CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM133947

Assay name Murray_2-3_T4-APH_Rep1_ATH1

GSE experiment GSE5747: Genome-wide cell cycle studies

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
339.0 100.0 24.1 At3g17260 3768760 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
319.9 100.0 92.2 At4g01970 828186 AtSTS (Arabidopsis thaliana stachyose synthase) Encodes a putative stachyose synthetase. O.I. C.G. H.G.
298.4 100.0 105.3 At4g21070 827854 ATBRCA1 Encodes AtBRCA1, an ortholog of the human breast cancer susceptibility gene 1. Contains one N-terminal RING finger, two C-terminal BRCT and the p300/CBP interacting domain. Strongly induced by gamma rays, consistent with a putative role in DNA repair and in cell cycle control. O.I. C.G. H.G.
225.6 100.0 21.5 At5g43000 834315 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MP O.I. C.G. H.G.
209.7 100.0 276.6 At2g04000 814926 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
199.2 100.0 72.1 At5g43980 834421 PDLP1 (PLASMODESMATA-LOCATED PROTEIN 1) Encodes a plasmodesmal protein that affects the intercellular movement of molecules through the plasmodesmata. The cytoplasmic C-terminal portion of the protein is connected to the apoplastic N-terminal portion of the protein by a single transmembrane domain (TMD). It is transported to the plasmodesmata through the secretory pathway. PDLP1 has two DUF26 domains and a signal peptide, but the proper localization of the protein appears to depend on the TMD. O.I. C.G. H.G.
192.7 100.0 76.3 At5g61740 836296 ATATH14 member of ATH subfamily O.I. C.G. H.G.
188.9 100.0 123.5 At4g02390 828049 APP (ARABIDOPSIS POLY(ADP-RIBOSE) POLYMERASE) Encodes a DNA dependent nuclear poly (ADP-ribose) polymerase (E.C.2.4.2.30), thought to be involved in post-translational modification . O.I. C.G. H.G.
178.2 100.0 103.6 At1g51380 841562 eukaryotic translation initiation factor 4A, putative / eIF-4A, putative F:helicase activity, ATP binding, ATP-dependent helicase activity, nucleic acid binding;P:unknown;C:cellular_component unknown;BOMFPAV O.I. C.G. H.G.
158.9 99.9 36.8 At1g44510 3767344 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
155.0 99.9 59.0 At5g20850 832208 ATRAD51 Encodes a homolog of yeast RAD51. Its mRNA is most abundant in early flower buds and is expressed at high levels in exponentially growing cells in suspension cultures and is induced in response to gamma radiation. O.I. C.G. H.G.
151.0 99.9 225.7 At1g19850 838573 MP (MONOPTEROS) Encodes a transcription factor (IAA24) mediating embryo axis formation and vascular development. Similar to AUXIN RESPONSIVE FACTOR 1 (ARF1) shown to bind to auxin responsive elements (AREs), and to the maize transcriptional activator VIVIPAROUS 1( VP1). In situ hybridization shows expression in provascular tissue of embryos, the emerging shoot primordia, then is restricted to provascular tissue, and in the root central vascular cylinder. O.I. C.G. H.G.
128.5 99.9 53.7 At4g01270 828038 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:unknown;MOPFBAV O.I. C.G. H.G.
126.3 99.9 40.2 At3g61340 825306 F-box family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO O.I. C.G. H.G.
125.2 99.9 149.5 At1g69770 843313 CMT3 (chromomethylase 3) Encodes a chromomethylase involved in methylating cytosine residues at non-CG sites. Involved in preferentially methylating transposon-related sequences, reducing their mobility. CMT3 interacts with an Arabidopsis homologue of HP1 (heterochromatin protein 1), which in turn interacts with methylated histones. Involved in gene silencing. O.I. C.G. H.G.
116.5 99.9 30.1 At4g01920 828197 DC1 domain-containing protein F:unknown;P:intracellular signaling cascade;C:cellular_component unknown;PMO O.I. C.G. H.G.
116.2 99.9 51.4 At3g19350 821469 MPC (MATERNALLY EXPRESSED PAB C-TERMINAL) Encodes a the C-terminal domain of poly(A) binding proteins. MPC is imprinted such that only the maternal allele is expressed in the endosperm. MPC is silenced by the action of MET1 and its expression is promoted by DEM. O.I. C.G. H.G.
100.1 99.9 189.7 At2g02560 814786 CAND1 (CULLIN-ASSOCIATED AND NEDDYLATION DISSOCIATED) Arabidopsis thaliana homolog of human CAND1 (cullin-associated and neddylation-dissociated). Putative similarity to TBP-interacting protein TIP120. Ubiquitously expressed in plant tissues throughout development. T-DNA insertion mutant plants were completely sterile and resistant to sirtinol and auxin, but not to gibberellins or brassinolide. Displayed developmental phenotypes similar to those of axr1, namely, short petioles, downwardly curling leaves, shorter inflorescence. Required for SCF function and appears to modulate SCF complex cycling. Physically interacts with CUL1. O.I. C.G. H.G.
99.5 99.9 34.5 At5g64060 836527 anac103 (Arabidopsis NAC domain containing protein 103) F:transcription factor activity;P:multicellular organismal development, regulation of transcription;C:cellular_component unknown;P O.I. C.G. H.G.
91.4 99.9 60.7 At1g59660 842256 nucleoporin family protein F:transporter activity;P:transport;C:chloroplast, nuclear pore;MBOFPVA O.I. C.G. H.G.
91.4 99.9 22.6 At5g44010 834424 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
91.3 99.9 147.0 At5g42970 834312 COP8 (CONSTITUTIVE PHOTOMORPHOGENIC 8) encodes subunit 4 of COP9 signalosome complex. sequence is similar to a subunit of the 19S regulatory particle of the 26S proteasome. recessive mutation causes derepression of photomorphogenesis. O.I. C.G. H.G.
91.2 99.9 72.9 At4g22960 828395 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPB O.I. C.G. H.G.
91.2 99.9 23.7 At1g20750 838665 helicase-related F:in 6 functions;P:nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;C:chloroplast;MOFBPA O.I. C.G. H.G.
89.4 99.9 259.8 At2g12240 3768292 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
89.4 99.9 255.7 At3g07800 819971 thymidine kinase, putative F:thymidine kinase activity, ATP binding;P:pyrimidine deoxyribonucleoside interconversion, anaerobic respiration;C:cellular_component unknown;BOVMPAF O.I. C.G. H.G.
89.4 99.9 15.4 At2g43270 818929 F-box family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO O.I. C.G. H.G.
89.3 99.9 29.8 At4g01930 828198 DC1 domain-containing protein F:protein binding, zinc ion binding;P:intracellular signaling cascade;C:cellular_component unknown;PMO O.I. C.G. H.G.
87.2 99.9 255.0 At2g10640 3767859 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
87.0 99.9 67.2 At1g66620 842980 seven in absentia (SINA) protein, putative F:ubiquitin-protein ligase activity, protein binding, zinc ion binding;P:multicellular organismal development, protein ubiquitination, ubiquitin-dependent protein catabolic process;C:nucleus;MOFPBVA O.I. C.G. H.G.
86.6 99.9 70.9 At1g23550 838965 SRO2 (SIMILAR TO RCD ONE 2) Encodes a protein with similarity to RCD1 but without the WWE domain. The protein does have a PARP signature upstream of the C-terminal protein interaction domain. The PARP signature may bind NAD+ and attach the ADP-ribose-moiety from NAD+ to the target molecule. Its presence suggests a role for the protein in ADP ribosylation. O.I. C.G. H.G.
86.0 99.9 173.7 At2g15690 816062 pentatricopeptide (PPR) repeat-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFBVA O.I. C.G. H.G.
83.9 99.9 259.0 At3g30396 3769077 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
82.7 99.9 23.9 At3g30360 822737 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
81.0 99.9 136.1 At2g16570 816156 ATASE1 (GLN PHOSPHORIBOSYL PYROPHOSPHATE AMIDOTRANSFERASE 1) Amidophosphoribosyltransferase (ATase: EC 2.4.2.14) is a key enzyme in the pathway of purine nucleotide biosynthesis O.I. C.G. H.G.
80.8 99.9 15.5 At1g33500 840244 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAV O.I. C.G. H.G.
79.6 99.9 49.4 At3g16980 820954 NRPB9A One of two highly similar, non-catalytic subunits common to nuclear DNA-directed RNA polymerases II, IV and V; homologous to budding yeast RPB9. Appears to be redundant with At4g16265 O.I. C.G. H.G.
78.7 99.9 51.4 At4g00930 827980 CIP4.1 Encodes COP1-interacting protein CIP4.1. O.I. C.G. H.G.
77.6 99.9 24.6 At3g29610 822626 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
76.6 99.9 54.7 At1g36180 840522 ACC2 (ACETYL-COA CARBOXYLASE 2) acetyl-CoA carboxylase 2 (ACC2) O.I. C.G. H.G.
76.4 99.9 13.2 At4g25330 828636 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
73.2 99.9 216.7 At2g12300 3768253 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
71.2 99.9 26.2 At5g03780 831726 TRFL10 (TRF-LIKE 10) Encodes a protein whose sequence is similar to human telomere proteins. This belongs to TRFL family 2, which do not show DNA binding in vitro. O.I. C.G. H.G.
71.0 99.9 72.3 At2g01640 814693 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POF O.I. C.G. H.G.
71.0 99.9 45.9 At4g01860 827918 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MBFOPA O.I. C.G. H.G.
70.1 99.9 35.4 At5g61690 836291 ATATH15 member of ATH subfamily O.I. C.G. H.G.
69.7 99.9 57.7 At5g53830 835464 VQ motif-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFBM O.I. C.G. H.G.
69.0 99.9 29.3 At2g01740 814704 pentatricopeptide (PPR) repeat-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBA O.I. C.G. H.G.
68.6 99.9 36.0 At3g20490 821595 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFBP O.I. C.G. H.G.
68.0 99.9 166.3 At5g43330 834351 malate dehydrogenase, cytosolic, putative F:in 6 functions;P:cellular carbohydrate metabolic process, glycolysis, malate metabolic process, carbohydrate metabolic process, metabolic process;C:plasma membrane;BOMPFA O.I. C.G. H.G.
68.0 99.9 81.4 At5g48720 834930 XRI1 (X-RAY INDUCED TRANSCRIPT 1) Encodes XRI1 (X-ray induced 1). Required for post-meiotic stages of pollen development and male and female meiosis. Maybe required for meiotic DNA repair. Inducible by X-ray. Homozygous xri1 mutants are sterile due to extensive chromosome fragmentation. O.I. C.G. H.G.
66.1 99.8 96.7 At2g45290 819137 transketolase, putative F:catalytic activity, transketolase activity;P:response to cadmium ion;C:chloroplast stroma, chloroplast;OBMFAP O.I. C.G. H.G.
65.1 99.8 55.4 At2g15790 816074 SQN (SQUINT) SQN encodes the Arabidopsis homolog of cyclophilin 40 (CyP40). It is specifically required for the vegetative but not the reproductive maturation of the shoot. O.I. C.G. H.G.
63.6 99.8 48.6 At1g20350 838623 ATTIM17-1 mitochondrial inner membrane translocase O.I. C.G. H.G.
63.4 99.8 33.6 At1g02970 839453 WEE1 (ARABIDOPSIS WEE1 KINASE HOMOLOG) Protein kinase that negatively regulates the entry into mitosis. O.I. C.G. H.G.
63.1 99.8 71.1 At5g47950 834846 transferase family protein F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFO O.I. C.G. H.G.
62.3 99.8 39.6 At1g20370 838625 tRNA pseudouridine synthase family protein F:pseudouridine synthase activity;P:tRNA processing, pseudouridine synthesis;C:cellular_component unknown;BOMFAP O.I. C.G. H.G.
61.9 99.8 36.1 At2g44510 819058 p21Cip1-binding protein-related F:molecular_function unknown;P:biological_process unknown;C:nucleolus;MFOP O.I. C.G. H.G.
59.6 99.8 80.7 At5g60250 836147 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding, nucleic acid binding;P:unknown;C:unknown;MFPOB O.I. C.G. H.G.
59.1 99.8 52.3 At5g43310 834349 COP1-interacting protein-related F:unknown;P:unknown;C:plasma membrane, membrane;MOFPBV O.I. C.G. H.G.
58.8 99.8 73.6 At1g60030 842297 xanthine/uracil permease family protein F:transmembrane transporter activity;P:transport;C:plasma membrane, membrane;BOMPFAV O.I. C.G. H.G.
57.9 99.8 99.1 At2g02860 814817 SUT2 (SUCROSE TRANSPORTER 2) encodes a sucrose transporter in sieve elements and a number of sink tissues and cell types. Gene expression is induced by wounding. O.I. C.G. H.G.
57.8 99.8 66.0 At1g33450 840238 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
57.2 99.8 26.2 At4g29170 829038 ATMND1 A homolog of yeast, mouse and human mnd1delta protein. Null mutants exhibit normal vegetative and flower development; however, during prophase I, chromosomes become fragmented resulting in random distribution of the fragments between polyads. Both male and female meiosis are defective and strong accumulation of AtRAD51 was observed in the inflorescence nuclei of mutant plants. Similarly to its yeast and animal homologues, AtMnd1 might play a role in DSB repair during meiosis. O.I. C.G. H.G.
56.9 99.8 74.5 At4g32880 829424 ATHB-8 (HOMEOBOX GENE 8) member of homeodomain-leucine zipper family, acting as a differentiation-promoting transcription factor of the vascular meristems. O.I. C.G. H.G.
56.5 99.8 66.6 At3g12510 820430 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PB O.I. C.G. H.G.
56.3 99.8 57.3 At1g51580 841583 KH domain-containing protein F:RNA binding, nucleic acid binding;P:unknown;C:unknown;MPFOBVA O.I. C.G. H.G.
56.2 99.8 170.9 At2g28510 817399 Dof-type zinc finger domain-containing protein F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleolus;POMFB O.I. C.G. H.G.
54.8 99.8 58.1 At2g28660 817415 copper-binding family protein F:copper ion binding, metal ion binding;P:copper ion transport, metal ion transport;C:chloroplast;OPMBF O.I. C.G. H.G.
54.6 99.8 23.0 At5g64990 836623 AtRABH1a (Arabidopsis Rab GTPase homolog H1a) F:GTP binding;P:protein transport, small GTPase mediated signal transduction;C:mitochondrion;MOFPBAV O.I. C.G. H.G.
54.3 99.8 31.5 At3g09070 820060 glycine-rich protein F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;MOPFBV O.I. C.G. H.G.
54.2 99.8 127.1 At5g14250 831275 COP13 (CONSTITUTIVE PHOTOMORPHOGENIC 13) Encodes subunit 3 of the COP9 signalosome. O.I. C.G. H.G.
54.1 99.8 198.9 At2g01610 814690 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.
53.8 99.8 208.3 At5g46700 834713 TRN2 (TORNADO 2) Encodes a transmembrane protein of the tetraspanin (TET) family, one of 17 members found in Arabidopsis. Double mutant analysis showed that TRN1 and TRN2 act in the same pathway. Required for the maintenance of both the radial pattern of tissue differentiation in the root and for the subsequent circumferential pattern within the epidermis. O.I. C.G. H.G.
53.8 99.8 35.5 At5g25580 832633 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOBV O.I. C.G. H.G.
53.2 99.8 40.4 At1g33460 3766895 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
53.2 99.8 34.5 At5g02220 831792 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
52.3 99.8 44.1 At4g01880 828223 methyltransferase F:methyltransferase activity;P:tRNA processing;C:unknown;MOFPAB O.I. C.G. H.G.
52.1 99.8 55.2 At5g06730 830562 peroxidase, putative F:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:plasma membrane;PFOBM O.I. C.G. H.G.
52.0 99.8 48.0 At5g24280 832495 - F:unknown;P:unknown;C:unknown;PMOBF O.I. C.G. H.G.
51.3 99.8 59.9 At3g18610 821392 ATRANGAP1 (RAN GTPASE-ACTIVATING PROTEIN 1) F:nucleotide binding, nucleic acid binding;P:unknown;C:unknown;MOFBPVA O.I. C.G. H.G.
50.8 99.8 175.8 At2g21790 816715 RNR1 (RIBONUCLEOTIDE REDUCTASE 1) encodes large subunit of ribonucleotide reductase involved in the production of deoxyribonucleoside triphosphates (dNTPs) for DNA replication and repair O.I. C.G. H.G.
50.5 99.8 47.1 At2g02880 814819 mucin-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFMB O.I. C.G. H.G.
50.4 99.8 181.9 At5g25450 832619 ubiquinol-cytochrome C reductase complex 14 kDa protein, putative F:ubiquinol-cytochrome-c reductase activity;P:mitochondrial electron transport, ubiquinol to cytochrome c;C:mitochondrion, mitochondrial respiratory chain complex III, membrane;MPFO O.I. C.G. H.G.
50.0 99.8 42.9 At1g79610 844299 sodium proton exchanger, putative (NHX6) F:solute:hydrogen antiporter activity, sodium:hydrogen antiporter activity;P:cation transport, sodium ion transport, regulation of pH;C:integral to membrane;BMOPFA O.I. C.G. H.G.
48.6 99.8 81.4 At5g61000 836221 replication protein, putative F:DNA binding, nucleic acid binding;P:DNA replication;C:nucleus;PMOFA O.I. C.G. H.G.
47.9 99.8 59.5 At3g16870 820942 zinc finger (GATA type) family protein F:transcription factor activity;P:regulation of transcription, DNA-dependent;C:nucleus;FPMO O.I. C.G. H.G.
47.3 99.8 15.2 At1g05490 837051 chr31 (chromatin remodeling 31) F:helicase activity, DNA binding, ATP binding, nucleic acid binding;P:biological_process unknown;C:unknown;MOBFPVA O.I. C.G. H.G.
46.8 99.8 96.6 At5g05340 830416 peroxidase, putative F:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:apoplast, cell wall;PFOBM O.I. C.G. H.G.
46.4 99.8 51.0 At4g37490 829904 CYCB1 Cyclin-dependent protein kinase CYCB1;1. Functions as an effector of growth control at G2/M. Regulated by TCP20. O.I. C.G. H.G.
46.3 99.8 20.7 At4g34320 829582 unknown protein F:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;PBOM O.I. C.G. H.G.
46.2 99.8 25.8 At2g02020 814733 proton-dependent oligopeptide transport (POT) family protein F:transporter activity;P:oligopeptide transport;C:membrane;BPMOF O.I. C.G. H.G.
46.0 99.8 243.4 At2g44450 819052 BGLU15 (BETA GLUCOSIDASE 15) F:cation binding, hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:cell wall, plant-type cell wall;BOPMFA O.I. C.G. H.G.
45.5 99.8 33.9 At1g22090 838814 emb2204 (embryo defective 2204) F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;P O.I. C.G. H.G.
44.6 99.8 122.8 At1g15420 838113 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBV O.I. C.G. H.G.
43.9 99.8 25.2 At5g40840 834084 SYN2 Cohesion family protein SYN2 (SYN2). O.I. C.G. H.G.
43.8 99.8 29.2 At2g45460 819154 forkhead-associated domain-containing protein / FHA domain-containing protein F:transcription factor activity;P:regulation of transcription, DNA-dependent;C:chloroplast;MOBFPAV O.I. C.G. H.G.
43.7 99.8 111.5 At2g01650 814694 PUX2 (PLANT UBX DOMAIN-CONTAINING PROTEIN 2) encodes a peripheral membrane protein that contains UBX domain and interacts with AtCDC48 in vitro and co-fractionates with membrane-associated but not soluble AtCDC48 in vivo. O.I. C.G. H.G.
43.7 99.8 14.8 At1g04650 839457 unknown protein F:unknown;P:unknown;C:cellular_component unknown;POM O.I. C.G. H.G.
43.5 99.8 31.6 At4g29770 829099 - Target of trans acting-siR480/255. 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.
339.0	100.0	24.1	At3g17260	3768760	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
319.9	100.0	92.2	At4g01970	828186	AtSTS (Arabidopsis thaliana stachyose synthase)	Encodes a putative stachyose synthetase.	O.I.	C.G.	H.G.
298.4	100.0	105.3	At4g21070	827854	ATBRCA1	Encodes AtBRCA1, an ortholog of the human breast cancer susceptibility gene 1. Contains one N-terminal RING finger, two C-terminal BRCT and the p300/CBP interacting domain. Strongly induced by gamma rays, consistent with a putative role in DNA repair and in cell cycle control.	O.I.	C.G.	H.G.
225.6	100.0	21.5	At5g43000	834315	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MP	O.I.	C.G.	H.G.
209.7	100.0	276.6	At2g04000	814926	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
199.2	100.0	72.1	At5g43980	834421	PDLP1 (PLASMODESMATA-LOCATED PROTEIN 1)	Encodes a plasmodesmal protein that affects the intercellular movement of molecules through the plasmodesmata. The cytoplasmic C-terminal portion of the protein is connected to the apoplastic N-terminal portion of the protein by a single transmembrane domain (TMD). It is transported to the plasmodesmata through the secretory pathway. PDLP1 has two DUF26 domains and a signal peptide, but the proper localization of the protein appears to depend on the TMD.	O.I.	C.G.	H.G.
192.7	100.0	76.3	At5g61740	836296	ATATH14	member of ATH subfamily	O.I.	C.G.	H.G.
188.9	100.0	123.5	At4g02390	828049	APP (ARABIDOPSIS POLY(ADP-RIBOSE) POLYMERASE)	Encodes a DNA dependent nuclear poly (ADP-ribose) polymerase (E.C.2.4.2.30), thought to be involved in post-translational modification .	O.I.	C.G.	H.G.
178.2	100.0	103.6	At1g51380	841562	eukaryotic translation initiation factor 4A, putative / eIF-4A, putative	F:helicase activity, ATP binding, ATP-dependent helicase activity, nucleic acid binding;P:unknown;C:cellular_component unknown;BOMFPAV	O.I.	C.G.	H.G.
158.9	99.9	36.8	At1g44510	3767344	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
155.0	99.9	59.0	At5g20850	832208	ATRAD51	Encodes a homolog of yeast RAD51. Its mRNA is most abundant in early flower buds and is expressed at high levels in exponentially growing cells in suspension cultures and is induced in response to gamma radiation.	O.I.	C.G.	H.G.
151.0	99.9	225.7	At1g19850	838573	MP (MONOPTEROS)	Encodes a transcription factor (IAA24) mediating embryo axis formation and vascular development. Similar to AUXIN RESPONSIVE FACTOR 1 (ARF1) shown to bind to auxin responsive elements (AREs), and to the maize transcriptional activator VIVIPAROUS 1( VP1). In situ hybridization shows expression in provascular tissue of embryos, the emerging shoot primordia, then is restricted to provascular tissue, and in the root central vascular cylinder.	O.I.	C.G.	H.G.
128.5	99.9	53.7	At4g01270	828038	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:unknown;MOPFBAV	O.I.	C.G.	H.G.
126.3	99.9	40.2	At3g61340	825306	F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO	O.I.	C.G.	H.G.
125.2	99.9	149.5	At1g69770	843313	CMT3 (chromomethylase 3)	Encodes a chromomethylase involved in methylating cytosine residues at non-CG sites. Involved in preferentially methylating transposon-related sequences, reducing their mobility. CMT3 interacts with an Arabidopsis homologue of HP1 (heterochromatin protein 1), which in turn interacts with methylated histones. Involved in gene silencing.	O.I.	C.G.	H.G.
116.5	99.9	30.1	At4g01920	828197	DC1 domain-containing protein	F:unknown;P:intracellular signaling cascade;C:cellular_component unknown;PMO	O.I.	C.G.	H.G.
116.2	99.9	51.4	At3g19350	821469	MPC (MATERNALLY EXPRESSED PAB C-TERMINAL)	Encodes a the C-terminal domain of poly(A) binding proteins. MPC is imprinted such that only the maternal allele is expressed in the endosperm. MPC is silenced by the action of MET1 and its expression is promoted by DEM.	O.I.	C.G.	H.G.
100.1	99.9	189.7	At2g02560	814786	CAND1 (CULLIN-ASSOCIATED AND NEDDYLATION DISSOCIATED)	Arabidopsis thaliana homolog of human CAND1 (cullin-associated and neddylation-dissociated). Putative similarity to TBP-interacting protein TIP120. Ubiquitously expressed in plant tissues throughout development. T-DNA insertion mutant plants were completely sterile and resistant to sirtinol and auxin, but not to gibberellins or brassinolide. Displayed developmental phenotypes similar to those of axr1, namely, short petioles, downwardly curling leaves, shorter inflorescence. Required for SCF function and appears to modulate SCF complex cycling. Physically interacts with CUL1.	O.I.	C.G.	H.G.
99.5	99.9	34.5	At5g64060	836527	anac103 (Arabidopsis NAC domain containing protein 103)	F:transcription factor activity;P:multicellular organismal development, regulation of transcription;C:cellular_component unknown;P	O.I.	C.G.	H.G.
91.4	99.9	60.7	At1g59660	842256	nucleoporin family protein	F:transporter activity;P:transport;C:chloroplast, nuclear pore;MBOFPVA	O.I.	C.G.	H.G.
91.4	99.9	22.6	At5g44010	834424	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
91.3	99.9	147.0	At5g42970	834312	COP8 (CONSTITUTIVE PHOTOMORPHOGENIC 8)	encodes subunit 4 of COP9 signalosome complex. sequence is similar to a subunit of the 19S regulatory particle of the 26S proteasome. recessive mutation causes derepression of photomorphogenesis.	O.I.	C.G.	H.G.
91.2	99.9	72.9	At4g22960	828395	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPB	O.I.	C.G.	H.G.
91.2	99.9	23.7	At1g20750	838665	helicase-related	F:in 6 functions;P:nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;C:chloroplast;MOFBPA	O.I.	C.G.	H.G.
89.4	99.9	259.8	At2g12240	3768292	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
89.4	99.9	255.7	At3g07800	819971	thymidine kinase, putative	F:thymidine kinase activity, ATP binding;P:pyrimidine deoxyribonucleoside interconversion, anaerobic respiration;C:cellular_component unknown;BOVMPAF	O.I.	C.G.	H.G.
89.4	99.9	15.4	At2g43270	818929	F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO	O.I.	C.G.	H.G.
89.3	99.9	29.8	At4g01930	828198	DC1 domain-containing protein	F:protein binding, zinc ion binding;P:intracellular signaling cascade;C:cellular_component unknown;PMO	O.I.	C.G.	H.G.
87.2	99.9	255.0	At2g10640	3767859	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
87.0	99.9	67.2	At1g66620	842980	seven in absentia (SINA) protein, putative	F:ubiquitin-protein ligase activity, protein binding, zinc ion binding;P:multicellular organismal development, protein ubiquitination, ubiquitin-dependent protein catabolic process;C:nucleus;MOFPBVA	O.I.	C.G.	H.G.
86.6	99.9	70.9	At1g23550	838965	SRO2 (SIMILAR TO RCD ONE 2)	Encodes a protein with similarity to RCD1 but without the WWE domain. The protein does have a PARP signature upstream of the C-terminal protein interaction domain. The PARP signature may bind NAD+ and attach the ADP-ribose-moiety from NAD+ to the target molecule. Its presence suggests a role for the protein in ADP ribosylation.	O.I.	C.G.	H.G.
86.0	99.9	173.7	At2g15690	816062	pentatricopeptide (PPR) repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFBVA	O.I.	C.G.	H.G.
83.9	99.9	259.0	At3g30396	3769077	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
82.7	99.9	23.9	At3g30360	822737	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
81.0	99.9	136.1	At2g16570	816156	ATASE1 (GLN PHOSPHORIBOSYL PYROPHOSPHATE AMIDOTRANSFERASE 1)	Amidophosphoribosyltransferase (ATase: EC 2.4.2.14) is a key enzyme in the pathway of purine nucleotide biosynthesis	O.I.	C.G.	H.G.
80.8	99.9	15.5	At1g33500	840244	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAV	O.I.	C.G.	H.G.
79.6	99.9	49.4	At3g16980	820954	NRPB9A	One of two highly similar, non-catalytic subunits common to nuclear DNA-directed RNA polymerases II, IV and V; homologous to budding yeast RPB9. Appears to be redundant with At4g16265	O.I.	C.G.	H.G.
78.7	99.9	51.4	At4g00930	827980	CIP4.1	Encodes COP1-interacting protein CIP4.1.	O.I.	C.G.	H.G.
77.6	99.9	24.6	At3g29610	822626	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
76.6	99.9	54.7	At1g36180	840522	ACC2 (ACETYL-COA CARBOXYLASE 2)	acetyl-CoA carboxylase 2 (ACC2)	O.I.	C.G.	H.G.
76.4	99.9	13.2	At4g25330	828636	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
73.2	99.9	216.7	At2g12300	3768253	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
71.2	99.9	26.2	At5g03780	831726	TRFL10 (TRF-LIKE 10)	Encodes a protein whose sequence is similar to human telomere proteins. This belongs to TRFL family 2, which do not show DNA binding in vitro.	O.I.	C.G.	H.G.
71.0	99.9	72.3	At2g01640	814693	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POF	O.I.	C.G.	H.G.
71.0	99.9	45.9	At4g01860	827918	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MBFOPA	O.I.	C.G.	H.G.
70.1	99.9	35.4	At5g61690	836291	ATATH15	member of ATH subfamily	O.I.	C.G.	H.G.
69.7	99.9	57.7	At5g53830	835464	VQ motif-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFBM	O.I.	C.G.	H.G.
69.0	99.9	29.3	At2g01740	814704	pentatricopeptide (PPR) repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBA	O.I.	C.G.	H.G.
68.6	99.9	36.0	At3g20490	821595	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFBP	O.I.	C.G.	H.G.
68.0	99.9	166.3	At5g43330	834351	malate dehydrogenase, cytosolic, putative	F:in 6 functions;P:cellular carbohydrate metabolic process, glycolysis, malate metabolic process, carbohydrate metabolic process, metabolic process;C:plasma membrane;BOMPFA	O.I.	C.G.	H.G.
68.0	99.9	81.4	At5g48720	834930	XRI1 (X-RAY INDUCED TRANSCRIPT 1)	Encodes XRI1 (X-ray induced 1). Required for post-meiotic stages of pollen development and male and female meiosis. Maybe required for meiotic DNA repair. Inducible by X-ray. Homozygous xri1 mutants are sterile due to extensive chromosome fragmentation.	O.I.	C.G.	H.G.
66.1	99.8	96.7	At2g45290	819137	transketolase, putative	F:catalytic activity, transketolase activity;P:response to cadmium ion;C:chloroplast stroma, chloroplast;OBMFAP	O.I.	C.G.	H.G.
65.1	99.8	55.4	At2g15790	816074	SQN (SQUINT)	SQN encodes the Arabidopsis homolog of cyclophilin 40 (CyP40). It is specifically required for the vegetative but not the reproductive maturation of the shoot.	O.I.	C.G.	H.G.
63.6	99.8	48.6	At1g20350	838623	ATTIM17-1	mitochondrial inner membrane translocase	O.I.	C.G.	H.G.
63.4	99.8	33.6	At1g02970	839453	WEE1 (ARABIDOPSIS WEE1 KINASE HOMOLOG)	Protein kinase that negatively regulates the entry into mitosis.	O.I.	C.G.	H.G.
63.1	99.8	71.1	At5g47950	834846	transferase family protein	F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFO	O.I.	C.G.	H.G.
62.3	99.8	39.6	At1g20370	838625	tRNA pseudouridine synthase family protein	F:pseudouridine synthase activity;P:tRNA processing, pseudouridine synthesis;C:cellular_component unknown;BOMFAP	O.I.	C.G.	H.G.
61.9	99.8	36.1	At2g44510	819058	p21Cip1-binding protein-related	F:molecular_function unknown;P:biological_process unknown;C:nucleolus;MFOP	O.I.	C.G.	H.G.
59.6	99.8	80.7	At5g60250	836147	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding, nucleic acid binding;P:unknown;C:unknown;MFPOB	O.I.	C.G.	H.G.
59.1	99.8	52.3	At5g43310	834349	COP1-interacting protein-related	F:unknown;P:unknown;C:plasma membrane, membrane;MOFPBV	O.I.	C.G.	H.G.
58.8	99.8	73.6	At1g60030	842297	xanthine/uracil permease family protein	F:transmembrane transporter activity;P:transport;C:plasma membrane, membrane;BOMPFAV	O.I.	C.G.	H.G.
57.9	99.8	99.1	At2g02860	814817	SUT2 (SUCROSE TRANSPORTER 2)	encodes a sucrose transporter in sieve elements and a number of sink tissues and cell types. Gene expression is induced by wounding.	O.I.	C.G.	H.G.
57.8	99.8	66.0	At1g33450	840238	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
57.2	99.8	26.2	At4g29170	829038	ATMND1	A homolog of yeast, mouse and human mnd1delta protein. Null mutants exhibit normal vegetative and flower development; however, during prophase I, chromosomes become fragmented resulting in random distribution of the fragments between polyads. Both male and female meiosis are defective and strong accumulation of AtRAD51 was observed in the inflorescence nuclei of mutant plants. Similarly to its yeast and animal homologues, AtMnd1 might play a role in DSB repair during meiosis.	O.I.	C.G.	H.G.
56.9	99.8	74.5	At4g32880	829424	ATHB-8 (HOMEOBOX GENE 8)	member of homeodomain-leucine zipper family, acting as a differentiation-promoting transcription factor of the vascular meristems.	O.I.	C.G.	H.G.
56.5	99.8	66.6	At3g12510	820430	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PB	O.I.	C.G.	H.G.
56.3	99.8	57.3	At1g51580	841583	KH domain-containing protein	F:RNA binding, nucleic acid binding;P:unknown;C:unknown;MPFOBVA	O.I.	C.G.	H.G.
56.2	99.8	170.9	At2g28510	817399	Dof-type zinc finger domain-containing protein	F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleolus;POMFB	O.I.	C.G.	H.G.
54.8	99.8	58.1	At2g28660	817415	copper-binding family protein	F:copper ion binding, metal ion binding;P:copper ion transport, metal ion transport;C:chloroplast;OPMBF	O.I.	C.G.	H.G.
54.6	99.8	23.0	At5g64990	836623	AtRABH1a (Arabidopsis Rab GTPase homolog H1a)	F:GTP binding;P:protein transport, small GTPase mediated signal transduction;C:mitochondrion;MOFPBAV	O.I.	C.G.	H.G.
54.3	99.8	31.5	At3g09070	820060	glycine-rich protein	F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;MOPFBV	O.I.	C.G.	H.G.
54.2	99.8	127.1	At5g14250	831275	COP13 (CONSTITUTIVE PHOTOMORPHOGENIC 13)	Encodes subunit 3 of the COP9 signalosome.	O.I.	C.G.	H.G.
54.1	99.8	198.9	At2g01610	814690	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.
53.8	99.8	208.3	At5g46700	834713	TRN2 (TORNADO 2)	Encodes a transmembrane protein of the tetraspanin (TET) family, one of 17 members found in Arabidopsis. Double mutant analysis showed that TRN1 and TRN2 act in the same pathway. Required for the maintenance of both the radial pattern of tissue differentiation in the root and for the subsequent circumferential pattern within the epidermis.	O.I.	C.G.	H.G.
53.8	99.8	35.5	At5g25580	832633	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOBV	O.I.	C.G.	H.G.
53.2	99.8	40.4	At1g33460	3766895	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
53.2	99.8	34.5	At5g02220	831792	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
52.3	99.8	44.1	At4g01880	828223	methyltransferase	F:methyltransferase activity;P:tRNA processing;C:unknown;MOFPAB	O.I.	C.G.	H.G.
52.1	99.8	55.2	At5g06730	830562	peroxidase, putative	F:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:plasma membrane;PFOBM	O.I.	C.G.	H.G.
52.0	99.8	48.0	At5g24280	832495	-	F:unknown;P:unknown;C:unknown;PMOBF	O.I.	C.G.	H.G.
51.3	99.8	59.9	At3g18610	821392	ATRANGAP1 (RAN GTPASE-ACTIVATING PROTEIN 1)	F:nucleotide binding, nucleic acid binding;P:unknown;C:unknown;MOFBPVA	O.I.	C.G.	H.G.
50.8	99.8	175.8	At2g21790	816715	RNR1 (RIBONUCLEOTIDE REDUCTASE 1)	encodes large subunit of ribonucleotide reductase involved in the production of deoxyribonucleoside triphosphates (dNTPs) for DNA replication and repair	O.I.	C.G.	H.G.
50.5	99.8	47.1	At2g02880	814819	mucin-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFMB	O.I.	C.G.	H.G.
50.4	99.8	181.9	At5g25450	832619	ubiquinol-cytochrome C reductase complex 14 kDa protein, putative	F:ubiquinol-cytochrome-c reductase activity;P:mitochondrial electron transport, ubiquinol to cytochrome c;C:mitochondrion, mitochondrial respiratory chain complex III, membrane;MPFO	O.I.	C.G.	H.G.
50.0	99.8	42.9	At1g79610	844299	sodium proton exchanger, putative (NHX6)	F:solute:hydrogen antiporter activity, sodium:hydrogen antiporter activity;P:cation transport, sodium ion transport, regulation of pH;C:integral to membrane;BMOPFA	O.I.	C.G.	H.G.
48.6	99.8	81.4	At5g61000	836221	replication protein, putative	F:DNA binding, nucleic acid binding;P:DNA replication;C:nucleus;PMOFA	O.I.	C.G.	H.G.
47.9	99.8	59.5	At3g16870	820942	zinc finger (GATA type) family protein	F:transcription factor activity;P:regulation of transcription, DNA-dependent;C:nucleus;FPMO	O.I.	C.G.	H.G.
47.3	99.8	15.2	At1g05490	837051	chr31 (chromatin remodeling 31)	F:helicase activity, DNA binding, ATP binding, nucleic acid binding;P:biological_process unknown;C:unknown;MOBFPVA	O.I.	C.G.	H.G.
46.8	99.8	96.6	At5g05340	830416	peroxidase, putative	F:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:apoplast, cell wall;PFOBM	O.I.	C.G.	H.G.
46.4	99.8	51.0	At4g37490	829904	CYCB1	Cyclin-dependent protein kinase CYCB1;1. Functions as an effector of growth control at G2/M. Regulated by TCP20.	O.I.	C.G.	H.G.
46.3	99.8	20.7	At4g34320	829582	unknown protein	F:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;PBOM	O.I.	C.G.	H.G.
46.2	99.8	25.8	At2g02020	814733	proton-dependent oligopeptide transport (POT) family protein	F:transporter activity;P:oligopeptide transport;C:membrane;BPMOF	O.I.	C.G.	H.G.
46.0	99.8	243.4	At2g44450	819052	BGLU15 (BETA GLUCOSIDASE 15)	F:cation binding, hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:cell wall, plant-type cell wall;BOPMFA	O.I.	C.G.	H.G.
45.5	99.8	33.9	At1g22090	838814	emb2204 (embryo defective 2204)	F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;P	O.I.	C.G.	H.G.
44.6	99.8	122.8	At1g15420	838113	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBV	O.I.	C.G.	H.G.
43.9	99.8	25.2	At5g40840	834084	SYN2	Cohesion family protein SYN2 (SYN2).	O.I.	C.G.	H.G.
43.8	99.8	29.2	At2g45460	819154	forkhead-associated domain-containing protein / FHA domain-containing protein	F:transcription factor activity;P:regulation of transcription, DNA-dependent;C:chloroplast;MOBFPAV	O.I.	C.G.	H.G.
43.7	99.8	111.5	At2g01650	814694	PUX2 (PLANT UBX DOMAIN-CONTAINING PROTEIN 2)	encodes a peripheral membrane protein that contains UBX domain and interacts with AtCDC48 in vitro and co-fractionates with membrane-associated but not soluble AtCDC48 in vivo.	O.I.	C.G.	H.G.
43.7	99.8	14.8	At1g04650	839457	unknown protein	F:unknown;P:unknown;C:cellular_component unknown;POM	O.I.	C.G.	H.G.
43.5	99.8	31.6	At4g29770	829099	-	Target of trans acting-siR480/255.	O.I.	C.G.	H.G.

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GSM ID	GSM133947
Assay name	Murray_2-3_T4-APH_Rep1_ATH1
GSE experiment	GSE5747: Genome-wide cell cycle studies

Microarray experiments to specifically-expressed genes

GSM ID GSM133947 Assay name Murray_2-3_T4-APH_Rep1_ATH1 GSE experiment GSE5747: Genome-wide cell cycle studies

GSM ID GSM133947

Assay name Murray_2-3_T4-APH_Rep1_ATH1

GSE experiment GSE5747: Genome-wide cell cycle studies