Table 2.

All Enriched Transcripts by Category

AGI No.aDescriptionGene Name(s)MeanbRatioc
Auxin
    At2g20610Tyr aminotransferaseSUPERROOT1 (SUR1); RTY/ALF18.75.5
    At4g31500Cytochrome P450 monooxygenaseSUPERROOT2 (SUR2); CYP83B131.918.0
    At3g62100Aux/IAA family transcriptional repressorIAA304.85.5
    At2g21050AAAP (amino acid/auxin permease); AUX1 family10.97.4
    At1g73590Auxin efflux carrierPIN-FORMED1 (AtPIN1)5.65.1
Gibberellin
    At4g02780ent-Kaurene synthetase AGA-DEFICIENT1 (GA1)2.03.0
    At5g25900Cytochrome P450 ent-kaurene oxidaseGA-DEFICIENT3 (GA3); CYP701A311.15.9
    At2g32440Cytochrome P450 ent-kaurene oxidaseCYP88A2.62.8
Brassinosteroid
    At1g55610LRR X receptor-like kinaseBRI1-LIKE (BRL1)1.42.8
Receptor-like kinases
    At4g21400DUF26 receptor-like kinase1.92.2
    At4g21410DUF26 receptor-like kinase2.42.9
    At3g58690Extensin2.42.0
    At3g53380Lectin receptor-like kinase2.53.2
    At1g34210LRR II1.92.2
    At5g45780LRR II1.62.2
    At5g67200LRR III2.22.4
    At5g51560LRR IV2.62.2
    At2g45340LRR IV4.76.5
    At1g11140LRR V2.42.4
    At1g53440LRR VIII-2; S-domain (type 1)1.52.0
    At5g48940LRR XI5.43.2
    At5g13290Receptor-like kinase1.72.3
    At5g39790Pro-rich receptor-like kinase1.42.0
    At5g56790Pro-rich receptor-like kinase10.46.8
    At5g15080RLCK VII1.81.9
Phosphatidylinositol and Ca2+ signaling
    At5g639803′(2′),5′-bisphosphate nucleotidase; PI signalingFIERY1 (FRY1); AtSAL110.02.8
    At5g10170Inositol-3-phosphate synthase3.94.9
    At4g05520Calcium ion binding EF hand1.82.0
    At3g56690Calmodulin binding protein2.01.8
    At1g72670Calmodulin binding protein1.61.9
Transcriptional regulation
    At1g25470AP21.61.7
    At1g72360AP22.53.1
    At2g41710AP22.01.9
    At3g20840AP2PLETHORA1 (PLT1)6.35.7
    At5g17430AP25.05.9
    At1g35460bHLHAtbHLH803.22.8
    At2g27230bHLH5.23.4
    At3g19500bHLHAtbHLH1132.82.7
    At1g12860bHLH with F-boxAtbHLH333.44.5
    At1g21740bZIP1.81.6
    At1g68640bZIPPERIANTHIA (PAN); AtbZIP464.15.6
    At3g60630GRASSCL63.91.9
    At2g01430HD-ZipAtHB-171.82.7
    At5g20240MADS box (type II)PISTILLATA (PI)4.17.3
    At5g47390Myb2.71.8
    At5g11510Myb (R2R3)AtMYB3R41.61.7
    At5g17800Myb (R2R3)AtMYB566.16.4
    At5g60890Myb (receptor-like kinase); Trp biosynthetic pathwayALTERED TRYPTOPHAN REGULATION (ATR1); AtMYB349.212.1
    At5g44190Myb; GARP1.31.8
    At1g69490NACNAC-LIKE; ACTIVATED BY AP3/PI (NAP)8.66.3
    At3g13000NAC1.52.0
    At2g13840Putative DNA binding1.71.8
    At4g22770Putative DNA binding1.92.1
    At5g48090Putative DNA binding1.21.6
    At5g51590Putative DNA binding3.01.8
    At5g54930Putative DNA binding1.81.9
    At1g14410Putative DNA binding; p24-related2.61.8
    At5g51910TCP2.82.8
    At1g16070TUBBYATLP81.62.6
    At1g76900TUBBY (F-box)ATLP14.32.5
    At5g48250Zn finger (C2C2) CO-like B-boxCOL101.61.8
    At3g50870Zn finger (C2C2) GATAHANABA TARANU (HAN)1.82.7
    At5g03150Zn finger (C2H2)2.42.9
    At3g20880Zn finger (C2H2)8.28.3
    At2g38970Zn finger (C3HC4 RING)4.14.1
    At5g40320Zn finger (CHP-rich)1.82.0
    At3g22780Zn finger (CPP1-related)TSO13.21.8
Transcription (general)
    At1g29940DNA-directed RNA polymerase subunit4.82.2
    At5g45140DNA-directed RNA polymerase subunit2.52.1
    At1g60620RNA polymerase subunit (isoform B)1.71.6
    At3g02980GCN5-related histone N-acetyltransferase (GNAT) family1.61.7
    At5g35330Methyl binding domain proteinMBD22.31.8
    At4g23800Nucleosome/chromatin assembly factor (HMG homolog)NFD65.32.9
    At3g03790Regulator of Chromosome Condensation (RCC1) family2.52.0
    At5g43990SET-domain histone methyltransferaseSDG18; SET18; SUVR21.91.9
    At2g18850SET-domain histone methyltransferase1.61.6
    At2g17900SET-domain histone methyltransferaseASHR1; SET371.61.7
    At5g44560SNF7 family3.92.8
Protein turnover
    At3g23880F-box A3 subfamily protein2.02.6
    At1g47340F-box A5 subfamily protein1.41.7
    At3g58530F-box B1 subfamily protein2.12.0
    At3g03360F-box B5 subfamily protein2.12.0
    At1g06630F-box B7 subfamily protein3.12.8
    At4g05460F-box C5 subfamily proteinAtFBL202.21.8
    At1g30090F-box D subfamily protein1.51.8
    At1g68050F-box E subfamily protein with PAS and Kelch repeatsFKF13.83.7
    At5g56380F-box family protein1.41.7
    At3g51530F-box family protein1.82.1
    At1g47570Ubiquitin ligase complex; zinc finger (C3HC4 RING)2.21.9
    At5g65450Ubiquitin C-terminal hydrolase-like1.51.7
RNA silencing
    At2g27040AGO1-related proteinARGONAUTE4 (AGO4)5.72.8
    At5g43810AGO1-related proteinPINHEAD (PNH)/ZLL/AGO104.95.5
    At3g03300DEAD/DEAH box helicaseDICER-LIKE2 (DCL2)2.12.3
    At2g19930RNA-dependent RNA polymerase1.31.6
Cell division
    At5g67260CyclinCYCD3;24.92.5
    At4g02060DNA replication licensing factorPROLIFERA (PRL1)2.92.1
DNA replication and repair
    At5g41880DNA polymerase α subunit (primase) activity2.41.9
    At4g24790DNA polymerase III–like γ subunit1.51.9
    At2g41460DNA (apurinic or apyrimidinic site) lyase (ARP)2.02.1
    At1g19485HhH-GPD superfamily base excision DNA repair protein1.82.0
    At3g22880Meiotic recombination proteinAtDMC12.32.6
    At3g24320MutS family; mitochondrial recombinationCHLOROPLAST MUTATOR (CHM)1.41.9
    At4g02390Poly(ADP-ribose) polymerase (PARP)APP1.61.9
    At2g31320Poly(ADP-ribose) polymerase (PARP)2.01.8
    At3g14890PARP, DNA ligase zinc finger (nick sensor)2.02.0
    At1g21710Purine-specific base lesion DNA N-glycosylase2.61.9
Cell wall
    At2g31960Callose synthase geneAtGSL32.62.5
    At2g35650Cellulose-synthase–like geneCslA72.62.0
    At4g31590Cellulose-synthase–like geneCslC53.22.6
    At2g28950ExpansinEXP61.92.5
    At3g15720Polygalacturonase (predicted GPI-anchored)2.44.1
    At3g53190Pectate and pectin lyase5.64.0
    At2g26440Pectin methyl esterase4.67.3
    At4g03210Xyloglucan endotransglucosylase/hydrolaseXTH94.65.4
Cytoskeleton
    At5g42480DNAJ plastid division protein (ARC6-like)2.72.3
    At5g48360Formin homology-2 (FH2) domain protein3.33.4
    At5g55000Formin homology (FH) binding proteinFIP22.52.1
    At5g60210Expressed protein slow myosin heavy chain 24.73.3
    At4g33200MyosinAtXI-I1.91.7
    At1g63640Kinesin2.31.7
    At5g60930Kinesin1.92.2
Transporter, carrier, or channel
    At2g28070ABC (ATP binding cassette) transporterWBC33.42.2
    At2g26900Bile acid:Na+ symporterAtSbf14.62.4
    At5g36940Cationic amino acid transporter–like2.01.7
    At5g53130Cyclic nucleotide/voltage-regulated cation channel2.52.3
    At5g57100Drug/metabolite transporter superfamily3.73.0
    At3g05290Mitochondrial carrierPHT23.02.2
    At5g01500Mitochondrial carrier4.62.6
    At5g09690Mitochondrial mRNA splicing-2 protein; Mg transporter2.63.0
    At1g33110Multiantimicrobial extrusion family (MATE) transporter3.44.0
    At3g17650Oligopeptide transporter OPT2.11.9
    At3g47950Plasma membrane H+-ATPaseAHA41.11.6
    At1g59740Proton-dependent oligopeptide transporterMRS25.77.3
    At2g26180SF sugar porter3.32.6
    At2g16990Tetracycline transporter–like1.62.2
    At4g33670Voltage-gated K+ channel β subunit3.42.2
Disease resistance
    At1g58410CNL (CC-NBS-LRR) class protein1.82.4
    At1g72840TNL (TIR-NBS-LRR) class protein3.73.9
    At1g72850TN (TIR-NBS) class putative disease resistance protein4.96.0
    At4g09940Avirulence-induced gene (AIG1) family2.13.9
Metabolism/enzyme
    At1g629601-Aminocyclopropane-1-carboxylate (1-ACC) synthaseACS101.71.9
    At1g204904-Coumarate:CoA ligase 1 (4-coumaroyl-CoA synthase 1)4CL14.84.1
    At4g39940Adenosine-5-phosphosulfate-kinase10.88.9
    At5g08380α-Galactosidase2.83.0
    At1g55510α-Galactosidase1.82.0
    At5g09300α-Ketoacid decarboxylase E1 subunit11.65.8
    At3g55850AmidohydrolaseLONG AFTER FAR-RED3 (LAF3)1.81.8
    At3g47040β-d-Glucan exohydrolase2.33.1
    At4g09510β-Fructofuranosidase1.91.7
    At5g57850Branched-chain amino acid aminotransferase1.61.7
    At1g50110Branched-chain amino acid aminotransferase2.61.9
    At1g53520Chalcone-flavanone isomerase-related1.62.0
    At1g69370Chorismate mutase (Phe biosynthesis)CM31.81.6
    At3g57470Cys-type endopeptidase activity1.72.2
    At2g46650Cytochrome b55.67.4
    At4g15920Cytochrome c oxidoreductase3.13.6
    At4g12300Cytochrome P450; flavonoid 3′,5′-hydroxylaseCYP706A2.53.2
    At4g39950Cytochrome P450; N-hydroxylase for TrpCYP79B29.615.7
    At1g72040Deoxyguanosine kinase3.62.5
    At3g23570Dienelactone hydrolase11.69.3
    At1g48430Dihydroxyacetone kinase1.42.0
    At1g12130Flavin-containing monooxygenase1.42.2
    At1g49390Flavonol synthase2.12.8
    At4g37550Formamidase1.72.7
    At1g66250Glucan endo-1,3-β-glucosidase3.32.7
    At4g29360Glucan endo-1,3-β-glucosidase2.73.1
    At5g56590Glucan endo-1,3-β-glucosidase1.81.8
    At5g27380Glutathione synthetaseGSH27.83.2
    At1g11820Glycoside hydrolase family 172.21.9
    At1g30530Glycosyl transferase1.12.1
    At3g21750Glycosyl transferase4.25.7
    At5g54690Glycosyl transferase1.62.0
    At3g07270GTP cyclohydrolase 14.52.0
    At1g79790Haloacid dehalogenase-like hydrolase family1.61.7
    At3g25470Hemolysin5.02.4
    At2g18950Homogentisate phytylprenyltransferase family protein2.53.2
    At3g16260Hydrolase1.61.7
    At3g48410Hydrolase5.44.3
    At2g04400Indole-3-glycerol phosphate synthase10.24.7
    At3g14360Lipid acylhydrolase–like2.12.0
    At3g53450Lys decarboxylase2.13.0
    At1g13270Met aminopeptidase2.02.6
    At5g55130Molybdenum cofactor synthesis protein 34.72.2
    At1g32160Obtusifoliol 14-α-demethylase1.51.7
    At2g39220Patatin-like acyl hydrolase2.23.2
    At5g13640Phosphatidylcholine-sterol O-acyltransferase2.62.1
    At1g48600Phosphoethanolamine N-methyltransferase13.95.6
    At1g74720Phosphoribosylanthranilate transferase1.72.2
    At1g16220Protein phosphatase 2C1.72.3
    At5g51140Pseudouridylate synthase activity3.12.1
    At2g40760Rhodanese-like protein2.32.0
    At3g23580Ribonucleoside-diphosphate reductase6.84.2
    At2g17640Ser acetyltransferase2.63.6
    At1g43710Ser decarboxylase9.02.0
    At4g11640Ser racemase; Thr dehydratase1.71.9
    At1g70560Similar to aliinase11.67.9
    At5g51970Sorbitol dehydrogenase4.92.6
    At3g14240Subtilisin-like Ser protease6.04.8
    At5g05980Tetrahydrofolylpolyglutamate synthase3.61.9
    At3g06730Thioredoxin1.62.0
    At2g41680Thioredoxin reductase, putative1.92.4
    At3g02660Tyrosyl-tRNA synthetase1.71.8
    At5g40870Uridine kinase3.73.0
Other
    At1g60860ARF GTPase-activating (GAP) protein2.62.3
    At4g03100Rac GTPase-activating (GAP) protein1.41.7
    At2g23460Extra-large GTP binding proteinXLG12.71.9
    At3g53800Armadillo/β-catenin repeat family2.02.2
    At4g33400Defective embryo and meristems (DEM)–like3.62.4
    At1g72070DNAJ chaperone1.41.9
    At5g16650DNAJ chaperone2.72.3
    At1g53140Dynamin2.92.0
    At3g60190DynaminADL41.82.1
    At3g19720Dynamin2.41.6
    At1g29980GPI-anchored protein14.39.8
    At1g21880GPI-anchored protein5.62.7
    At2g36730Pentatricopeptide (PPR) protein1.21.7
    At2g23050Phototropic-responsive NPH3 family; phosphorelay12.610.7
    At5g4642016S rRNA processing protein2.01.8
    At2g47250RNA helicase3.82.1
    At3g26120RNA binding protein1.82.2
    At5g23690Poly A polymerase–like1.61.8
    At1g35610Putative electron transport activity1.72.2
    At1g50240Armadillo/β-catenin repeat family2.52.0
    At2g19430Transducin/WD-40 repeat family2.51.6
    At5g15550Transducin/WD-40 repeat family5.32.3
    At4g37110tRNA aminacylation; protein translation1.62.2
    At3g46210tRNA nucleotidyl transferase; protein translation2.32.0
    At1g13030tRNA splicing2.42.0
Unknown
    At1g08020Unknown1.52.2
    At1g09450Unknown1.41.9
    At1g09980Unknown5.53.3
    At1g17650Unknown1.41.7
    At1g21560Unknown1.92.1
    At1g23370Unknown1.32.0
    At1g29270Unknown4.68.0
    At1g35612Unknown5.17.3
    At1g48460Unknown2.32.1
    At1g53460Unknown3.92.8
    At1g61065Unknown1.81.6
    At1g63260Unknown3.33.4
    At1g67660Unknown1.51.8
    At1g68080Unknown1.41.9
    At1g68220Unknown3.62.2
    At1g68820Unknown2.92.8
    At2g03280Unknown1.11.8
    At2g03780Unknown1.81.8
    At2g25270Unknown2.32.2
    At2g26200Unknown1.91.7
    At2g32590Unknown2.22.2
    At2g38370Unknown5.16.5
    At2g39070Unknown1.91.7
    At2g45830Unknown3.43.7
    At3g01810Unknown5.23.4
    At3g09000Unknown1.81.7
    At3g15351Unknown2.72.2
    At3g17680Unknown2.82.4
    At3g22970Unknown4.32.8
    At3g26750Unknown1.41.9
    At3g29185Unknown1.41.9
    At3g43240Unknown3.92.4
    At3g43540Unknown1.42.0
    At3g50190Unknown1.32.1
    At3g50620Unknown1.72.0
    At3g51290Unknown1.52.3
    At3g53540Unknown1.72.3
    At3g63090Unknown2.22.4
    At4g02790Unknown1.72.1
    At4g13140Unknown1.71.9
    At4g16620Unknown1.51.9
    At4g18570Unknown3.93.3
    At4g19400Unknown3.32.4
    At4g22890Unknown1.92.0
    At4g24750Unknown2.32.0
    At4g25170Unknown1.92.8
    At4g35910Unknown2.72.2
    At5g02010Unknown2.32.6
    At5g12080Unknown5.73.9
    At5g15170Unknown1.71.9
    At5g23780Unknown1.32.2
    At5g27400Unknown3.52.5
    At5g29771Unknown3.92.0
    At5g37010Unknown1.81.8
    At5g41620Unknown4.66.2
    At5g44650Unknown1.52.1
    At5g47440Unknown6.69.1
    At5g48960Unknown1.61.8
    At5g51850Unknown2.14.4
    At5g63040Unknown1.31.7
    At5g65685Unknown2.11.8
    At5g66180Unknown2.52.3
  • a Arabidopsis Genome Initiative number.

  • b Mean normalized expression of AGL42IV:GFP sort.

  • c Average ratio of AGL42IV:GFP sort to five other root tissue sorts.