5/12/05

MeV (MultiExperiment Viewer) a Java application designed to allow the analysis of microarray data to identify patterns of gene expression and differentially expressed genes.

http://www.tm4.org/mev.html

MIDAS (Microarray Data Analysis System)

MADAM (MicroArray Data Manager)

Spotfinder

ArrayViewer

R and Bioconductor

http://www.bioconductor.org/

http://www.r-project.org/

dChip

http://www.biostat.harvard.edu/complab/dchip/info_file.htm

NASCArrays

http://affymetrix.arabidopsis.info/narrays/experimentbrowse.pl

TAIR

Ara-Cyc

http://www.arabidopsis.org/tools/aracyc

http://www.arabidopsis.org/tools/bulk/microarray/analysis/index.jsp

MapMan (GABI & the group of Mark Stitt)

http://gabi.rzpd.de/projects/MapMan/

Genevestigator (Gruissem Laboratory , ETH Zurich, Switzerland)

https://www.genevestigator.ethz.ch/

PathMAPA (Yale University, USA)

http://bioinformatics.med.yale.edu/pathmapa.htm

http://plantgenomics.biology.yale.edu/

4. Useful Gene Expression Databases

AtGenExpress (multinational effort coordinated by Weigel, Altmann & Nover)

http://www.arabidopsis.org/info/expression/ATGenExpress.jsp

Gene Expression Omnibus (GEO) (NCBI's expression database)

http://www.ncbi.nlm.nih.gov/geo/

NASCArrays

http://affymetrix.arabidopsis.info/narrays/experimentbrowse.pl

Genevestigator (The Gruissem Lab, ETH Zurich, Switzerland)

https://www.genevestigator.ethz.ch/

Arabidopsis Tiling Array Transcriptome Express Tool (The Ecker Lab, Salk)

http://signal.salk.edu/cgi-bin/atta

MPSS (Massively Parallel Signature Sequencing)

Blake Meyers Lab

http://mpss.udel.edu/

SAGE (Serial Analysis of Gene Expression)

Gregory May Lab

http://www.ncbi.nlm.nih.gov/geo/query/browse.cgi?view=samples&email=zdu@noble.org

5. Informative Functional Genomic Websites

TAIR (The Arabidopsis Information Resource)

http://www.arabidopsis.org/

PlaNet

http://mips.gsf.de/projects/plants/PlaNetPortal/index_html

http://mips.gsf.de/projects/plants/PlaNetPortal/databases.html

AGRIS (The Arabidopsis Gene Regulatory Information Server at Ohio State U)

http://arabidopsis.med.ohio-state.edu/

The Database of Arabidopsis Transcription Factors (DATF)

http://datf.cbi.pku.edu.cn/

AthaMap (a genome-wide map of putative transcription factor)

http://www.athamap.de/

RARTF (RIKEN Arabidopsis Transcription Factor database)

http://rarge.gsc.riken.go.jp/rartf/

PlantCARE (cis-acting regulatory element)

http://oberon.fvms.ugent.be:8080/PlantCARE/index.html

PLACE (A Database of Plant Cis-acting Regulatory DNA Elements)

http://www.dna.affrc.go.jp/PLACE/

PlantsP (Functional genomics of plant phosphorylation)

http://plantsp.genomics.purdue.edu/

PlantsT (functional genomics of plant transporters)

http://plantst.sdsc.edu/

PlantsUBQ

A Functional Genomics Database for the Ubiquitin/26S Proteasome Proteolytic Pathway

http://plantsubq.sdsc.edu/

Yale Plant Genomics

http://plantgenomics.biology.yale.edu/

The Plant Chromatin Database (ChromDB)

http://www.chromdb.org/

Arabidopsis Transcription Regulators & Regulatory pathways (Sheen Lab)

http://genetics.mgh.harvard.edu/sheenweb/AraTRs.html

http://genetics.mgh.harvard.edu/sheenweb/Ara_pathways.html

Integrated Arabidopsis Gene Functional Annotation (Sheen Lab)

http://genetics.mgh.harvard.edu/sheenweb/Ara_gene_families.html

MAPKs & CDPKs & TRs, ATH1 gene annotation & Regulatory pathways (Sheen Lab)

http://genetics.mgh.harvard.edu/sheenweb/main_page.html

The Integrated Microarray Database System (IMDS, Ausubel Lab)

http://ausubellab.mgh.harvard.edu/imds/

John OHLROGGE Plant Lipid Metabolism Lab, Michigan State U

http://www.plantbiology.msu.edu/ohlrogge/index.shtml

Developing Seeds array data (The Ohlrogge Lab, Michigan State U)

http://www.bpp.msu.edu/Seed/SeedArray.htm

MAPK cascades & AGC PKs (Laszlo Bögre Lab, University of London)

http://personal.rhul.ac.uk/ujba/110/bogrelab.htm

Receptor PKs (Shin-Han Shiu, U of Chicago, Dept of Ecology & Evolution)

http://pondside.uchicago.edu/~lilab/people/shinhan.htm

AMPL Arabidopsis Membrane Protein Lab

http://www.cbs.umn.edu/arabidopsis/

Plant morphogenetics (Jim Haseloff's Lab, Dept Plant Sciences, U Cambridge)

http://www.plantsci.cam.ac.uk/Haseloff/index.htm

AREX: The Arabidopsis Gene Expression Database (Benfey Lab)

http://www.arexdb.org/database.jsp

Functional Genomics of Model Plants (Sundaresan Lab, UC Davis)

http://www-plb.ucdavis.edu/Labs/sundar/index.asp

The Arabidopsis Small RNA Project (The Carrington Lab, Oregon State U)

http://asrp.cgrb.oregonstate.edu/

Plant snoRNA database

http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home

Osmotic Stress Microarray Database (Stress Genomics Consortium, USA)

http://www.osmid.org/

ABA-dependent Guard Cell and Mesophyll Cell expression arrays (The Schroeder Lab, UCSD)

http://www-biology.ucsd.edu/labs/schroeder/guardcellchips.html

Cold responses (The Tomashow Lab, MSU-DOE PRL, Michigan State U, USA)

http://www.msu.edu/~mftlab/

Seedgenes project (The Meike Lab, Oklahoma State University)

http://www.seedgenes.org/

Functional genomics of Arabidopsis P450 (The Schuler Lab, U Ill)

http://arabidopsis-p450.biotec.uiuc.edu/

The Functional Genomics Plant Polyploid

http://polyploid.agronomy.wisc.edu/

SIGnAL (Salk Institute Genomic Analysis Lab)

http://signal.salk.edu/index.html

The Arabidopsis TILLING Project

http://tilling.fhcrc.org:9366/

Arabidopsis insertion database

http://atidb.org/cgi-perl/index

RIKEN Transposon Mutant Keyword Search

http://rarge.gsc.riken.go.jp/dsmutant/keyword.pl

Plant genes involved in Agrobacterium-mediated genetic transformation (Gelvin Lab)

http://www.biology.purdue.edu/people/faculty/gelvin/gelvinweb/main.html

Center for plant cell biology at UC Riverside (Raikhel Lab)

http://cepceb.ucr.edu/members/raikhel.htm

Functional and Comparative Genomics of Disease Resistance Gene Homologs (Michelmore Lab)

http://www.niblrrs.ucdavis.edu/data_links1.html

ARABI-COIL (Arabidopsis Coiled-Coil Protein Database)

http://www.coiled-coil.org/arabidopsis/

Arabidopsis Nucleolar Protein Database

http://bioinf.scri.sari.ac.uk/cgi-bin/atnopdb/home

Arabidopsis seed protein proteome

http://seed.proteome.free.fr/

PDB (a specialized proteome database dedicated to plant plastids, the van Wijk Lab, Cornell U)

http://cbsusrv01.tc.cornell.edu/users/ppdb/

Arabidopsis Databases (mitochondria AMPDB, MPIMP, SUBA)

http://www.mitoz.bcs.uwa.edu.au/pmbg/Databases.php

Proteins of Arabidopsis thaliana database (a part of the Encyclopedia of Life EOL project)

http://pat.sdsc.edu/perl/browser.pl?tax=Arabidopsis%20thaliana

Plant cell imaging (The Ehrhardt Lab, Stanford U/Carnegie)

http://deepgreen.stanford.edu/

Naturalvariation

http://www.naturalvariation.org/

The Net Center for Plant Genomics

http://plantgenome.sdsc.edu/dw_NCPG.html

The CATMA (Complete Arabidopsis Transcriptome MicroArray)

http://www.catma.org/

The AGRIKOLA project (Arabidopsis Genomic RNAi Knock-out Line Analysis)

http://www.agrikola.org/

ORFEUS (Open Reading Frames for European Union Scientists)

http://www.orfeome.org/index.php

Systematic analysis of Arabidopsis promoters

http://www.psb.ugent.be/SAP/

Gateway™ vectors for functional studies in plant cells

(Plant Systems Biology (VIB-Ghent U, Belgium)

http://www.psb.ugent.be/gateway/

The Arabidopsis Book (Somerville & Meyerowitz, ASPP)

http://www.aspb.org/publications/arabidopsis/index.cfm