Table II.

Genes up-regulated by BRs

Gene NameAccession No.Function or CommentAffymetrix No.det2WT
AmplifiedNo-Amp.AmplifiedNo-Amp.
FC ± seFC ± seFC ±seFC ± se
IAA3/SHY2 U18406 Auxin-inducible nuclear protein/suppressor of phyB13301_at2.4 ± 0.422.7 ± 0.291.3 ± 0.101.3 ± 0.10
IAA5 U18407 Auxin-inducible nuclear protein13660_i_at16.8 ± 4.647.8 ± 1.023.3 ± 0.351.8 ± 0.00
SAUR-AC1/−15 S70188 Small auxin up RNA from Arabidopsis Columbia12608_i_at9.9 ± 0.559.6 ± 1.223.3 ± 0.003.7 ± 0.25
IAA19 U49075 Member of IAA gene family/IAA1 binding protein13296_at3.1 ± 0.252.9 ± 0.151.8 ± 0.002.1 ± 0.20
BAS1/CYP72B1 AC003105/F18A8.8Activation-tagged suppressor of phyB12543_at3.8 ± 0.274.2 ± 1.162.7 ± 0.053.1 ± 0.00
TCH2 AF026473 Touch-induced gene 2/calmodulin-related protein18300_at2.5 ± 0.192.7 ± 0.241.9 ± 0.151.8 ± 0.05
TCH4 AF051338 Touch-induced gene 4/xyloglucan endotransglycosylase16620_s_at8.8 ± 0.8116.8 ± 4.626.5 ± 0.358.2 ± 0.75
XTR6 U43488 Xyloglucan endotransglycosylase-related protein 617533_s_at9.0 ± 1.105.7 ± 0.965.5 ± 0.451.4 ± 2.50
MSS3 AC004450/F14B2.23Suppressor of snf4/calmodulin-like protein (EF-hand)20689_at3.2 ± 0.353.8 ± 0.581.6 ± 0.151.8 ± 0.25
ZAT7 X98676 Zinc finger protein15778_at4.2 ± 0.472.0 ± 0.151.4 ± 0.150.1 ± 1.20
ATPA2 X99952 Root-specific peroxidase12356_at4.0 ± 2.093.0 ± 0.431.4 ± 0.201.7 ± 0.40
KCS1 AF053345 Fatty acid elongase 3-ketoacyl-CoA synthase 117961_at2.7 ± 0.283.0 ± 0.291.3 ± 0.051.3 ± 0.10
OPR1 U92460 12-Oxophytodienoate reductase (jasmonate biosynthesis)18253_s_at2.0 ± 0.032.1 ± 0.031.4 ± 0.101.4 ± 0.10
AtPMEpcrB AF033206 Pectin methylesterase homolog19267_s_at4.1 ± 0.324.4 ± 0.463.3 ± 0.153.5 ± 0.10
ATP24a Y11788 Peroxidase18946_at2.3 ± 0.152.4 ± 0.300.0 ± 1.051.1 ± 0.05
CYP94C1 AC005824/F15K20.21P450 monooxygenase19288_at10.1 ± 3.324.0 ± 0.972.0 ± 0.201.7 ± 0.25
CYP86A2 AF013293/A_IG005I10.21P450 monooxygenase17966_at2.0 ± 0.092.2 ± 0.151.3 ± 0.001.3 ± 0.00
BRU2/SAUR-25 AL035528/F18A5.180Auxin-inducible SAUR gene family13395_at5.3 ± 0.632.6 ± 0.381.6 ± 0.051.6 ± 0.50
BRU3/SAUR-9 AL022373/T19K4.240Auxin-inducible SAUR gene family12947_at9.0 ± 0.219.2 ± 0.654.9 ± 0.354.9 ± 0.20
BRU4/SAUR16 AL035656/T9A14.140Auxin-inducible SAUR gene family13322_at5.8 ± 0.686.5 ± 1.002.2 ± 0.052.5 ± 0.30
BRU5/SAUR-10 AC006201/T27K22.12Auxin-inducible SAUR gene family13781_at3.0 ± 0.663.0 ± 0.061.6 ± 0.151.7 ± 0.20
BRU6/GH3-22-a AL035601/F6G17.40Auxin-inducible GH3 gene family13565_at2.3 ± 0.172.2 ± 0.151.3 ± 0.051.8 ± 0.35
BRU7/GH3-10 AC005275/F4C21.36Auxin-inducible GH3 gene family13812_at2.2 ± 0.212.3 ± 0.151.7 ± 0.201.8 ± 0.40
BRU8 AC004512/T8F5.9Putative xyloglucan endotransglycosylase (TCH4 homolog)17960_at7.7 ± 0.488.0 ± 0.432.1 ± 0.352.0 ± 0.30
BRU9 AC007067/T10O24.17Putative endoxyloglucan transferase (EXGT-A3 homolog)19490_at22.0 ± 9.1710.9 ± 2.545.2 ± 0.103.7 ± 0.00
AtExp8 AC002336/T2P4.4Putative expansin (expansin2-homolog)19660_at3.3 ± 0.573.7 ± 0.571.3 ± 0.051.3 ± 0.05
BRU11 AL035539/F22I13.170Putative expansin (pollen allergen protein homolog)19976_at6.2 ± 0.427.2 ± 0.922.0 ± 0.002.1 ± 0.10
BRU12 AC005169/F6F22.19Putative extensin with Leu-rich repeat (LRX1 homolog)18525_at3.3 ± 0.092.4 ± 0.451.3 ± 0.20−0.1 ± 1.10
BRU13 AC005698/T3P18.1Putative extensin with Leu-rich repeat (LRX1 homolog)18998_at2.2 ± 0.152.3 ± 0.292.0 ± 0.402.0 ± 0.50
BRU14 AL049608/T9E8.80Putative extensin with Leu-rich repeat (LRX1 homolog)20537_at2.8 ± 0.153.1 ± 0.151.6 ± 0.001.8 ± 0.00
BRU15 AC003027/F21M11.20Putative arabinogalactan protein (fasciclin-domain)16438_at0.6 ± 0.802.2 ± 0.101.6 ± 0.101.7 ± 0.10
BRU16 AL035601/F6GT17.100Putative arabinogalactan protein14947_at1.5 ± 0.282.5 ± 0.181.8 ± 0.001.8 ± 0.00
BRU17 AF060874 Putative arabinogalactan protein (AtAGP4 homolog)15107_s_at1.7 ± 0.372.4 ± 0.241.5 ± 0.001.5 ± 0.00
BRU18 AF069298/T14P8.14Putative pectinesterase14612_at4.0 ± 0.184.2 ± 0.263.3 ± 0.403.6 ± 0.55
BRU19 AL022580/T5K18.200Putative pectinacetylesterase19905_at3.0 ± 0.283.6 ± 0.732.5 ± 0.453.3 ± 0.95
BRU20 AC004077/T31E10.15Endo-1,4-β-xylanase homolog15271_at2.7 ± 0.172.9 ± 0.121.5 ± 0.051.6 ± 0.10
BRU21 AL030978/M4122.170Ca2+-binding protein homolog15431_at3.1 ± 0.253.6 ± 0.492.3 ± 0.102.2 ± 0.00
BRU22 AL022198/F6I18.90Putative calmodulin-binding protein19857_at2.7 ± 0.202.7 ± 0.171.7 ± 0.102.0 ± 0.20
BRU23 AC005970/T6P5.14Putative protein kinase14030_at2.2 ± 0.102.4 ± 0.331.5 ± 0.151.7 ± 0.15
BRU24 AC002339/T11A7.8Putative receptor kinase (CLV1 homolog)14112_at3.4 ± 0.902.4 ± 0.321.7 ± 0.251.8 ± 0.10
BRU25 AC004238/F19I3.16Leu-rich repeat domain12251_at4.5 ± 0.674.7 ± 0.723.5 ± 0.852.6 ± 0.25
BRU26 AC002354/F6P23.7NAM/NAC gene homolog13806_at2.9 ± 0.443.0 ± 0.701.8 ± 0.301.6 ± 0.05
BRU27 AC006533/F20M17.23Ethylene-Regulated protein ER33 homolog15403_s_at3.7 ± 0.253.8 ± 0.291.9 ± 0.152.1 ± 0.20
BRU28 AF128396/T3H13.3Phosphate-induced gene phl-1 homolog14077_at3.2 ± 0.355.8 ± 0.293.6 ± 0.303.5 ± 0.30
BRU29 AL021711/F13C5.140Pro-rich protein (APG) homolog (GDSL-motif)16434_at2.8 ± 0.153.0 ± 0.032.4 ± 0.402.4 ± 0.35
BRU30 AL035353/F16A16.110Pro-rich protein (APG) homolog (GDSL-motif)17196_at3.9 ± 0.384.7 ± 0.481.9 ± 0.202.3 ± 0.25
BRU31 AC005917/F3P11.22Pollen-specific protein (SF21) homolog15892_at2.4 ± 0.182.7 ± 0.321.8 ± 0.151.8 ± 0.25
BRU32 AC005679/F9K20.9Carrot (Daucus carota) EP1 homolog17440_i_at2.7 ± 0.323.2 ± 0.551.6 ± 0.201.6 ± 0.25
BRU33 AC007060/T5I8.14Phosphatidylinositol/phosphatidylcholine transfer protein homolog12046_at3.6 ± 0.343.8 ± 0.251.9 ± 0.101.9 ± 0.15
BRU34 AP007269/A_IG002N01.14Unknown12953_at3.1 ± 0.353.3 ± 0.491.6 ± 0.051.8 ± 0.05
BRU35 AC005169/F6F22.17Unknown13916_at2.2 ± 0.123.6 ± 0.203.6 ± 0.203.8 ± 0.45
BRU36 AC005106/T25N20.6Unknown14913_at3.7 ± 0.343.4 ± 0.470.1 ± 1.050.0 ± 1.10
BRU37 AL049481/T5L19.20Unknown14951_at2.6 ± 0.262.8 ± 0.322.0 ± 0.102.2 ± 0.20
BRU38 AC002535/T30B22.26Unknown19880_at2.6 ± 0.152.9 ± 0.251.6 ± 0.201.6 ± 0.10
BRU39 AC007138/T7B11.21Unknown19992_at3.0 ± 0.213.4 ± 0.321.6 ± 0.101.6 ± 0.05
BRU40 AL022224/F1C12.90Unknown12027_at2.8 ± 0.322.5 ± 0.541.2 ± 0.050.0 ± 1.05
BRU41 AC000348/T7N9.22Unknown14443_at2.1 ± 0.172.1 ± 0.121.8 ± 0.202.0 ± 0.25
BRU42 AC006921/F2H17.17Unknown18885_at2.0 ± 0.122.1 ± 0.122.0 ± 0.002.2 ± 0.10
BRU43 AC004521/F411.31Unknown12584_at2.1 ± 0.152.8 ± 0.571.4 ± 0.101.5 ± 0.45

When genes have names on publications or on database, we adopted their names. Otherwise, we designated genes from BRU2 to BRU43. Ampified and No-Amp., Before and after signal amplification with antibody, respectively.