Table 1 Rice Genes Upregulated (≥2 Fold) Following Cellulase Treatment
Probe set IDa | Public IDb | FCAc | Gene descriptiond | Homolog (E score)e |
|---|---|---|---|---|
Cell growth/division | ||||
 Os.10388.1.S1_at | AK120374 | 2.74 | MEE59 (maternal effect embryo arrest 59) | NP_195447 (3e-22) |
 OsAffx.7876.1.S1_s_at | 9640.m04245 | 2.46 | Os12g0626500 (Seed maturation protein domain containing protein) | NP_001067326 (2e-35) |
 Os.38249.2.S1_at | CB638262 | 2.39 | Putative early flowering 3 | BAA83571 (6e-28) |
Cell structure | ||||
 OsAffx.22303.1.S1_at | 9635.m03076 | 5.06 | Expansin-like B1 precursor (OsEXLB1) (Expansin-related 1) | Q850K7 (3e-147) |
 Os.37723.1.S1_at | AK072531 | 2.27 | Putative tonoplast membrane integral protein | AAS98488 (3e-95) |
 Os.5754.1.S1_at | AK099590 | 2.23 | Putative plastid developmental DAG protein | BAD03018 (8e-91) |
 Os.36975.3.S1_x_at | NM_189551 | 2.17 | Putative MAR binding filament-like protein 1 | BAD68082 (0.0) |
 Os.24307.1.S1_at | AK066849 | 2.01 | TMP14 (THYLAKOID MEMBRANE PHOSPHOPROTEIN OF 14 KDA) | NP_566086 (1e-24) |
Disease/defense | ||||
 Os.53444.1.S1_at | AK072661 | 4.61 | Putative pathogen-induced protein 2–4 | BAD08038 (7e-17) |
 Os.11575.3.S1_x_at | AK065363 | 3.04 | Ankyrin-repeat protein/OsNPR3 | ABE11617 (0.0) |
 Os.10546.1.S1_s_at | AU183565 | 2.92 | Putative UDP-glucose:salicylic acid glucosyltransferase | BAD34356 (2e-33) |
 OsAffx.30138.1.S1_at | 9637.m02954 | 2.9 | Putative UDP-glucose:salicylic acid glucosyltransferase | BAD34356 (0.0) |
 Os.8760.1.S1_a_at | AK099869 | 2.6 | Putative nodulin-like protein | BAD34227 (0.0) |
 Os.36969.1.S1_at | AK120328 | 2.43 | NB-ARC domain containing protein | EAY99786 (3e-25) |
 Os.11179.1.S1_at | CB647801 | 2.37 | Ankyrin repeat family protein, putative, expressed | ABF95250 (1e-43) |
 Os.25266.1.S1_at | AK058891 | 2.34 | Putative beta 1,3-glucanase | BAB63855 (2e-167) |
 OsAffx.23277.2.S1_at | 9629.m01656 | 2.3 | Ribosome inactivating protein, expressed | ABF98182 (1e-08) |
 Os.38249.1.S1_at | AK065173 | 2.23 | Nematode responsive protein-like | BAD45081 (0.0) |
 Os.4327.1.S1_at | AF384030 | 2.21 | Seven transmembrane protein MLO2 | AF384030_1 (0.0) |
 Os.11831.1.S1_at | AK062130 | 2.12 | Putative benzothiadiazole-induced S-adenosyl-L-methionine:salicylic acid Carboxyl methyltransferase1 | BAD45797 (0.0) |
 Os.11575.1.S1_at | AK065952 | 2.09 | Ankyrin-repeat protein/OsNPR3 | ABE11617 (0.0) |
 Os.15355.1.S1_x_at | AK067000 | 2.07 | Putative bacterial-induced peroxidase precursor | BAD28871 (2e-166) |
Energy | ||||
 OsAffx.12379.1.S1_at | 9630.m03520 | 3.26 | Putative oxygen-evolving enhancer protein 3-2, chloroplast precursor (OEE3) | BAD29563 (8e-61) |
 OsAffx.32230.1.A1_at | X15901 | 2.96 | ATP synthase CF1 epsilon subunit | NP_039389 (4e-65) |
 Os.52588.1.S1_at | AK068191 | 2.85 | 2Fe-2S iron-sulfur cluster protein-like/ferredoxin-related | BAC80058 (5e-86) |
 Os.19061.1.S1_s_at | AK099499 | 2.77 | 4Fe-4S ferredoxin, iron-sulfur binding; Heat shock protein DnaJ | ABP02426 (2e-21) |
 Os.26744.1.A1_at | CA762807 | 2.66 | Chloroplast photosystem I assembly protein Ycf3 | BAD81968 (7e-16) |
 Os.44475.1.S1_x_at | AK121213 | 2.66 | Putative NADH dehydrogenase (ubiquinone oxidoreductase) | BAC15811 (0.0) |
 Os.29056.1.S2_at | AK110782 | 2.54 | Apocytochrome f precursor, putative | AAP53263.2 (4e-54) |
 Os.27830.1.S1_at | AK068377 | 2.54 | PsbQ domain protein family/oxygen evolving enhancer 3 | BAC10375 (4e-105) |
 OsAffx.32225.1.A1_at | X15901 | 2.5 | Photosystem I assembly protein Ycf3 | NP_039384 (3e-95) |
 Os.3406.1.S1_at | AB004865 | 2.48 | Alternative oxidase | BAA28771 (0.0) |
 Os.11570.1.S1_s_at | AK101484 | 2.22 | Putative glycerol-3-phosphate dehydrogenase | AAU44049 (0.0) |
Intracellular traffic | ||||
 Os.8700.1.S1_at | AK066218 | 2.74 | Dynein light chain type 1-like | BAD28635 (2e-36) |
 Os.31464.1.S1_a_at | AK101489 | 2.6 | Os04g0527400 | NP_001053367 (0.0) |
 Os.40002.1.S1_s_at | CF315096 | 2.17 | Got1-like family | NP_001060166 (1e-07) |
Metabolism | ||||
 Os.18490.1.S1_x_at | AK120238 | 3.16 | Thiamine biosynthesis protein ThiC, putative, expressed | ABF98201 (0.0) |
 Os.56682.1.S1_at | AK110292 | 3.1 | GDSL-lipase-like | BAD61697 (0.0) |
 Os.23154.2.S1_at | AK111360 | 2.68 | Putative proline-rich protein APG (GDSL-lipase-like) | BAD15755 (1e-61) |
 Os.52414.1.S1_at | AK066972 | 2.41 | Hydrolase, alpha/beta fold family protein-like | BAD23358 (8e-145) |
 OsAffx.27752.1.S1_s_at | 9634.m02096 | 2.41 | Putative aldose 1-epimerase | BAD05401 (4e-149) |
 Os.50951.1.S1_at | AK059666 | 2.21 | Metallo-beta-lactamase protein-like | BAD28843 (6e-136) |
 OsAffx.32255.1.A1_at | X15901 | 2.19 | Acetyl-coa carboxylase beta subunit | NP_039394 (5e-56) |
 Os.8957.1.S1_at | AK071523 | 2.19 | Phosphatidic acid phosphatase-related/PAP2-related | NP_190970 (6e-128) |
 Os.47381.2.S1_at | AK120916 | 2.12 | Putative 3-oxoacyl-[acyl-carrier-protein] synthase I, chloroplast precursor | BAD35225 (0.0) |
 Os.8957.1.S1_a_at | AK071523 | 2.06 | Phosphatidic acid phosphatase-related/PAP2-related | NP_190970 (3e-128) |
Otherf | ||||
 OsAffx.5746.1.S1_s_at | 9636.m00746 | 8.72 | Hypothetical protein OsJ_025189 | EAZ41706 (3e-20) |
 Os.4618.1.S1_at | AK062310 | 4.71 | Hypothetical protein OsI_002101 | EAY74254 (2e-50) |
 Os.40007.1.S1_x_at | CF318727 | 3.86 | Os03g0120600 | NP_001048790 (4e-18) |
 Os.6288.1.S1_at | AK106356 | 3.58 | Unknown protein/Os08g0412700 | NP_001061796 (2e-169) |
 Os.20548.1.S1_at | AK066753 | 3.58 | Hypothetical protein OsI_016689 | EAY95456 (9e-34) |
 Os.30528.1.S1_at | AK108716 | 3.45 | Unknown protein/Os08g0412800 | NP_001061797 (0.0) |
 Os.46544.1.A1_at | AK066066 | 3.38 | Expressed protein/Os10g0389500 | NP_001064501 (3e-113) |
 Os.21260.1.S1_at | AK067400 | 3.38 | Os03g0184100 | NP_001049187 (2e-120) |
 Os.6516.1.S1_at | CF303902 | 3.37 | No significant similarity found |  |
 Os.52004.1.S1_at | AK064520 | 3.31 | Hypothetical protein LOC_Os12g17920 | ABA97088 (3e-06) |
 Os.27218.1.A1_at | CB649864 | 3.23 | Os05g0575000 | NP_001056395 (5e-33) |
 Os.57343.1.S1_at | AK111335 | 3.06 | Os02g0733900 | NP_001048037 (2e-36) |
 Os.22703.1.S1_at | AK066033 | 3.03 | Unknown protein /Os07g0618700 | BAC79871 (1e-112) |
 Os.27764.1.S1_at | CB629248 | 3 | Os05g0464200 | NP_001055778 (4e-04) |
 Os.51529.1.S1_at | AK063010 | 2.99 | Os12g0174200 | NP_001066286 (1e-16) |
 Os.39942.2.S1_x_at | CF321166 | 2.81 | Osjnbb0058j09.9 | CAD39870 (9e-06) |
 Os.7944.1.S1_at | AK120788 | 2.76 | No significant similarity found |  |
 Os.5823.1.S1_at | AK109216 | 2.75 | Os02g0718200 | NP_001047938 (0.003) |
 Os.51299.1.S1_at | AK062470 | 2.75 | Os05g0464300 | NP_001055779 (2e-14) |
 Os.4773.1.S1_at | CF325704 | 2.67 | Os06g0133500 | NP_001056709 (3e-30) |
 Os.57191.1.S1_at | AK111114 | 2.63 | Os06g0147300 | NP_001056802 (2e-50) |
 Os.18712.1.S1_at | AK108985 | 2.63 | Hypothetical protein OsI_028900 | EAZ07668 (7e-127) |
 Os.2426.1.A1_at | CA759372 | 2.49 | Expressed protein | ABA92028 (2e-21) |
 Os.12342.1.S2_at | CB668460 | 2.43 | No significant similarity found |  |
 Os.39725.1.S1_at | CA763989 | 2.35 | No significant similarity found |  |
 Os.7130.2.S1_x_at | AU032629 | 2.27 | No significant similarity found |  |
 OsAffx.7530.1.S1_s_at | 9640.m00831 | 2.26 | Expressed protein | ABA96042 (6e-24) |
 Os.38992.1.A1_x_at | D43281 | 2.23 | No significant similarity found |  |
 OsAffx.27741.1.S1_s_at | 9634.m02034 | 2.23 | Hypothetical protein | BAD62179 (2e-21) |
 Os.50952.1.S1_at | AK059668 | 2.19 | No Significant similarity |  |
 Os.10823.2.S1_at | AK064162 | 2.07 | Os05g0487300/unknown protein | NP_001055881 (1e-05) |
 Os.55407.1.S1_at | AK108023 | 2.02 | Os03g0799300 | NP_001051576 (3e-26) |
Protein synthesis/Turnover | Â | Â | Â | Â |
 Os.55628.1.S1_at | AK108443 | 3.69 | Eukaryotic translation initiation factor SUI1, putative | NP_175831 (3e-30) |
 OsAffx.26671.1.S1_x_at | 9632.m05851 | 3.34 | Eukaryotic translation initiation factor SUI1, putative | NP_175831 (4e-30) |
 Os.8724.1.S1_at | AK072982 | 3.02 | Cyclin-like-F-box family protein | NP_567629 (5e-09) |
 OsAffx.24862.1.S1_at | 9630.m05377 | 2.43 | F-box domain containing protein | AAP54337.2 (1e-27) |
 Os.46325.1.A1_at | AK120658 | 2.32 | Zinc finger (C3HC4-type RING finger) family protein | NP_568096 (3e-146) |
 Os.27569.1.S2_at | AK121706 | 2.26 | Calcium-binding EF-hand family protein-like | BAD08916 (8e-49) |
Secondary metabolism | ||||
 Os.50053.1.A1_at | AK119780 | 3.9 | 9-cis-epoxycarotenoid dioxygenase 4 | AAW21320 (0.0) |
 Os.6376.1.S1_at | AK121461 | 3.41 | Chalcone-flavanone isomerase | NP_001057086 (0.0) |
 Os.27507.1.S1_at | AK109673 | 2.97 | Reticuline oxidase precursor, putative/berberine bridge enzyme-like protein | ABA93766 (1e-132) |
 OsAffx.32219.1.A1_x_at | X15901 | 2.61 | Terpene synthase family, metal binding domain containing protein | ABF96083 (0.0) |
Signal transduction | ||||
 Os.1606.1.S1_at | AK111969 | 5.05 | Putative receptor-like protein kinase | AAL87185 (8e-137) |
 Os.15247.1.S1_s_at | AB125310 | 3.15 | Serine/threonine-protein kinase SAPK9 | BAD18005 (0.0) |
 Os.10254.1.S1_at | AK066150 | 3.12 | Copine I-like | BAD10026 (0.0) |
 Os.9585.1.S1_at | AB060552 | 3.04 | Calmodulin-2 | BAB69673 (8e-66) |
 Os.26226.1.S1_at | AK103704 | 2.96 | Putative serine/threonine protein kinase | BAD08131 (0.0) |
 Os.9585.1.S1_s_at | AB060552 | 2.62 | Calmodulin, putative, expressed | ABA99816 (5e-66) |
 Os.35013.1.S1_at | AK069274 | 2.16 | Putative Serine/threonine phosphatases | AAP06902 (0.0) |
 OsAffx.11760.1.S1_at | 9629.m06614 | 2 | Putative S-receptor kinase | BAD82381 (0.0) |
Stress | ||||
 Os.51546.1.S1_at | AK063042 | 10.2 | Senescence-associated protein-related | NP_197570 (1e-08) |
 OsAffx.32080.1.S1_at | 9640.m03722 | 7.34 | Metallothionein-like protein 1, putative, expressed | ABA99660 (8e-30) |
 Os.37783.1.S1_a_at | AK105219 | 4.52 | Metallothionein-like protein 4C (OsMT-I-4c) | Q2QNC3 (2e-22) |
 OsAffx.7826.2.S1_at | 9640.m03694 | 4.02 | Metallothionein-like protein 1, putative, expressed | ABA99599 (1e-10) |
 Os.37773.1.S1_at | AU165294 | 3.82 | Low molecular mass heat shock protein | AAC78392 (2e-37) |
 Os.37783.2.S1_x_at | AU070898 | 3.73 | Metallothionein-like protein 1, putative, expressed | ABA99639 (4e-24) |
 Os.14105.1.S1_at | AK106404 | 3.63 | Cytochrome P450 | AAX92767 (0.0) |
 Os.4671.1.S1_a_at | AF435970 | 3.47 | Jacalin-related lectin like /Protein mannose-binding lectin | P24120 (2e-78) |
 Os.37773.1.S1_x_at | AU165294 | 3.46 | Alpha-crystallin-Hsps/17.4 kda class I heat shock protein, putative | AAP06883 (6e-38) |
 Os.6092.1.S1_at | AB120515 | 3.17 | Trehalose-6-phosphate phosphatase | BAD12596 (0.0) |
 Os.7756.1.S1_at | AK060639 | 2.7 | Putative stress-responsive protein (pectinesterase inhibitor domain containing) | AAM94917 (2e-83) |
 Os.15428.1.S1_at | AK065414 | 2.61 | Putative wound inducive gene | BAD81783 (2e-174) |
 Os.8741.1.S1_at | AK102303 | 2.57 | RADICAL-INDUCED CELL DEATH1 | ABF94777 (0.0) |
 Os.33675.1.S1_at | AK099569 | 2.5 | Rbcx protein having a possible chaperonin-like function | NP_001061837 (2e-82) |
 Os.8774.1.S1_at | AK071331 | 2.43 | Peroxidase-like protein | BAD82471 (7e-127) |
 Os.5363.1.S1_at | AU174652 | 2.4 | Putative cadmium-induced protein | BAC19956 (1e-29) |
 Os.53236.1.S1_at | AK071507 | 2.28 | Putative zinc finger protein/Salt tolerance-like protein | BAD25819 (7e-95) |
 Os.49030.1.A1_s_at | CR292984 | 2.27 | Putative glutathione S-transferase OsGSTU5 | AF309377_1 (3e-09) |
Transcription | ||||
 OsAffx.17366.1.S1_at | 9636.m03709 | 6.54 | Ethylene-binding protein-AP2 domain containing | BAD38371 (4e-41) |
 Os.6043.1.S1_at | AB040744 | 5.3 | RERJ1(Helix-loop-helix domain containing transcriptin factor) | AB040744 (8e-111) |
 OsAffx.27442.1.S1_at | NM_185471 | 5.23 | Transcription factor CBF1 | BAA90812 (3e-73) |
 Os.4463.1.S1_s_at | AY327040 | 4.57 | Transcription factor CBF1 | BAA90812 (3e-73) |
 Os.15849.1.S1_s_at | AK062882 | 4.34 | AP2 domain-containing transcription factor-like | BAD17116 (4e-15) |
 Os.49746.1.S1_at | AY581256 | 3.87 | Induced protein mgi1(MYB-like DNA-binding domain) | AAS90600 (1e-76) |
 Os.55259.1.S1_at | AK107750 | 3.77 | ZIM motif family protein, expressed | ABF94311 (1e-07) |
 Os.46849.1.S1_at | AK107854 | 3.46 | ZIM motif family protein, expressed | AAP53563 (7e-23) |
 Os.54501.1.S1_at | AK105440 | 3.44 | PHD-finger, putative | AAX94898 (0.0) |
 Os.5335.1.S1_at | AK101209 | 3.19 | Putative MYB transcription factor | BAD61826 (1e-33) |
 Os.3400.1.S1_s_at | AB001888 | 3.05 | Zinc finger protein | BAA33206 (0.0) |
 Os.12977.1.S1_at | AK072192 | 2.96 | Zinc finger protein/COL9 (CONSTANS-LIKE 9); transcription factor | BAA33206 (4e-141) |
 Os.55550.1.S1_at | AK108297 | 2.88 | Transcription factor GT-3b | AAP13348 (3e-04) |
 Os.9923.1.S1_s_at | AK120087 | 2.58 | ZIM motif family protein, expressed | ABF94311 (9e-57) |
 Os.35681.1.S1_at | AY344493 | 2.54 | Putative heat shock transcription factor 8 | BAB68070 (2e-124) |
 Os.35343.1.A1_at | AK067922 | 2.51 | No apical meristem protein (NAC domain containing) | ABA95706 (2e-116) |
 Os.10411.1.S1_at | AY077725 | 2.45 | C2H2 zinc finger protein | BAD81699 (2e-72) |
 Os.23778.1.S1_at | AK101934 | 2.44 | Putative heat stress transcription factor | BAD25410 (0.0) |
 Os.7130.1.S1_at | AK073475 | 2.42 | Transcription factor jumonji, putative, expressed | ABB48025 (0.0) |
 Os.8031.1.S1_at | AK111775 | 2.38 | Putative ethylene response factor 2/AP2 domain-containing transcription factor | BAB92777 (1e-73) |
 Os.49787.1.S1_at | AK111571 | 2.36 | Putative MYB-like transcription factor | AAT69605 (6e-50) |
 Os.20750.1.S1_at | CB635910 | 2.33 | bZIP transcription factor-like | BAB89012 (5e-54) |
 Os.19899.1.S1_x_at | AK106830 | 2.12 | Transcription factor PCF8 | BAC01119 (4e-38) |
 Os.11046.1.S1_at | AK119729 | 2.1 | Putative ethylene-responsive transcriptional coactivator | BAD32863 (8e-60) |
 Os.10356.1.S1_at | AK073589 | 2.09 | ZIM motif family protein, expressed | ABF94310 (2e-82) |
 OsAffx.3006.1.S1_at | 9630.m04817 | 2.08 | MYB-like transcription factor-like | BAD13038 (1e-15) |
Transporter | ||||
 Os.47946.1.S1_s_at | AK070124 | 4.22 | Putative glucose-6-phosphate/phosphate- translocator precursor | BAC57673 (2e-90) |
 Os.11800.1.S1_s_at | AK108373 | 3.37 | MDR-like ABC transporter | CAD59587 (3e-141) |
 Os.11800.1.S1_at | AK108373 | 3.13 | MDR-like ABC transporter | CAD59587 (4e-140) |
Transposons | ||||
 Os.18078.1.S1_at | C97547 | 3.91 | Rtac1 | AAX95969 (0.17) |
 Os.39994.1.S1_at | CF319063 | 3.8 | Rtac1 | AAL86017 (1e-10) |
 Os.6901.1.S1_at | AK102892 | 2.72 | Os10g0378500/retrotransposon protein, putative | NP_001064482 (2e-31) |