CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM252682

Assay name Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep4

GSE experiment GSE9996: Organ regeneration in plants is independent of stem cell niche activity

Click Gene ID to show a list of GSM assays in which the gene are specifically expressed.

Std2 GX %ile Std GX Gene ID Repr. ID Gene name Functional description O.I. C.G. H.G. Other DB
125.5 99.9 176.6 At5g35940 833584 jacalin lectin family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POBM O.I. C.G. H.G.
71.6 99.9 163.5 At1g73620 843696 thaumatin-like protein, putative / pathogenesis-related protein, putative F:unknown;P:response to other organism;C:membrane;PMFBO O.I. C.G. H.G.
55.8 99.8 103.5 At3g04320 819587 endopeptidase inhibitor F:endopeptidase inhibitor activity;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
41.6 99.8 27.9 At2g23050 816835 NPY4 (NAKED PINS IN YUC MUTANTS 4) A member of the NPY gene family (NPY1/AT4G31820, NPY2/AT2G14820, NPY3/AT5G67440, NPY4/AT2G23050, NPY5/AT4G37590). Involved in auxin-mediated organogenesis. O.I. C.G. H.G.
37.8 99.8 41.0 At5g51500 835224 pectinesterase family protein F:enzyme inhibitor activity, pectinesterase activity;P:cell wall modification;C:endomembrane system, cell wall, plant-type cell wall;PBFMO O.I. C.G. H.G.
37.5 99.7 67.6 At1g54890 841928 late embryogenesis abundant protein-related / LEA protein-related F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
32.1 99.7 68.6 At1g74500 843791 bHLH family protein F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;P O.I. C.G. H.G.
30.2 99.7 127.9 At1g05205 839266 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
29.8 99.7 335.6 At4g15910 827273 ATDI21 (ARABIDOPSIS THALIANA DROUGHT-INDUCED 21) encodes a gene whose transcript level in root and leaves increases to progressive drought stress. The transcript level is also affected by changes of endogenous or exogenous abscisic acid level. It appears to be a member of plant-specific gene family that includes late embryo-abundant and zinc- IAA-induced proteins in other plants. O.I. C.G. H.G.
29.0 99.7 29.1 At5g57980 835909 RPB5C (RNA POLYMERASE II FIFTH LARGEST SUBUNIT, C) NRPB5-like protein of unknown function; homologous to budding yeast RPB5 O.I. C.G. H.G.
28.1 99.7 268.9 At2g43610 818963 glycoside hydrolase family 19 protein F:chitin binding, chitinase activity;P:cell wall macromolecule catabolic process;C:plasma membrane;PBFOVM O.I. C.G. H.G.
27.9 99.7 143.3 At2g25980 817139 jacalin lectin family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBO O.I. C.G. H.G.
25.8 99.7 46.3 At5g48110 834863 terpene synthase/cyclase family protein F:lyase activity, magnesium ion binding;P:metabolic process;C:chloroplast;PMO O.I. C.G. H.G.
25.3 99.6 94.6 At1g50490 841471 UBC20 (ubiquitin-conjugating enzyme 20) Encodes one of two ubiquitin-conjugating enzymes belonging to the E2-C gene family (the other being UBC19). Transcript is always found in diving cells, but also in other non-dividing cells. O.I. C.G. H.G.
23.5 99.6 31.5 At5g48940 834952 leucine-rich repeat transmembrane protein kinase, putative F:protein binding, protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:unknown;MPOBFVA O.I. C.G. H.G.
23.1 99.6 33.3 At3g13175 820507 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
23.0 99.6 56.5 At3g55170 824683 60S ribosomal protein L35 (RPL35C) F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic large ribosomal subunit, ribosome;MOBAFP O.I. C.G. H.G.
23.0 99.6 17.6 At4g10640 826656 IQD16 (IQ-domain 16) F:calmodulin binding;P:biological_process unknown;C:cellular_component unknown;PMOF O.I. C.G. H.G.
22.9 99.6 12.9 At3g49630 824125 2-oxoacid-dependent oxidase, putative F:oxidoreductase activity, iron ion binding;P:aging, cellular response to starvation;C:endomembrane system;POBFM O.I. C.G. H.G.
22.8 99.6 11.0 At5g59070 836024 glycosyl transferase family 1 protein F:transferase activity, transferring glycosyl groups;P:biosynthetic process;C:endomembrane system;BOAPMF O.I. C.G. H.G.
22.3 99.6 92.2 At5g60950 836216 COBL5 (COBRA-LIKE PROTEIN 5 PRECURSOR) F:unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
22.3 99.6 71.7 At5g20400 832162 oxidoreductase, 2OG-Fe(II) oxygenase family protein encodes a protein whose sequence is similar to flavanone 3 hydroxylase from Malus. O.I. C.G. H.G.
21.5 99.6 28.7 At4g23590 828459 aminotransferase class I and II family protein F:1-aminocyclopropane-1-carboxylate synthase activity, pyridoxal phosphate binding, transferase activity, transferring nitrogenous groups, transaminase activity, catalytic activity;P:cellular amino acid and derivative metabolic process, biosynthetic process;C:cellular_component unknown;BOPMAF O.I. C.G. H.G.
21.1 99.6 204.0 At2g40360 818629 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:rRNA processing;C:nucleus;BMOFPVA O.I. C.G. H.G.
21.1 99.6 17.1 At3g06840 819868 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
20.7 99.6 65.9 At5g19520 832072 MSL9 (MECHANOSENSITIVE CHANNEL OF SMALL CONDUCTANCE-LIKE 9) F:mechanically-gated ion channel activity;P:detection of mechanical stimulus;C:nucleus, plasma membrane, membrane;BOFPAV O.I. C.G. H.G.
20.6 99.6 53.8 At1g13590 837920 ATPSK1 (PHYTOSULFOKINE 1 PRECURSOR) Encodes a phytosulfokine-alpha (PSK) precursor, a unique plant peptide growth factor first described in Asparagus. O.I. C.G. H.G.
20.4 99.6 29.4 At3g18510 821381 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
19.9 99.6 74.1 At4g22930 828392 PYR4 (PYRIMIDIN 4) Encodes dihydroorotase (PYR4). O.I. C.G. H.G.
19.7 99.6 16.1 At1g73160 843647 glycosyl transferase family 1 protein F:transferase activity, transferring glycosyl groups;P:biosynthetic process;C:unknown;BOAFPM O.I. C.G. H.G.
19.5 99.6 53.6 At2g20515 816573 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
19.5 99.6 24.0 At1g56680 842124 glycoside hydrolase family 19 protein F:chitinase activity;P:cell wall macromolecule catabolic process;C:endomembrane system;PBOMFV O.I. C.G. H.G.
18.9 99.5 59.8 At4g37160 829870 sks15 (SKU5 Similar 15) F:oxidoreductase activity, copper ion binding;P:unknown;C:endomembrane system;FBPMOA O.I. C.G. H.G.
18.3 99.5 143.6 At4g00585 828026 unknown protein F:molecular_function unknown;P:photorespiration;C:mitochondrial membrane, respiratory chain complex I;PFMO O.I. C.G. H.G.
18.3 99.5 84.1 At1g16000 838170 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
18.3 99.5 10.2 At5g52170 835293 HDG7 (HOMEODOMAIN GLABROUS 7) Encodes a homeobox-leucine zipper family protein belonging to the HD-ZIP IV family. O.I. C.G. H.G.
18.1 99.5 39.6 At2g14460 815934 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
17.8 99.5 29.4 At3g23470 821928 cyclopropane-fatty-acyl-phospholipid synthase F:cyclopropane-fatty-acyl-phospholipid synthase activity;P:lipid biosynthetic process;C:endomembrane system;OBFPAM O.I. C.G. H.G.
17.7 99.5 165.5 At1g54690 841910 GAMMA-H2AX (GAMMA HISTONE VARIANT H2AX) Encodes HTA3, a histone H2A protein. H2AX is a meiosis-specific isoform of histone H2A. Upon DSB formation, rapid accumulation of phosphorylated H2AX (γ-H2AX) occurs around the break site. H2AX foci accumulate in early G2. Immunolocalization studies in spread preparations of wild-type meiocytes at G2/early leptotene revealed the accumulation of numerous rather diffuse γ-H2AX foci throughout the chromatin. However, their accumulation is not contemporaneous with that of AtSPO11-1. At 3 h post-S, no γ-H2AX foci are detected. During the 3- to 5-h window when AtSPO11-1 foci rapidly disappear, there is an equally swift accumulation of γ-H2AX to a maximum of >50 diffuse foci. The level of γH2AX then remains constant for a further 13 h before undergoing a gradual decrease to 10�20 foci in the 18- to 24-h post-S period. By 30 h the foci have disappeared from the chromatin. O.I. C.G. H.G.
17.7 99.5 109.0 At2g41800 818779 - F:molecular_function unknown;P:biological_process unknown;C:cell wall, plant-type cell wall;P O.I. C.G. H.G.
17.7 99.5 15.8 At5g43030 834318 DC1 domain-containing protein F:unknown;P:intracellular signaling cascade;C:cellular_component unknown;PMO O.I. C.G. H.G.
17.5 99.5 95.6 At1g07070 837218 60S ribosomal protein L35a (RPL35aA) F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic large ribosomal subunit, ribosome;MOFPA O.I. C.G. H.G.
17.2 99.5 56.6 At3g62810 825456 complex 1 family protein / LVR family protein F:catalytic activity;P:unknown;C:unknown;MFPO O.I. C.G. H.G.
17.1 99.5 87.3 At5g16060 831463 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PFOM O.I. C.G. H.G.
16.2 99.5 11.5 At1g03840 839396 MGP (Magpie) MGP is a nuclear-localized putative transcription factor with three zinc finger domains. MGP can interact with three proteins implicated in root patterning: SCR, SHR, and JKD in Y2H assays, and these interactions depend on the first zinc finger in MGP. MGP appears to be a direct transcriptional target of SHR and SCR, based on promoter binding assays, though it is not expressed in the QC, based on in situ hybridizations. O.I. C.G. H.G.
16.0 99.5 37.0 At2g04090 814945 MATE efflux family protein F:drug transporter activity, antiporter activity, transporter activity;P:multidrug transport;C:membrane;BOPFMA O.I. C.G. H.G.
15.8 99.5 30.7 At3g52740 824440 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
15.8 99.5 5.8 At1g43040 840903 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:unknown;P O.I. C.G. H.G.
15.7 99.5 25.4 At1g02430 839242 ATARFD1B (ADP-ribosylation factor D1B) A member of ARF GTPase family. A thaliana has 21 members of this family, known to be essential for vesicle coating and uncoating and functions in GTP-binding. Gene encoding ADP-ribosylation factor and similar to other ARFs and ARF-like proteins. O.I. C.G. H.G.
15.6 99.5 180.2 At2g39390 818524 60S ribosomal protein L35 (RPL35B) F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic ribosome, cytosolic large ribosomal subunit, ribosome;MOBAFP O.I. C.G. H.G.
15.6 99.5 111.6 At3g06320 819806 ribosomal protein L33 family protein F:structural constituent of ribosome;P:translation;C:ribosome, intracellular, large ribosomal subunit;BOPMF O.I. C.G. H.G.
15.6 99.5 54.9 At1g62810 842580 copper amine oxidase, putative F:amine oxidase activity, quinone binding, copper ion binding;P:cellular amine metabolic process;C:endomembrane system;FBMOPA O.I. C.G. H.G.
15.1 99.4 19.0 At5g60730 836194 anion-transporting ATPase family protein F:ATP binding;P:cellular metal ion homeostasis, anion transport;C:membrane;BOAMFP O.I. C.G. H.G.
15.1 99.4 18.1 At3g62280 825401 carboxylesterase/ hydrolase, acting on ester bonds F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBFOM O.I. C.G. H.G.
14.9 99.4 18.3 At2g30340 817584 LBD13 (LOB DOMAIN-CONTAINING PROTEIN 13) F:molecular_function unknown;P:biological_process unknown;C:membrane;PMOFVBA O.I. C.G. H.G.
14.8 99.4 54.9 At1g79150 844256 binding F:binding;P:biological_process unknown;C:cellular_component unknown;OMFBPVA O.I. C.G. H.G.
14.7 99.4 211.1 At3g10090 820170 40S ribosomal protein S28 (RPS28A) F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic small ribosomal subunit, cytosolic ribosome, ribosome, cell wall;MOAPF O.I. C.G. H.G.
14.7 99.4 16.1 At5g07040 830595 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:endomembrane system;PMOFV O.I. C.G. H.G.
14.4 99.4 119.1 At5g09590 830818 MTHSC70-2 (MITOCHONDRIAL HSP70 2) heat shock protein 70 (Hsc70-5); nuclear O.I. C.G. H.G.
14.4 99.4 18.2 At1g26660 839206 c-myc binding protein, putative / prefoldin, putative F:unfolded protein binding;P:protein folding;C:prefoldin complex;MFOPAB O.I. C.G. H.G.
14.3 99.4 71.7 At1g79390 844277 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
14.3 99.4 26.5 At4g31930 829323 mitochondrial glycoprotein family protein / MAM33 family protein F:molecular_function unknown;P:biological_process unknown;C:mitochondrion, mitochondrial matrix;PFO O.I. C.G. H.G.
14.2 99.4 9.2 At3g59850 825155 polygalacturonase, putative / pectinase, putative F:polygalacturonase activity;P:carbohydrate metabolic process;C:endomembrane system;FPBOMAV O.I. C.G. H.G.
14.1 99.4 95.5 At2g30000 817551 - F:unknown;P:unknown;C:cellular_component unknown;MFOP O.I. C.G. H.G.
14.1 99.4 87.0 At2g35605 818127 SWIB complex BAF60b domain-containing protein F:molecular_function unknown;P:biological_process unknown;C:unknown;OPBFMV O.I. C.G. H.G.
14.0 99.4 134.4 At2g03870 814913 small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative F:molecular_function unknown;P:unknown;C:small nucleolar ribonucleoprotein complex, nucleus;MFAOP O.I. C.G. H.G.
14.0 99.4 3.5 At3g30740 3769121 - F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
13.9 99.4 596.3 At4g39200 830075 40S ribosomal protein S25 (RPS25E) F:structural constituent of ribosome;P:translation;C:cytosolic small ribosomal subunit, cytosolic ribosome, ribosome;MFPOA O.I. C.G. H.G.
13.9 99.4 88.4 At4g02840 828163 small nuclear ribonucleoprotein D1, putative / snRNP core protein D1, putative / Sm protein D1, putative F:molecular_function unknown;P:unknown;C:nucleolus, small nucleolar ribonucleoprotein complex, nucleus, plasma membrane, membrane;MFOP O.I. C.G. H.G.
13.8 99.4 84.5 At1g04870 839393 PRMT10 Encodes a type I protein arginine methyltransferase based on the At1g04870.2 gene model. PRMT10 can catalyze the asymmetric dimethylation of arginine 3 on histone 4 and can also methylate myelin basic protein in vitro. Mutants lacking PRMT10 flower late due to defects in the autonomous pathway and they have elevated levels of FLC transcripts. O.I. C.G. H.G.
13.8 99.4 72.5 At3g01740 821088 - F:molecular_function unknown;P:biological_process unknown;C:unknown;MPFO O.I. C.G. H.G.
13.7 99.4 64.9 At1g73940 843731 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
13.7 99.4 27.2 At2g41810 818780 - F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PB O.I. C.G. H.G.
13.6 99.4 44.3 At2g43780 818981 unknown protein F:molecular_function unknown;P:biological_process unknown;C:mitochondrion;P O.I. C.G. H.G.
13.4 99.4 16.1 At4g37940 829950 AGL21 encodes a MADS box protein, highly expressed in the root. O.I. C.G. H.G.
13.4 99.4 11.1 At3g46720 823825 UDP-glucoronosyl/UDP-glucosyl transferase family protein F:transferase activity, transferring hexosyl groups, UDP-glycosyltransferase activity, transferase activity, transferring glycosyl groups;P:metabolic process;C:cellular_component unknown;PMBVOF O.I. C.G. H.G.
13.3 99.4 104.6 At5g62340 836355 invertase/pectin methylesterase inhibitor family protein F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
13.2 99.4 56.3 At1g61580 842454 RPL3B (R-PROTEIN L3 B) F:structural constituent of ribosome;P:translation;C:cytosolic large ribosomal subunit, ribosome, membrane;BOMAPFV O.I. C.G. H.G.
13.2 99.4 24.9 At5g01620 831716 unknown protein F:unknown;P:unknown;C:endomembrane system;PM O.I. C.G. H.G.
13.2 99.4 24.8 At1g29270 839801 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
13.0 99.4 44.0 At5g57120 835816 - F:molecular_function unknown;P:biological_process unknown;C:nucleolus;MOBFPVA O.I. C.G. H.G.
13.0 99.4 22.4 At1g23100 838918 10 kDa chaperonin, putative F:ATP binding;P:protein folding;C:mitochondrion;BOMPFV O.I. C.G. H.G.
12.7 99.3 36.3 At4g31320 829259 auxin-responsive protein, putative / small auxin up RNA (SAUR_C) F:calmodulin binding;P:response to auxin stimulus;C:cellular_component unknown;PO O.I. C.G. H.G.
12.7 99.3 17.8 At3g57360 824903 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MP O.I. C.G. H.G.
12.6 99.3 69.7 At1g14620 838024 DECOY (DECOY) F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;FMPOB O.I. C.G. H.G.
12.6 99.3 31.9 At4g10620 826654 - F:unknown;P:biological_process unknown;C:chloroplast;BMFOPA O.I. C.G. H.G.
12.5 99.3 353.6 At2g22170 816751 lipid-associated family protein F:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast, membrane;PMO O.I. C.G. H.G.
12.5 99.3 126.0 At1g16740 838245 ribosomal protein L20 family protein F:structural constituent of ribosome, RNA binding;P:translation, ribosome biogenesis;C:ribosome, intracellular;BOPM O.I. C.G. H.G.
12.4 99.3 203.7 At1g54000 841838 myrosinase-associated protein, putative F:lipase activity, hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:vacuolar membrane, plasma membrane, vacuole, plant-type cell wall, plant-type vacuole;PBOFM O.I. C.G. H.G.
12.4 99.3 51.3 At2g45730 819181 eukaryotic initiation factor 3 gamma subunit family protein F:translation initiation factor activity;P:translational initiation, regulation of translational initiation;C:cellular_component unknown;MFOP O.I. C.G. H.G.
12.3 99.3 329.7 At5g02450 831907 60S ribosomal protein L36 (RPL36C) F:structural constituent of ribosome;P:translation;C:cytosolic large ribosomal subunit, ribosome, plasma membrane;MOFP O.I. C.G. H.G.
12.2 99.3 16.5 At5g42060 834211 unknown protein F:unknown;P:unknown;C:cellular_component unknown;P O.I. C.G. H.G.
12.2 99.3 9.0 At1g62520 842549 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PFOB O.I. C.G. H.G.
12.0 99.3 75.7 At4g31120 829240 SKB1 (SHK1 BINDING PROTEIN 1) Involved in vernalization. Required for epigenetic silencing of FLC, and for vernalization-mediated histone modification. O.I. C.G. H.G.
12.0 99.3 15.1 At4g40000 830161 NOL1/NOP2/sun family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BOMFAP O.I. C.G. H.G.
11.9 99.3 19.6 At4g33100 829447 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPO O.I. C.G. H.G.
11.9 99.3 15.2 At3g27950 822419 early nodule-specific protein, putative F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBOFM O.I. C.G. H.G.
11.9 99.3 15.2 At5g35400 833501 tRNA pseudouridine synthase family protein F:pseudouridine synthase activity;P:tRNA processing, pseudouridine synthesis;C:unknown;BOMPAF O.I. C.G. H.G.
11.8 99.3 251.1 At1g57660 842142 60S ribosomal protein L21 (RPL21E) F:structural constituent of ribosome;P:translation;C:ribosome, intracellular;MOAFP O.I. C.G. H.G.
11.8 99.3 33.7 At5g44560 834483 VPS2.2 F:unknown;P:vesicle-mediated transport;C:ESCRT III complex;MPFOB O.I. C.G. H.G.

Std2 GX	%ile	Std GX	Gene ID	Repr. ID	Gene name	Functional description	O.I.	C.G.	H.G.
125.5	99.9	176.6	At5g35940	833584	jacalin lectin family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POBM	O.I.	C.G.	H.G.
71.6	99.9	163.5	At1g73620	843696	thaumatin-like protein, putative / pathogenesis-related protein, putative	F:unknown;P:response to other organism;C:membrane;PMFBO	O.I.	C.G.	H.G.
55.8	99.8	103.5	At3g04320	819587	endopeptidase inhibitor	F:endopeptidase inhibitor activity;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
41.6	99.8	27.9	At2g23050	816835	NPY4 (NAKED PINS IN YUC MUTANTS 4)	A member of the NPY gene family (NPY1/AT4G31820, NPY2/AT2G14820, NPY3/AT5G67440, NPY4/AT2G23050, NPY5/AT4G37590). Involved in auxin-mediated organogenesis.	O.I.	C.G.	H.G.
37.8	99.8	41.0	At5g51500	835224	pectinesterase family protein	F:enzyme inhibitor activity, pectinesterase activity;P:cell wall modification;C:endomembrane system, cell wall, plant-type cell wall;PBFMO	O.I.	C.G.	H.G.
37.5	99.7	67.6	At1g54890	841928	late embryogenesis abundant protein-related / LEA protein-related	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
32.1	99.7	68.6	At1g74500	843791	bHLH family protein	F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;P	O.I.	C.G.	H.G.
30.2	99.7	127.9	At1g05205	839266	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
29.8	99.7	335.6	At4g15910	827273	ATDI21 (ARABIDOPSIS THALIANA DROUGHT-INDUCED 21)	encodes a gene whose transcript level in root and leaves increases to progressive drought stress. The transcript level is also affected by changes of endogenous or exogenous abscisic acid level. It appears to be a member of plant-specific gene family that includes late embryo-abundant and zinc- IAA-induced proteins in other plants.	O.I.	C.G.	H.G.
29.0	99.7	29.1	At5g57980	835909	RPB5C (RNA POLYMERASE II FIFTH LARGEST SUBUNIT, C)	NRPB5-like protein of unknown function; homologous to budding yeast RPB5	O.I.	C.G.	H.G.
28.1	99.7	268.9	At2g43610	818963	glycoside hydrolase family 19 protein	F:chitin binding, chitinase activity;P:cell wall macromolecule catabolic process;C:plasma membrane;PBFOVM	O.I.	C.G.	H.G.
27.9	99.7	143.3	At2g25980	817139	jacalin lectin family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBO	O.I.	C.G.	H.G.
25.8	99.7	46.3	At5g48110	834863	terpene synthase/cyclase family protein	F:lyase activity, magnesium ion binding;P:metabolic process;C:chloroplast;PMO	O.I.	C.G.	H.G.
25.3	99.6	94.6	At1g50490	841471	UBC20 (ubiquitin-conjugating enzyme 20)	Encodes one of two ubiquitin-conjugating enzymes belonging to the E2-C gene family (the other being UBC19). Transcript is always found in diving cells, but also in other non-dividing cells.	O.I.	C.G.	H.G.
23.5	99.6	31.5	At5g48940	834952	leucine-rich repeat transmembrane protein kinase, putative	F:protein binding, protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:unknown;MPOBFVA	O.I.	C.G.	H.G.
23.1	99.6	33.3	At3g13175	820507	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
23.0	99.6	56.5	At3g55170	824683	60S ribosomal protein L35 (RPL35C)	F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic large ribosomal subunit, ribosome;MOBAFP	O.I.	C.G.	H.G.
23.0	99.6	17.6	At4g10640	826656	IQD16 (IQ-domain 16)	F:calmodulin binding;P:biological_process unknown;C:cellular_component unknown;PMOF	O.I.	C.G.	H.G.
22.9	99.6	12.9	At3g49630	824125	2-oxoacid-dependent oxidase, putative	F:oxidoreductase activity, iron ion binding;P:aging, cellular response to starvation;C:endomembrane system;POBFM	O.I.	C.G.	H.G.
22.8	99.6	11.0	At5g59070	836024	glycosyl transferase family 1 protein	F:transferase activity, transferring glycosyl groups;P:biosynthetic process;C:endomembrane system;BOAPMF	O.I.	C.G.	H.G.
22.3	99.6	92.2	At5g60950	836216	COBL5 (COBRA-LIKE PROTEIN 5 PRECURSOR)	F:unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
22.3	99.6	71.7	At5g20400	832162	oxidoreductase, 2OG-Fe(II) oxygenase family protein	encodes a protein whose sequence is similar to flavanone 3 hydroxylase from Malus.	O.I.	C.G.	H.G.
21.5	99.6	28.7	At4g23590	828459	aminotransferase class I and II family protein	F:1-aminocyclopropane-1-carboxylate synthase activity, pyridoxal phosphate binding, transferase activity, transferring nitrogenous groups, transaminase activity, catalytic activity;P:cellular amino acid and derivative metabolic process, biosynthetic process;C:cellular_component unknown;BOPMAF	O.I.	C.G.	H.G.
21.1	99.6	204.0	At2g40360	818629	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:rRNA processing;C:nucleus;BMOFPVA	O.I.	C.G.	H.G.
21.1	99.6	17.1	At3g06840	819868	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
20.7	99.6	65.9	At5g19520	832072	MSL9 (MECHANOSENSITIVE CHANNEL OF SMALL CONDUCTANCE-LIKE 9)	F:mechanically-gated ion channel activity;P:detection of mechanical stimulus;C:nucleus, plasma membrane, membrane;BOFPAV	O.I.	C.G.	H.G.
20.6	99.6	53.8	At1g13590	837920	ATPSK1 (PHYTOSULFOKINE 1 PRECURSOR)	Encodes a phytosulfokine-alpha (PSK) precursor, a unique plant peptide growth factor first described in Asparagus.	O.I.	C.G.	H.G.
20.4	99.6	29.4	At3g18510	821381	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
19.9	99.6	74.1	At4g22930	828392	PYR4 (PYRIMIDIN 4)	Encodes dihydroorotase (PYR4).	O.I.	C.G.	H.G.
19.7	99.6	16.1	At1g73160	843647	glycosyl transferase family 1 protein	F:transferase activity, transferring glycosyl groups;P:biosynthetic process;C:unknown;BOAFPM	O.I.	C.G.	H.G.
19.5	99.6	53.6	At2g20515	816573	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
19.5	99.6	24.0	At1g56680	842124	glycoside hydrolase family 19 protein	F:chitinase activity;P:cell wall macromolecule catabolic process;C:endomembrane system;PBOMFV	O.I.	C.G.	H.G.
18.9	99.5	59.8	At4g37160	829870	sks15 (SKU5 Similar 15)	F:oxidoreductase activity, copper ion binding;P:unknown;C:endomembrane system;FBPMOA	O.I.	C.G.	H.G.
18.3	99.5	143.6	At4g00585	828026	unknown protein	F:molecular_function unknown;P:photorespiration;C:mitochondrial membrane, respiratory chain complex I;PFMO	O.I.	C.G.	H.G.
18.3	99.5	84.1	At1g16000	838170	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
18.3	99.5	10.2	At5g52170	835293	HDG7 (HOMEODOMAIN GLABROUS 7)	Encodes a homeobox-leucine zipper family protein belonging to the HD-ZIP IV family.	O.I.	C.G.	H.G.
18.1	99.5	39.6	At2g14460	815934	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
17.8	99.5	29.4	At3g23470	821928	cyclopropane-fatty-acyl-phospholipid synthase	F:cyclopropane-fatty-acyl-phospholipid synthase activity;P:lipid biosynthetic process;C:endomembrane system;OBFPAM	O.I.	C.G.	H.G.
17.7	99.5	165.5	At1g54690	841910	GAMMA-H2AX (GAMMA HISTONE VARIANT H2AX)	Encodes HTA3, a histone H2A protein. H2AX is a meiosis-specific isoform of histone H2A. Upon DSB formation, rapid accumulation of phosphorylated H2AX (γ-H2AX) occurs around the break site. H2AX foci accumulate in early G2. Immunolocalization studies in spread preparations of wild-type meiocytes at G2/early leptotene revealed the accumulation of numerous rather diffuse γ-H2AX foci throughout the chromatin. However, their accumulation is not contemporaneous with that of AtSPO11-1. At 3 h post-S, no γ-H2AX foci are detected. During the 3- to 5-h window when AtSPO11-1 foci rapidly disappear, there is an equally swift accumulation of γ-H2AX to a maximum of >50 diffuse foci. The level of γH2AX then remains constant for a further 13 h before undergoing a gradual decrease to 10�20 foci in the 18- to 24-h post-S period. By 30 h the foci have disappeared from the chromatin.	O.I.	C.G.	H.G.
17.7	99.5	109.0	At2g41800	818779	-	F:molecular_function unknown;P:biological_process unknown;C:cell wall, plant-type cell wall;P	O.I.	C.G.	H.G.
17.7	99.5	15.8	At5g43030	834318	DC1 domain-containing protein	F:unknown;P:intracellular signaling cascade;C:cellular_component unknown;PMO	O.I.	C.G.	H.G.
17.5	99.5	95.6	At1g07070	837218	60S ribosomal protein L35a (RPL35aA)	F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic large ribosomal subunit, ribosome;MOFPA	O.I.	C.G.	H.G.
17.2	99.5	56.6	At3g62810	825456	complex 1 family protein / LVR family protein	F:catalytic activity;P:unknown;C:unknown;MFPO	O.I.	C.G.	H.G.
17.1	99.5	87.3	At5g16060	831463	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PFOM	O.I.	C.G.	H.G.
16.2	99.5	11.5	At1g03840	839396	MGP (Magpie)	MGP is a nuclear-localized putative transcription factor with three zinc finger domains. MGP can interact with three proteins implicated in root patterning: SCR, SHR, and JKD in Y2H assays, and these interactions depend on the first zinc finger in MGP. MGP appears to be a direct transcriptional target of SHR and SCR, based on promoter binding assays, though it is not expressed in the QC, based on in situ hybridizations.	O.I.	C.G.	H.G.
16.0	99.5	37.0	At2g04090	814945	MATE efflux family protein	F:drug transporter activity, antiporter activity, transporter activity;P:multidrug transport;C:membrane;BOPFMA	O.I.	C.G.	H.G.
15.8	99.5	30.7	At3g52740	824440	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
15.8	99.5	5.8	At1g43040	840903	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;P	O.I.	C.G.	H.G.
15.7	99.5	25.4	At1g02430	839242	ATARFD1B (ADP-ribosylation factor D1B)	A member of ARF GTPase family. A thaliana has 21 members of this family, known to be essential for vesicle coating and uncoating and functions in GTP-binding. Gene encoding ADP-ribosylation factor and similar to other ARFs and ARF-like proteins.	O.I.	C.G.	H.G.
15.6	99.5	180.2	At2g39390	818524	60S ribosomal protein L35 (RPL35B)	F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic ribosome, cytosolic large ribosomal subunit, ribosome;MOBAFP	O.I.	C.G.	H.G.
15.6	99.5	111.6	At3g06320	819806	ribosomal protein L33 family protein	F:structural constituent of ribosome;P:translation;C:ribosome, intracellular, large ribosomal subunit;BOPMF	O.I.	C.G.	H.G.
15.6	99.5	54.9	At1g62810	842580	copper amine oxidase, putative	F:amine oxidase activity, quinone binding, copper ion binding;P:cellular amine metabolic process;C:endomembrane system;FBMOPA	O.I.	C.G.	H.G.
15.1	99.4	19.0	At5g60730	836194	anion-transporting ATPase family protein	F:ATP binding;P:cellular metal ion homeostasis, anion transport;C:membrane;BOAMFP	O.I.	C.G.	H.G.
15.1	99.4	18.1	At3g62280	825401	carboxylesterase/ hydrolase, acting on ester bonds	F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBFOM	O.I.	C.G.	H.G.
14.9	99.4	18.3	At2g30340	817584	LBD13 (LOB DOMAIN-CONTAINING PROTEIN 13)	F:molecular_function unknown;P:biological_process unknown;C:membrane;PMOFVBA	O.I.	C.G.	H.G.
14.8	99.4	54.9	At1g79150	844256	binding	F:binding;P:biological_process unknown;C:cellular_component unknown;OMFBPVA	O.I.	C.G.	H.G.
14.7	99.4	211.1	At3g10090	820170	40S ribosomal protein S28 (RPS28A)	F:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic small ribosomal subunit, cytosolic ribosome, ribosome, cell wall;MOAPF	O.I.	C.G.	H.G.
14.7	99.4	16.1	At5g07040	830595	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:endomembrane system;PMOFV	O.I.	C.G.	H.G.
14.4	99.4	119.1	At5g09590	830818	MTHSC70-2 (MITOCHONDRIAL HSP70 2)	heat shock protein 70 (Hsc70-5); nuclear	O.I.	C.G.	H.G.
14.4	99.4	18.2	At1g26660	839206	c-myc binding protein, putative / prefoldin, putative	F:unfolded protein binding;P:protein folding;C:prefoldin complex;MFOPAB	O.I.	C.G.	H.G.
14.3	99.4	71.7	At1g79390	844277	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
14.3	99.4	26.5	At4g31930	829323	mitochondrial glycoprotein family protein / MAM33 family protein	F:molecular_function unknown;P:biological_process unknown;C:mitochondrion, mitochondrial matrix;PFO	O.I.	C.G.	H.G.
14.2	99.4	9.2	At3g59850	825155	polygalacturonase, putative / pectinase, putative	F:polygalacturonase activity;P:carbohydrate metabolic process;C:endomembrane system;FPBOMAV	O.I.	C.G.	H.G.
14.1	99.4	95.5	At2g30000	817551	-	F:unknown;P:unknown;C:cellular_component unknown;MFOP	O.I.	C.G.	H.G.
14.1	99.4	87.0	At2g35605	818127	SWIB complex BAF60b domain-containing protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;OPBFMV	O.I.	C.G.	H.G.
14.0	99.4	134.4	At2g03870	814913	small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative	F:molecular_function unknown;P:unknown;C:small nucleolar ribonucleoprotein complex, nucleus;MFAOP	O.I.	C.G.	H.G.
14.0	99.4	3.5	At3g30740	3769121	-	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
13.9	99.4	596.3	At4g39200	830075	40S ribosomal protein S25 (RPS25E)	F:structural constituent of ribosome;P:translation;C:cytosolic small ribosomal subunit, cytosolic ribosome, ribosome;MFPOA	O.I.	C.G.	H.G.
13.9	99.4	88.4	At4g02840	828163	small nuclear ribonucleoprotein D1, putative / snRNP core protein D1, putative / Sm protein D1, putative	F:molecular_function unknown;P:unknown;C:nucleolus, small nucleolar ribonucleoprotein complex, nucleus, plasma membrane, membrane;MFOP	O.I.	C.G.	H.G.
13.8	99.4	84.5	At1g04870	839393	PRMT10	Encodes a type I protein arginine methyltransferase based on the At1g04870.2 gene model. PRMT10 can catalyze the asymmetric dimethylation of arginine 3 on histone 4 and can also methylate myelin basic protein in vitro. Mutants lacking PRMT10 flower late due to defects in the autonomous pathway and they have elevated levels of FLC transcripts.	O.I.	C.G.	H.G.
13.8	99.4	72.5	At3g01740	821088	-	F:molecular_function unknown;P:biological_process unknown;C:unknown;MPFO	O.I.	C.G.	H.G.
13.7	99.4	64.9	At1g73940	843731	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
13.7	99.4	27.2	At2g41810	818780	-	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PB	O.I.	C.G.	H.G.
13.6	99.4	44.3	At2g43780	818981	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:mitochondrion;P	O.I.	C.G.	H.G.
13.4	99.4	16.1	At4g37940	829950	AGL21	encodes a MADS box protein, highly expressed in the root.	O.I.	C.G.	H.G.
13.4	99.4	11.1	At3g46720	823825	UDP-glucoronosyl/UDP-glucosyl transferase family protein	F:transferase activity, transferring hexosyl groups, UDP-glycosyltransferase activity, transferase activity, transferring glycosyl groups;P:metabolic process;C:cellular_component unknown;PMBVOF	O.I.	C.G.	H.G.
13.3	99.4	104.6	At5g62340	836355	invertase/pectin methylesterase inhibitor family protein	F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
13.2	99.4	56.3	At1g61580	842454	RPL3B (R-PROTEIN L3 B)	F:structural constituent of ribosome;P:translation;C:cytosolic large ribosomal subunit, ribosome, membrane;BOMAPFV	O.I.	C.G.	H.G.
13.2	99.4	24.9	At5g01620	831716	unknown protein	F:unknown;P:unknown;C:endomembrane system;PM	O.I.	C.G.	H.G.
13.2	99.4	24.8	At1g29270	839801	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
13.0	99.4	44.0	At5g57120	835816	-	F:molecular_function unknown;P:biological_process unknown;C:nucleolus;MOBFPVA	O.I.	C.G.	H.G.
13.0	99.4	22.4	At1g23100	838918	10 kDa chaperonin, putative	F:ATP binding;P:protein folding;C:mitochondrion;BOMPFV	O.I.	C.G.	H.G.
12.7	99.3	36.3	At4g31320	829259	auxin-responsive protein, putative / small auxin up RNA (SAUR_C)	F:calmodulin binding;P:response to auxin stimulus;C:cellular_component unknown;PO	O.I.	C.G.	H.G.
12.7	99.3	17.8	At3g57360	824903	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MP	O.I.	C.G.	H.G.
12.6	99.3	69.7	At1g14620	838024	DECOY (DECOY)	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;FMPOB	O.I.	C.G.	H.G.
12.6	99.3	31.9	At4g10620	826654	-	F:unknown;P:biological_process unknown;C:chloroplast;BMFOPA	O.I.	C.G.	H.G.
12.5	99.3	353.6	At2g22170	816751	lipid-associated family protein	F:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast, membrane;PMO	O.I.	C.G.	H.G.
12.5	99.3	126.0	At1g16740	838245	ribosomal protein L20 family protein	F:structural constituent of ribosome, RNA binding;P:translation, ribosome biogenesis;C:ribosome, intracellular;BOPM	O.I.	C.G.	H.G.
12.4	99.3	203.7	At1g54000	841838	myrosinase-associated protein, putative	F:lipase activity, hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:vacuolar membrane, plasma membrane, vacuole, plant-type cell wall, plant-type vacuole;PBOFM	O.I.	C.G.	H.G.
12.4	99.3	51.3	At2g45730	819181	eukaryotic initiation factor 3 gamma subunit family protein	F:translation initiation factor activity;P:translational initiation, regulation of translational initiation;C:cellular_component unknown;MFOP	O.I.	C.G.	H.G.
12.3	99.3	329.7	At5g02450	831907	60S ribosomal protein L36 (RPL36C)	F:structural constituent of ribosome;P:translation;C:cytosolic large ribosomal subunit, ribosome, plasma membrane;MOFP	O.I.	C.G.	H.G.
12.2	99.3	16.5	At5g42060	834211	unknown protein	F:unknown;P:unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
12.2	99.3	9.0	At1g62520	842549	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PFOB	O.I.	C.G.	H.G.
12.0	99.3	75.7	At4g31120	829240	SKB1 (SHK1 BINDING PROTEIN 1)	Involved in vernalization. Required for epigenetic silencing of FLC, and for vernalization-mediated histone modification.	O.I.	C.G.	H.G.
12.0	99.3	15.1	At4g40000	830161	NOL1/NOP2/sun family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BOMFAP	O.I.	C.G.	H.G.
11.9	99.3	19.6	At4g33100	829447	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPO	O.I.	C.G.	H.G.
11.9	99.3	15.2	At3g27950	822419	early nodule-specific protein, putative	F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBOFM	O.I.	C.G.	H.G.
11.9	99.3	15.2	At5g35400	833501	tRNA pseudouridine synthase family protein	F:pseudouridine synthase activity;P:tRNA processing, pseudouridine synthesis;C:unknown;BOMPAF	O.I.	C.G.	H.G.
11.8	99.3	251.1	At1g57660	842142	60S ribosomal protein L21 (RPL21E)	F:structural constituent of ribosome;P:translation;C:ribosome, intracellular;MOAFP	O.I.	C.G.	H.G.
11.8	99.3	33.7	At5g44560	834483	VPS2.2	F:unknown;P:vesicle-mediated transport;C:ESCRT III complex;MPFOB	O.I.	C.G.	H.G.

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GSM ID	GSM252682
Assay name	Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep4
GSE experiment	GSE9996: Organ regeneration in plants is independent of stem cell niche activity

Microarray experiments to specifically-expressed genes

GSM ID GSM252682 Assay name Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep4 GSE experiment GSE9996: Organ regeneration in plants is independent of stem cell niche activity

GSM ID GSM252682

Assay name Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep4

GSE experiment GSE9996: Organ regeneration in plants is independent of stem cell niche activity