PLANT GENE FUNCTION CATOGORIESRESOURCESTAIR Gene FamiliesTAIR/Mendel TFsKEGG, TIGR, GO, MIPS* (MIPS experts list at the end)AGI, Nature 408, 796, Dec. 2000 (The Arabidopsis Genome Sequence)Proteins are sorted by cellular function (610 genes)METABOLIC PATHWAYSSucrose, glucose and fructose utilizationOther sugar utilizationGluconeogenesisSecondary MetabolismAlkaloid BiosynthesisGlucosinolate BiosynthesisPhenylalanine/hydroxycinnamate pathwayIsoprenoid metabolismPierre BenvenisteTerpenoid MetabolismMatthew Jenks and Bertrand Lemieux(AraCyc)Vitamins and CofactorsCamalexin BiosynthesisShikimic acid pathwayPhotosynthesis(AraCyc) Photosynthesis (plant)PhotorespirationRespirationAlternative oxidaseL McIntosh/J SiedowNitrogen metabolismStorage ProteinsLipid metabolismAlternative Lipid Gene Classificationhttp://www.plantbiology.msu.edu/lipids/genesurvey/table2.htmlPhytoremediation of Toxic Elemental and Organic PollutantsCell Wall MetabolismCellulose metabolism(future AraCyc)Hemicellulose metabolism(future AraCyc)(future AraCyc)Glycoside HydrolasesCell wall proteinsAlternative Cell Wall Gene ClassificationORGANELLESChloroplast and Mitochondria Structure, Import & Function Gene FamiliesProtein Targeting & Trafficking MachineryChromosomeRNA MetabolismRibosomeProteosomeCytoskeletonVesicle/Trafficking/SecretionPlasmodesmataGolgiVacuolePeroxisomeGlyxoysomePlasma MembraneMicrosomeGENE FAMILIESTransporter/ChannelTransporters/assimilationRedoxTranscription Regulators(More information in summary table for 2,863 genes. Please refer to the table for detailed notes.)RCD gene familyThe NPH3/RPT2 familyPeroxin genesREGULATORY PATHWAYSSIGNAL TRANSDUCTIONABA biosynthesis, metabolism, transport & signalingBob Creelman et al.Polyamine Biosynthesis, metabolism, transport and signaling (Aracyc)Stomatal Development in ArabidopsisStress SignalingColdJian Kang Zhu et al.DroughtUVOxidative & AntioxidativeOxidative Stress and Acclimation Mechanisms in PlantsHypoxiaFloodDetoxificxationMechanicalWoundingTouchingSecond messengersProtein PhosphataseReceptor KinasesMAPK CasacadesAMPK and SNF-Related PK (SnRPK) Gene FamilyCasein kinaseTwo-ComponentDefense/ImmunityCell DeathProteasesDNaesCell CycleCytokinesisGerd Jurgens and Uli MeyerMIPS Gene Family ExpertsNSF Plant Genome and 2010 Projects & websites (2001 & 2002)Nitrogen networkTranscriptional NetworksTwo-Component(NCU) Arabidopsis 2010: Analysis of Two-Component Signaling Elements from ArabidopsisTransportersStarch Granule Metabolism1ARABIDOPSIS GENE FUNCTIONANNOTATION(J Sheen, 9/1/03)Data Resources include websites, papers, reviews, domainblast, etc.PLANT GENE FUNCTION CATOGORIES1. METABOLIC PATHWAYS (GO: Molecular Function)2. GENE FAMILIES (GO: Molecular Function)3. ORGANELLES (GO: Cellular Component/Biological Process)4. REGULATORY PATHWAYS/SIGNAL TRANSDUCTION (GO: Biological Process)RESOURCESTAIR AraCyc http://luggagefast.stanford.edu/group/arabprotein/TAIR Gene FamiliesPresently there are 555 Gene Families4,670 Genes, e.g., Arabidopsis cytochrome P450 databaseTAIR/Mendel TFsKEGG, TIGR, GO, MIPS* (MIPS experts list at the end)AGI, Nature 408, 796, Dec. 2000 (The Arabidopsis Genome Sequence)The Arabidopsis Book (C Somerville & EM, ASPB), 2002The Plant Cell Signal Transduction Special Issues, 2002Other sources of plant gene function reviews: TIPS, COPB, Annu Rev PB, Plant Physiol and Plant Physiol Arabidopsis special issues (2000-2003), Science STKEThe 620 Arabidopsis Mutants (David W. Meinke, Plant Physiol, 131, 409-418, 2003)2The NSF 2010 and Plant Genome Projects (list at the end)http://www.nsf.gov/bio/pubs/awards/2010fy01.htmhttp://www.nsf.gov/bio/pubs/awards/2010fy02.htm**Sheen Lab, Arabidopsis Transcription Regulator (AtTR) Gene List(One summary Word file, one xls summary table file, and one large xls gene list file)**Sheen Lab, Regulatory Pathway Gene List(One xls summary table and one large xls gene list file)**Sheen Lab, Arabidopsis Gene Family List(One xls summary table file and one large xls gene family list file)**Sheen Lab, Integrated Arabidopsis Gene Function List(One master xls gene list file)**Microarray and Affychip Papers (reference list)(One Word file)Comprehensive Reviews and Websites Transcription factors (Science 2000, 290, 2105; COPB 2002, 5, 430, The Arabidopsis book, 2002)AtTFDB & AGRIS website (Ohio State U) http://arabidopsis.med.ohio-state.edu.ChromDB website (U Arizona)NSF plant genome project www.chromdb.orgGene list http://chromdb.biosci.arizona.edu/cgi-bin/v3/gene_loc.cgiPlantsP website for PK and PPs (1286 PK genes, including receptorkinase genes)A review for PP genes, Plant Physiology, 129, 908–925, 2002)http://plantsp.sdsc.edu PlantsT for plant transportershttp://plantst.sdsc.edu3SeedGenes (NSF 2010 Project, D. Meinke website)http://www.seedgenes.org/Stress Genomic consortium (Plant Genome Project, Hans Bohnert)The Plant Lipids website (Michigan State U)Proteins are sorted by cellular function (610 genes)http://www.plantbiology.msu.edu/ohlrogge/index.shtmlhttp://www.plantbiology.msu.edu/lipids/genesurvey/master_table.htmhttp://blue.butler.edu/~kschmid/lipids.htmlThe Plant Cell Wall Genomics website (Purdue U)http://cellwall.genomics.purdue.edu/http://cellwall.genomics.purdue.edu/families/index.htmlRichmond, T. A., C. R. Somerville. 2001. Integrative approaches todetermining Csl function. Plant Mol. Biol. 47, 131-143.http://cellwall.stanford.edu/The Cellulose Synthase SuperfamilyCallose Synthases/Glucan Synthaseshttp://xyloglucan.prl.msu.edu/cell wall databasehttp://xyloglucan.prl.msu.edu/cgi-bin/gene.pl?index=geneMAPK, CDPK, Two-component & Sugar (Sheen Lab reviews/website)http://genetics.mgh.harvard.edu/sheenweb/main_page.htmlNitrogen Networks (NSF 2010 project, including glutamine receptors, New York U, Gloria Goruzzi, website)Arabidopsis Ub/26S Proteosome (1327 genes)TIPS 8, 135- 1442, 2003 (R. Vierstra)F-box proteins (694 members)PNAS 99, 11519-11524, 2002Small G-protein review (Plant Physiol, 131, 1191-1208, 2003)4Pfam domains, Plant Physiol 125, 77-80, 2001 (Table 1)TIPS 7(12), 544-549 (Dec. 2002), (Table 1, 2) TIPS 7 (12), 565, Dec 2002 (Box 1, Specific interest database)Signaling protein domains (TIPS 7, 544-549, 2002)METABOLIC PATHWAYSCarbon MetabolismStarch synthesis and metabolism Sucrose(Aracyc)Glycolysis, Pentose phosophate cycle(future AraCyc)TCA cycleAlternate oxidase pathway(future AraCyc)Sucrose, glucose and fructose utilization Fructokinases, hexokinases, invertasae, sucrose synthaseOther sugar