including microarray data. Integrated with other NCBI databases.
• Stanford Microarray Database
• ArrayExpress: microarray data public repository maintained by European Bioinformatics Institute.
• Gene Expression Database (GXD): a database of Mouse Genome Informatics at the Jackson laboratory.
• Human Gene Expression Index (HuGE Index): aims to provide a comprehensive database to understand the expression of human genes in normal human tissues.
• Oncomine: curates public cancer microarray studies and provides data-mining tools so that genes and datasets of interest may be queried efficiently and groups of studies meta-analyzed.
• READ (RIKEN cDNA Expression Array Database): A database maintained by RIKEN (The institute of Physical and Chemical Research), Japan.
• Saccharomyces Genome Database (SGD) - Expression Connection: search gene expression data in the Saccharomyces genome database at Stanford University.
• Yale Microarray Database

Genomics Data Analysis Tools

Gene Ontology Analysis

• A comprehensive list of Gene Ontology analysis tools: hosted by The Gene Ontology Project site

Biological Pathway Analysis

• ArrayXpath
• BioMiner
• GenMAPP: a good tool for both pathway and gene ontology analysis
• PathFinder
• PathMAPA: for Arabidopsis
• PathwayExplorer: pathway resources include KEGG, BioCarta and GenMAPP.
• Pathway Express
• Pathway Miner
• Major pathway databases: KEGG, BioCarta, CMAP

Genomics_Related Discussion Groups

• nodalpoint.org - A bioinformatics weblog
• Microarray group @ Yahoo! Groups
• Real-time qPCR group @ Yahoo! Groups
• SAM (Significance Analysis of Microarrays) group @ Yahoo! Groups
• GeneSpring users group @ Yahoo! Groups
• GenMAPP google group
• The Bioconductor project mailing list

Journals

• Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
• Bioinformatics
• BMC Bioinformatics
• BMC Genomics
• Comparative and Functional Genomics
• Current Genomics
• Functional & Integrative Genomics
• Genome Biology
• Genome Research
• Genomics (publisher link, ScienceDirect link)
• Genomics & Human Genetics - Annual Reviews
• Journal of Biomedical Informatics
• Journal of Structural and Functional Genomics
• Nature
• Nature Genetics
• Nucleic Acids Research
• Online Journal of Bioinformatics (OJB)
• Physiological Genomics
• PLoS Biology
• PLoS Computational Biology
• PNAS
• Science

Organizations

• Genome.gov
• International Society for Computational Biology
• Microarray Gene Expression Data (MGED) Society