CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g18035

Gene name HON4

Module size 92 genes

NF 0.27

%ile 31.1

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

Co-expressed genes

Click gene/probe ID to show a list of genes that are co-expressed with the gene.

VF %ile CC Gene ID Repr. ID Gene name Func. O.I. H.G. S.X. Other DB
1.00 100.0 1.00 At3g18035 821328 HON4 A linker histone like protein O.I. H.G. S.X.
0.44 57.2 0.89 At4g22360 828331 SWIB complex BAF60b domain-containing protein F:molecular_function unknown;P:biological_process unknown;C:unknown;PFMBO O.I. H.G. S.X.
0.42 53.9 0.90 At5g52040 835279 ATRSP41 encodes an arginine/serine-rich splicing factor. transcript is alternatively spliced and is differentially expressed in different tissues (flowers, roots, stems, and leaves) examined. O.I. H.G. S.X.
0.40 50.8 0.91 At1g18450 838425 ATARP4 Encodes a gene similar to actin-related proteins in other organisms. Member of nuclear ARP family of genes. Component of chromatin remodeling complexes, involved in chromatin-mediated gene regulation. Phenotype of the arp4-1 mutant allele revealed partial sterility due to defects in anther development. Targeting the distinct, 3' UTR of AtARP4 transcripts with RNA interference caused a drastic reduction in the level of AtARP4 protein expression, and resulted in strong pleiotropic phenotypes such as altered organization of plant organs, early flowering, delayed flower senescence and high levels of sterility. Western blot analysis and immunolabelling demonstrated a clear correlation between reductions in the level of AtARP4 expression and severity of the phenotypes. O.I. H.G. S.X.
0.39 48.4 0.90 At3g54350 824602 emb1967 (embryo defective 1967) F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;MPOF O.I. H.G. S.X.
0.38 46.7 0.90 At1g06760 837187 histone H1, putative F:DNA binding;P:nucleosome assembly;C:nucleus, nucleosome;BOMFPVA O.I. H.G. S.X.
0.38 46.7 0.89 At5g14170 831267 CHC1 CHC1 is predicted to encode a protein that belongs to the chromodomain remodeling complex. Two RNAi knock-down lines have a dwarf phenotype and reduced rates of Agrobacterium-mediated transformation. The low rate of root-mediated transformation rate may result from altered root morphology or reduced root growth rates. O.I. H.G. S.X.
0.37 45.0 0.90 At5g01020 831918 protein kinase family protein F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:plasma membrane;MPOBFVA O.I. H.G. S.X.
0.37 45.0 0.89 At3g56860 824853 UBP1 interacting protein 2a (UBA2a) encodes a nuclear protein that binds to RNA with a specificity for oligouridylates in vitro. Along with UBP1 and UBA1a, it may act as a component of a complex recognizing U-rich sequences in plant 3'-UTRs and contributing to the stabilization of mRNAs in the nucleus. O.I. H.G. S.X.
0.36 43.6 0.90 At4g32660 829401 AME3 Encodes protein kinase AME3. O.I. H.G. S.X.
0.35 41.6 0.90 At3g33520 823150 ATARP6 Encodes ACTIN-RELATED PROTEIN6 (ARP6), a putative component of a chromatin-remodeling complex. Required for both histone acetylation and methylation of the FLC chromatin in Arabidopsis. Along with PIE1 forms a complex to deposit modified histone H2A.Z at several loci within the genome. This modification alters the expression of the target genes (i.e. FLC, MAF4, MAF6. Located at specific regions of the nuclear periphery. Expression throughout plants shown by in-situ and immunolocalization methods. Mutants show defects in fertility, leaf, flower and inflorescence development and shorter flowering times. O.I. H.G. S.X.
0.35 41.6 0.91 At5g64610 836582 HAM1 (HISTONE ACETYLTRANSFERASE OF THE MYST FAMILY 1) Encodes an enzyme with histone acetyltransferase activity. HAM1 primarily acetylate histone H4, but also display some ability to acetylate H3. Prior acetylation of lysine 5 on histone H4 reduces radioactive acetylation by either HAM1. HAM1 acetylates histone H4 lysine 5. O.I. H.G. S.X.
0.35 41.6 0.90 At5g16505 3770617 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.34 39.8 0.90 At3g06960 819881 PDE320 (PIGMENT DEFECTIVE 320) F:molecular_function unknown;P:acylglycerol transport;C:endoplasmic reticulum, chloroplast;P O.I. H.G. S.X.
0.34 39.8 0.91 At1g48620 841283 HON5 (High Mobility Group Family A 5) This gene is predicted to encodes a histone H1/H5 family member. A plant line expressing an RNAi construct targeted against HON5 shows a reduced level of agrobacterium-mediated root transformation. O.I. H.G. S.X.
0.34 39.8 0.89 At3g22990 821873 LFR (LEAF AND FLOWER RELATED) Armadillo-repeat containing protein. Involved in leaf and flower development. Located in nucleus. Broadly expressed throughout vegetative and floral tissues. O.I. H.G. S.X.
0.34 39.8 0.89 At2g45700 819178 sterile alpha motif (SAM) domain-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPFBA O.I. H.G. S.X.
0.34 39.8 0.89 At4g36960 829850 RNA recognition motif (RRM)-containing protein F:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPOFBA O.I. H.G. S.X.
0.33 38.1 0.90 At4g00830 827998 RNA recognition motif (RRM)-containing protein F:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MOFPBVA O.I. H.G. S.X.
0.33 38.1 0.89 At5g16310 831492 UCH1 F:ubiquitin thiolesterase activity;P:shoot development, shoot morphogenesis, leaf development, ubiquitin-dependent protein catabolic process;C:nucleus, intracellular, cytoplasm;MFOPB O.I. H.G. S.X.
0.33 38.1 0.89 At3g54190 824586 - F:molecular_function unknown;P:biological_process unknown;C:unknown;PO O.I. H.G. S.X.
0.33 38.1 0.90 At1g14510 838013 AL7 (ALFIN-LIKE 7) AL7 encodes a member of the Alfin-Like family of nuclear-localized PhD domain containing homeodomain proteins. Binds to H3K4 di or trimethylated DNA. O.I. H.G. S.X.
0.32 35.7 0.89 At5g09860 830846 nuclear matrix protein-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPA O.I. H.G. S.X.
0.32 35.7 0.89 At3g55000 824665 TON1A (TONNEAU 1) Encodes a protein of unknown function that is involved in cortical microtubule organization. Mutants exhibit abnormal cell growth and patterns of division. TON1A can functionally complement TON1B and their roles appear to be redundant in plants. Encodes a novel protein that is similar to human FOP and OFD1 centrosomal proteins. Localizes to the preprophase band, cytoplasm and cell cortex where it is probably associated with the cortical cytoskeleton. TON1A associates with plant centrins CEN1 and CEN2. O.I. H.G. S.X.
0.32 35.7 0.89 At3g60250 825196 CKB3 Regulatory (beta) subunit of the protein kinase CK2. Involved in regulation of the circadian clock in Arabidopsis O.I. H.G. S.X.
0.32 35.7 0.90 At2g25970 817137 KH domain-containing protein F:RNA binding, nucleic acid binding;P:unknown;C:unknown;MBFOPVA O.I. H.G. S.X.
0.32 35.7 0.90 At5g42820 834293 U2AF35B U2 auxiliary factor small subunit. The atU2AF35b protein and its homolog, atU2AF35a, contain most of the conserved domains of hsU2AF35, including the psiRRM, one RS domain, two zinc fingers, and the two regions for interacting with U2AF large subunit. Both proteins lack the stretch of glycines present in human U2AF35. The sequences are overall 83% identical, and each Arabidopsis homolog shows approximately 70% similarity to hsU2AF35. U2AF(35) homologs were also identified from maize, rice and other plants with large-scale EST projects. Both genes are expressed in all major tissues, with atU2AF(35)a expressed at a higher level than atU2AF(35)b in most tissues. The expression patterns were different in roots: atU2AF(35)b expressed strongly in whole young roots and root tips and atU2AF(35)a limited to root vascular regions. O.I. H.G. S.X.
0.32 35.7 0.90 At3g24010 821986 ING1 (INHIBITOR OF GROWTH 1) ING1 encodes a member of the Inhibitor of Growth family of nuclear-localized PhD domain containing homeodomain proteins. Binds to H3K4 di or trimethylated DNA. O.I. H.G. S.X.
0.31 33.8 0.90 At3g59990 825169 MAP2B (METHIONINE AMINOPEPTIDASE 2B) Encodes a MAP2 like methionine aminopeptidase O.I. H.G. S.X.
0.31 33.8 0.89 At2g47900 819402 AtTLP3 (TUBBY LIKE PROTEIN 3) Member of TLP family O.I. H.G. S.X.
0.31 33.8 0.89 At3g56750 824842 unknown protein F:molecular_function unknown;P:biological_process unknown;C:Golgi apparatus;PO O.I. H.G. S.X.
0.31 33.8 0.89 At2g40930 818691 UBP5 (UBIQUITIN-SPECIFIC PROTEASE 5) Encodes ubiquitin-specific protease with nuclear localization signals that is likely to be involved in ubiquitin-mediated protein degradation. O.I. H.G. S.X.
0.31 33.8 0.89 At5g04280 830307 glycine-rich RNA-binding protein F:RNA binding, zinc ion binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:nucleolus;MPFOBVA O.I. H.G. S.X.
0.31 33.8 0.91 At1g14570 838019 UBX domain-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOB O.I. H.G. S.X.
0.31 33.8 0.91 At1g49480 841372 RTV1 (related to vernalization1 1) F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:cellular_component unknown;PM O.I. H.G. S.X.
0.30 32.1 0.90 At4g32551 829390 LUG (LEUNIG) LEUNIG regulates floral organ identity,gynoecium and ovule development. Negatively regulates AGAMOUS . Encodes a glutamine-rich protein with seven WD repeats similar to transcriptional corepressors. O.I. H.G. S.X.
0.30 32.1 0.89 At5g01160 831742 e-cadherin binding protein-related F:protein binding, zinc ion binding;P:biological_process unknown;C:intracellular;MOFPB O.I. H.G. S.X.
0.30 32.1 0.89 At5g64960 836620 CDKC2 (Cyclin dependent kinase group C 2) Encodes CDKC;2, part of a CDKC kinase complex that is targeted by Cauliflower mosaic virus (CaMV) for transcriptional activation of viral genes. Also regulates plant growth and development. Co-localizes with spliceosomal components in a manner dependent on the transcriptional status of the cells and on CDKC2-kinase activity. Expression of CDKC2 modifies the location of spliceosomal components. O.I. H.G. S.X.
0.30 32.1 0.89 At5g05080 830390 UBC22 (ubiquitin-conjugating enzyme 22) F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:cellular_component unknown;MFOPV O.I. H.G. S.X.
0.30 32.1 0.91 At5g06140 830501 SNX1 (SORTING NEXIN 1) Homolog of yeast retromer subunit VPS5. Part of a retromer-like protein complex involved in endosome to lysosome protein transport. In roots it co-localizes with the PIN2 auxin efflux carrier. Involved in endocytic sorting of membrane proteins including PIN2, BOR1 and BRI1. O.I. H.G. S.X.
0.30 32.1 0.89 At1g54610 841903 protein kinase family protein F:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:plasma membrane;MPOFBVA O.I. H.G. S.X.
0.30 32.1 0.89 At3g22520 821823 unknown protein F:unknown;P:biological_process unknown;C:chloroplast stroma, chloroplast, chloroplast envelope;OMBFPA O.I. H.G. S.X.
0.30 32.1 0.89 At5g28850 833004 calcium-binding EF hand family protein F:calcium ion binding;P:biological_process unknown;C:endomembrane system;MOPF O.I. H.G. S.X.
0.28 30.3 0.89 At1g61010 842393 CPSF73-I (CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 73-I) F:protein binding;P:mRNA polyadenylation;C:mRNA cleavage and polyadenylation specificity factor complex, nucleus;BOMAFPV O.I. H.G. S.X.
0.27 26.2 0.89 At1g54390 841881 PHD finger protein-related ING2 encodes a member of the Inhibitor of Growth family of nuclear-localized PhD domain containing homeodomain proteins. Binds to H3K4 di or trimethylated DNA. O.I. H.G. S.X.
0.27 26.2 0.89 At5g21160 832242 La domain-containing protein / proline-rich family protein F:molecular_function unknown;P:biological_process unknown;C:cytosol, nucleus;MFPBOVA O.I. H.G. S.X.
0.27 26.2 0.90 At2g05230 815071 DNAJ heat shock N-terminal domain-containing protein F:heat shock protein binding;P:protein folding;C:cellular_component unknown;BOMPFAV O.I. H.G. S.X.
0.27 26.2 0.89 At2g25740 817117 ATP-dependent protease La (LON) domain-containing protein F:ATP-dependent peptidase activity;P:N-terminal protein myristoylation, ATP-dependent proteolysis;C:cellular_component unknown;BOMPF O.I. H.G. S.X.
0.27 26.2 0.90 At3g22170 821781 FHY3 (FAR-RED ELONGATED HYPOCOTYLS 3) A component of the PHYA signaling network, mediates the FR-HIR response to far-red light in concert with FAR1. O.I. H.G. S.X.
0.26 24.4 0.89 At4g22140 828303 DNA binding / protein binding / zinc ion binding F:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:cellular_component unknown;MPFO O.I. H.G. S.X.
0.26 24.4 0.89 At2g29080 817456 ftsh3 (FtsH protease 3) encodes an FtsH protease that is localized to the mitochondrion O.I. H.G. S.X.
0.26 24.4 0.89 At1g73840 843720 ESP1 (ENHANCED SILENCING PHENOTYPE 1) Resembles the CstF64 family of RNA processing factors that are conserved between yeast and mammals. In mammals, CstF64 is a component of the CstF complex which is required for mRNA 3'end formation along with other factors. O.I. H.G. S.X.
0.26 24.4 0.89 At1g11930 837744 alanine racemase family protein F:pyridoxal phosphate binding;P:biological_process unknown;C:cellular_component unknown;OBMFPA O.I. H.G. S.X.
0.25 22.6 0.90 At2g38560 818438 TFIIS (TRANSCRIPT ELONGATION FACTOR IIS) Encodes RNA polymerase II transcript elongation factor TFIIS. Complements yeast TFIIS mutation. Mutant plants display essentially normal development, but they flower slightly earlier than the wild type and show clearly reduced seed dormancy. O.I. H.G. S.X.
0.25 22.6 0.90 At4g19150 827653 ankyrin repeat family protein F:protein binding;P:biological_process unknown;C:unknown;MOFBPVA O.I. H.G. S.X.
0.25 22.6 0.91 At2g30620 817612 histone H1.2 F:DNA binding;P:nucleosome assembly;C:nucleolus, nucleus, nucleosome;BMOFPVA O.I. H.G. S.X.
0.25 22.6 0.89 At3g06670 819852 binding F:binding;P:biological_process unknown;C:cellular_component unknown;MOFPBV O.I. H.G. S.X.
0.25 22.6 0.89 At2g28390 817387 SAND family protein F:unknown;P:unknown;C:chloroplast;MFOBPAV O.I. H.G. S.X.
0.25 22.6 0.89 At2g36720 818244 PHD finger transcription factor, putative F:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:nucleus;MPFO O.I. H.G. S.X.
0.25 22.6 0.89 At3g51310 824294 VPS35C (VPS35 HOMOLOG C) Homolog of yeast retromer subunit VPS35. Part of a retromer-like protein complex involved in endosome to lysosome protein transport. O.I. H.G. S.X.
0.25 22.6 0.89 At3g12130 820388 KH domain-containing protein / zinc finger (CCCH type) family protein F:transcription factor activity, nucleic acid binding;P:regulation of transcription;C:unknown;MPOFB O.I. H.G. S.X.
0.24 20.7 0.89 At1g02080 839244 transcriptional regulator-related F:transcription regulator activity;P:unknown;C:membrane;MOFBP O.I. H.G. S.X.
0.24 20.7 0.89 At4g20280 827775 TAF11 (TBP-ASSOCIATED FACTOR 11) Encodes TAF11, a putative TBP-associated factor (TBP: TATA binding protein). O.I. H.G. S.X.
0.24 20.7 0.90 At3g55460 824712 SCL30 encodes an SC35-like splicing factor that is localized to nuclear specks. O.I. H.G. S.X.
0.24 20.7 0.89 At2g21230 816660 bZIP family transcription factor F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus, chloroplast;OPMBFAV O.I. H.G. S.X.
0.24 20.7 0.89 At4g27690 828883 VPS26B (VACUOLAR PROTEIN SORTING 26B) F:molecular_function unknown;P:intracellular protein transport, vacuolar transport, retrograde transport, endosome to Golgi;C:retromer complex;MOFP O.I. H.G. S.X.
0.23 19.3 0.89 At4g15415 827211 ATB' GAMMA B' regulatory subunit of PP2A (AtB'gamma) O.I. H.G. S.X.
0.23 19.3 0.89 At1g43190 840918 polypyrimidine tract-binding protein, putative / heterogeneous nuclear ribonucleoprotein, putative F:RNA binding, nucleotide binding, nucleic acid binding;P:mRNA processing;C:nucleus;MPOF O.I. H.G. S.X.
0.23 19.3 0.89 At5g04240 830303 ELF6 (EARLY FLOWERING 6) Early Flowering 6 (ELF6) encodes a Jumonji N/C and zinc finger domain-containing protein that acts as a repressor in the photoperiod pathway. ELF6 interacts with BES1 in a Y2H assay, in vitro, and in Arabidosis protoplasts (based on BiFC). ELF6 may play a role in brassinosteroid signaling by affecting histone methylation in the promoters of BR-responsive genes. O.I. H.G. S.X.
0.23 19.3 0.89 At5g46210 834663 CUL4 (CULLIN4) Arabidopsis CULLIN4 (CUL4) forms an E3 ubiquitin ligase with the CDD complex and a common catalytic subunit RBX1 in mediating light control of development. This CUL4-based E3 ligase is essential for the repression of photomorphogenesis. The partial loss of CUL4 function resulted in a constitutive photomorphogenic phenotype with respect to morphogenesis and light-regulated gene expression. CUL4 exhibits a synergistic genetic interaction with COP10 and DET1. O.I. H.G. S.X.
0.23 19.3 0.89 At3g05530 819718 RPT5A (REGULATORY PARTICLE TRIPLE-A ATPASE 5A) Encodes RPT5a (Regulatory Particle 5a), one of the six AAA-ATPases of the proteasome regulatory particle. Essential for gametophyte development. In Arabidopsis, the RPT5 subunit is encoded by two highly homologous genes, RPT5a and RPT5b. RPT5a and RPT5b show accession-dependent functional redundancy. In Wassilewskija (Ws) accession: mutant alleles of RPT5a displayed 50% pollen lethality, indicating that RPT5a is essential for male gametophyte development. In the Columbia (Col) accession, a rpt5a mutant allele did not display such a phenotype because the RPT5b Col allele complements the rpt5a defect in the male gametophyte, whereas the RPT5b Ws allele does not. Double rpt5a rpt5b mutants in Col background showed a complete male and female gametophyte lethal phenotype. O.I. H.G. S.X.
0.23 19.3 0.89 At3g61600 825333 ATPOB1 POZ/BTB containing-protein AtPOB1 O.I. H.G. S.X.
0.23 19.3 0.89 At5g17070 831570 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFO O.I. H.G. S.X.
0.23 19.3 0.89 At5g63110 836431 HDA6 (HISTONE DEACETYLASE 6) RPD3-like histone deacetylase. HDA6 mutations specifically increase the expression of auxin-responsive transgenes, suggesting a role in transgene silencing. O.I. H.G. S.X.
0.23 19.3 0.89 At4g05420 825890 DDB1A (DAMAGED DNA BINDING PROTEIN 1A) Structurally similar to damaged DNA binding proteins.DDB1a is part of a 350 KDa nuclear localized DET1 protein complex. This complex may physically interact with histone tails and while bound to chromatin- repress transcription of genes involved in photomorphogenesis. O.I. H.G. S.X.
0.22 17.5 0.89 At5g19330 832053 armadillo/beta-catenin repeat family protein / BTB/POZ domain-containing protein F:protein binding, binding;P:unknown;C:plasma membrane;MPOFVBA O.I. H.G. S.X.
0.21 15.8 0.89 At5g13570 831201 DCP2 (DECAPPING 2) Encodes DCP2 with mRNA decapping activity. DCP2 forms a mRNA decapping complex with DCP1 (At1g08370) and VCS (VARICOSE) (At3g13300). Recombinant DCP2 is enzymatically active in vitro, generating from capped mRNAs m7GDP, and 5�-phosphorylated mRNAs. DCP1, DCP2 and VCS colocalize in cytoplasmic loci, which are putative Arabidopsis mRNA processing bodies. Null mutants of DCP1, DCP2, and VCS accumulate capped mRNAs with a reduced degradation rate. These mutants also share a similar lethal phenotype at the seedling cotyledon stage, with disorganized veins, swollen root hairs, and altered epidermal cell morphology. The protein was shown by immunoprecipitation not to interact with DCP1. O.I. H.G. S.X.
0.21 15.8 0.89 At1g04950 839370 TAF6 (TBP-ASSOCIATED FACTOR 6) Encodes one of two Arabidopsis proteins with significant similarity to the histone fold TBP-associated factor TAF6. Mutants are embryo lethal and transmission of the mutant allele through the male gametophyte is significantly reduced. This is due to reduced pollen tube growth of the mutant. O.I. H.G. S.X.
0.20 14.4 0.89 At5g55230 835616 ATMAP65-1 (MICROTUBULE-ASSOCIATED PROTEINS 65-1) Binds and bundles microtubules. Plays a role in stabilizing anti-parallel microtubules in the central spindle at anaphase to early cytokinesis but is not essential at the midline of the phragmoplast at later stages. The timing with which the MAP65-1 was targeted to the spindle appears to be regulated by a phosphorylation sensitive switch. Enhances microtubule polymerization, promotes nucleation and stabilizes microtubules against cold treatment and dilution. O.I. H.G. S.X.
0.20 14.4 0.89 At1g52740 841707 HTA9 (HISTONE H2A PROTEIN 9) Encodes HTA9, a histone H2A protein. O.I. H.G. S.X.
0.19 12.7 0.89 At3g05090 819671 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFOBPAV O.I. H.G. S.X.
0.19 12.7 0.89 At4g40030 830164 histone H3.2 F:DNA binding;P:nucleosome assembly;C:nucleus, nucleosome;MFPO O.I. H.G. S.X.
0.18 11.4 0.89 At2g45810 819189 DEAD/DEAH box helicase, putative F:helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding;P:unknown;C:cellular_component unknown;OMBFPAV O.I. H.G. S.X.
0.18 11.4 0.89 At2g43770 818980 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MFOBPAV O.I. H.G. S.X.
0.17 10.2 0.89 At5g65960 836726 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOF O.I. H.G. S.X.
0.17 10.2 0.89 At5g42560 834262 abscisic acid-responsive HVA22 family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOBV O.I. H.G. S.X.
0.17 10.2 0.89 At1g72550 843587 tRNA synthetase beta subunit family protein F:phenylalanine-tRNA ligase activity, RNA binding, magnesium ion binding, nucleotide binding, ATP binding;P:phenylalanyl-tRNA aminoacylation, translation;C:phenylalanine-tRNA ligase complex, cytoplasm;BOMAFP O.I. H.G. S.X.
0.16 8.8 0.89 At2g30980 817649 ASKdZeta (Arabidopsis SHAGGY-related protein kinase dZeta) Encodes a GSK3-like protein kinase. This protein can interact with the BZR1 protein involved in brassinosteroid-mediated signaling in a Y2H assay and promotes BZR1 phosphorylation in protoplasts. O.I. H.G. S.X.
0.16 8.8 0.90 At2g21240 816663 BPC4 (BASIC PENTACYSTEINE 4) F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;PMB O.I. H.G. S.X.
0.16 8.8 0.89 At4g29870 829109 - F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;MPO O.I. H.G. S.X.
0.15 7.8 0.89 At1g27600 839652 glycosyl transferase family 43 protein F:transferase activity, transferring glycosyl groups;P:protein amino acid glycosylation;C:membrane;MPO O.I. H.G. S.X.
0.14 6.8 0.89 At3g10850 820255 GLY2 glyoxalase II cytoplasmic isozyme (Glx2-2) mRNA, complete O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
1.00	100.0	1.00	At3g18035	821328	HON4	A linker histone like protein	O.I.	H.G.	S.X.
0.44	57.2	0.89	At4g22360	828331	SWIB complex BAF60b domain-containing protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;PFMBO	O.I.	H.G.	S.X.
0.42	53.9	0.90	At5g52040	835279	ATRSP41	encodes an arginine/serine-rich splicing factor. transcript is alternatively spliced and is differentially expressed in different tissues (flowers, roots, stems, and leaves) examined.	O.I.	H.G.	S.X.
0.40	50.8	0.91	At1g18450	838425	ATARP4	Encodes a gene similar to actin-related proteins in other organisms. Member of nuclear ARP family of genes. Component of chromatin remodeling complexes, involved in chromatin-mediated gene regulation. Phenotype of the arp4-1 mutant allele revealed partial sterility due to defects in anther development. Targeting the distinct, 3' UTR of AtARP4 transcripts with RNA interference caused a drastic reduction in the level of AtARP4 protein expression, and resulted in strong pleiotropic phenotypes such as altered organization of plant organs, early flowering, delayed flower senescence and high levels of sterility. Western blot analysis and immunolabelling demonstrated a clear correlation between reductions in the level of AtARP4 expression and severity of the phenotypes.	O.I.	H.G.	S.X.
0.39	48.4	0.90	At3g54350	824602	emb1967 (embryo defective 1967)	F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;MPOF	O.I.	H.G.	S.X.
0.38	46.7	0.90	At1g06760	837187	histone H1, putative	F:DNA binding;P:nucleosome assembly;C:nucleus, nucleosome;BOMFPVA	O.I.	H.G.	S.X.
0.38	46.7	0.89	At5g14170	831267	CHC1	CHC1 is predicted to encode a protein that belongs to the chromodomain remodeling complex. Two RNAi knock-down lines have a dwarf phenotype and reduced rates of Agrobacterium-mediated transformation. The low rate of root-mediated transformation rate may result from altered root morphology or reduced root growth rates.	O.I.	H.G.	S.X.
0.37	45.0	0.90	At5g01020	831918	protein kinase family protein	F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:plasma membrane;MPOBFVA	O.I.	H.G.	S.X.
0.37	45.0	0.89	At3g56860	824853	UBP1 interacting protein 2a (UBA2a)	encodes a nuclear protein that binds to RNA with a specificity for oligouridylates in vitro. Along with UBP1 and UBA1a, it may act as a component of a complex recognizing U-rich sequences in plant 3'-UTRs and contributing to the stabilization of mRNAs in the nucleus.	O.I.	H.G.	S.X.
0.36	43.6	0.90	At4g32660	829401	AME3	Encodes protein kinase AME3.	O.I.	H.G.	S.X.
0.35	41.6	0.90	At3g33520	823150	ATARP6	Encodes ACTIN-RELATED PROTEIN6 (ARP6), a putative component of a chromatin-remodeling complex. Required for both histone acetylation and methylation of the FLC chromatin in Arabidopsis. Along with PIE1 forms a complex to deposit modified histone H2A.Z at several loci within the genome. This modification alters the expression of the target genes (i.e. FLC, MAF4, MAF6. Located at specific regions of the nuclear periphery. Expression throughout plants shown by in-situ and immunolocalization methods. Mutants show defects in fertility, leaf, flower and inflorescence development and shorter flowering times.	O.I.	H.G.	S.X.
0.35	41.6	0.91	At5g64610	836582	HAM1 (HISTONE ACETYLTRANSFERASE OF THE MYST FAMILY 1)	Encodes an enzyme with histone acetyltransferase activity. HAM1 primarily acetylate histone H4, but also display some ability to acetylate H3. Prior acetylation of lysine 5 on histone H4 reduces radioactive acetylation by either HAM1. HAM1 acetylates histone H4 lysine 5.	O.I.	H.G.	S.X.
0.35	41.6	0.90	At5g16505	3770617	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.34	39.8	0.90	At3g06960	819881	PDE320 (PIGMENT DEFECTIVE 320)	F:molecular_function unknown;P:acylglycerol transport;C:endoplasmic reticulum, chloroplast;P	O.I.	H.G.	S.X.
0.34	39.8	0.91	At1g48620	841283	HON5 (High Mobility Group Family A 5)	This gene is predicted to encodes a histone H1/H5 family member. A plant line expressing an RNAi construct targeted against HON5 shows a reduced level of agrobacterium-mediated root transformation.	O.I.	H.G.	S.X.
0.34	39.8	0.89	At3g22990	821873	LFR (LEAF AND FLOWER RELATED)	Armadillo-repeat containing protein. Involved in leaf and flower development. Located in nucleus. Broadly expressed throughout vegetative and floral tissues.	O.I.	H.G.	S.X.
0.34	39.8	0.89	At2g45700	819178	sterile alpha motif (SAM) domain-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPFBA	O.I.	H.G.	S.X.
0.34	39.8	0.89	At4g36960	829850	RNA recognition motif (RRM)-containing protein	F:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPOFBA	O.I.	H.G.	S.X.
0.33	38.1	0.90	At4g00830	827998	RNA recognition motif (RRM)-containing protein	F:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MOFPBVA	O.I.	H.G.	S.X.
0.33	38.1	0.89	At5g16310	831492	UCH1	F:ubiquitin thiolesterase activity;P:shoot development, shoot morphogenesis, leaf development, ubiquitin-dependent protein catabolic process;C:nucleus, intracellular, cytoplasm;MFOPB	O.I.	H.G.	S.X.
0.33	38.1	0.89	At3g54190	824586	-	F:molecular_function unknown;P:biological_process unknown;C:unknown;PO	O.I.	H.G.	S.X.
0.33	38.1	0.90	At1g14510	838013	AL7 (ALFIN-LIKE 7)	AL7 encodes a member of the Alfin-Like family of nuclear-localized PhD domain containing homeodomain proteins. Binds to H3K4 di or trimethylated DNA.	O.I.	H.G.	S.X.
0.32	35.7	0.89	At5g09860	830846	nuclear matrix protein-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPA	O.I.	H.G.	S.X.
0.32	35.7	0.89	At3g55000	824665	TON1A (TONNEAU 1)	Encodes a protein of unknown function that is involved in cortical microtubule organization. Mutants exhibit abnormal cell growth and patterns of division. TON1A can functionally complement TON1B and their roles appear to be redundant in plants. Encodes a novel protein that is similar to human FOP and OFD1 centrosomal proteins. Localizes to the preprophase band, cytoplasm and cell cortex where it is probably associated with the cortical cytoskeleton. TON1A associates with plant centrins CEN1 and CEN2.	O.I.	H.G.	S.X.
0.32	35.7	0.89	At3g60250	825196	CKB3	Regulatory (beta) subunit of the protein kinase CK2. Involved in regulation of the circadian clock in Arabidopsis	O.I.	H.G.	S.X.
0.32	35.7	0.90	At2g25970	817137	KH domain-containing protein	F:RNA binding, nucleic acid binding;P:unknown;C:unknown;MBFOPVA	O.I.	H.G.	S.X.
0.32	35.7	0.90	At5g42820	834293	U2AF35B	U2 auxiliary factor small subunit. The atU2AF35b protein and its homolog, atU2AF35a, contain most of the conserved domains of hsU2AF35, including the psiRRM, one RS domain, two zinc fingers, and the two regions for interacting with U2AF large subunit. Both proteins lack the stretch of glycines present in human U2AF35. The sequences are overall 83% identical, and each Arabidopsis homolog shows approximately 70% similarity to hsU2AF35. U2AF(35) homologs were also identified from maize, rice and other plants with large-scale EST projects. Both genes are expressed in all major tissues, with atU2AF(35)a expressed at a higher level than atU2AF(35)b in most tissues. The expression patterns were different in roots: atU2AF(35)b expressed strongly in whole young roots and root tips and atU2AF(35)a limited to root vascular regions.	O.I.	H.G.	S.X.
0.32	35.7	0.90	At3g24010	821986	ING1 (INHIBITOR OF GROWTH 1)	ING1 encodes a member of the Inhibitor of Growth family of nuclear-localized PhD domain containing homeodomain proteins. Binds to H3K4 di or trimethylated DNA.	O.I.	H.G.	S.X.
0.31	33.8	0.90	At3g59990	825169	MAP2B (METHIONINE AMINOPEPTIDASE 2B)	Encodes a MAP2 like methionine aminopeptidase	O.I.	H.G.	S.X.
0.31	33.8	0.89	At2g47900	819402	AtTLP3 (TUBBY LIKE PROTEIN 3)	Member of TLP family	O.I.	H.G.	S.X.
0.31	33.8	0.89	At3g56750	824842	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:Golgi apparatus;PO	O.I.	H.G.	S.X.
0.31	33.8	0.89	At2g40930	818691	UBP5 (UBIQUITIN-SPECIFIC PROTEASE 5)	Encodes ubiquitin-specific protease with nuclear localization signals that is likely to be involved in ubiquitin-mediated protein degradation.	O.I.	H.G.	S.X.
0.31	33.8	0.89	At5g04280	830307	glycine-rich RNA-binding protein	F:RNA binding, zinc ion binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:nucleolus;MPFOBVA	O.I.	H.G.	S.X.
0.31	33.8	0.91	At1g14570	838019	UBX domain-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOB	O.I.	H.G.	S.X.
0.31	33.8	0.91	At1g49480	841372	RTV1 (related to vernalization1 1)	F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:cellular_component unknown;PM	O.I.	H.G.	S.X.
0.30	32.1	0.90	At4g32551	829390	LUG (LEUNIG)	LEUNIG regulates floral organ identity,gynoecium and ovule development. Negatively regulates AGAMOUS . Encodes a glutamine-rich protein with seven WD repeats similar to transcriptional corepressors.	O.I.	H.G.	S.X.
0.30	32.1	0.89	At5g01160	831742	e-cadherin binding protein-related	F:protein binding, zinc ion binding;P:biological_process unknown;C:intracellular;MOFPB	O.I.	H.G.	S.X.
0.30	32.1	0.89	At5g64960	836620	CDKC2 (Cyclin dependent kinase group C 2)	Encodes CDKC;2, part of a CDKC kinase complex that is targeted by Cauliflower mosaic virus (CaMV) for transcriptional activation of viral genes. Also regulates plant growth and development. Co-localizes with spliceosomal components in a manner dependent on the transcriptional status of the cells and on CDKC2-kinase activity. Expression of CDKC2 modifies the location of spliceosomal components.	O.I.	H.G.	S.X.
0.30	32.1	0.89	At5g05080	830390	UBC22 (ubiquitin-conjugating enzyme 22)	F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:cellular_component unknown;MFOPV	O.I.	H.G.	S.X.
0.30	32.1	0.91	At5g06140	830501	SNX1 (SORTING NEXIN 1)	Homolog of yeast retromer subunit VPS5. Part of a retromer-like protein complex involved in endosome to lysosome protein transport. In roots it co-localizes with the PIN2 auxin efflux carrier. Involved in endocytic sorting of membrane proteins including PIN2, BOR1 and BRI1.	O.I.	H.G.	S.X.
0.30	32.1	0.89	At1g54610	841903	protein kinase family protein	F:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:plasma membrane;MPOFBVA	O.I.	H.G.	S.X.
0.30	32.1	0.89	At3g22520	821823	unknown protein	F:unknown;P:biological_process unknown;C:chloroplast stroma, chloroplast, chloroplast envelope;OMBFPA	O.I.	H.G.	S.X.
0.30	32.1	0.89	At5g28850	833004	calcium-binding EF hand family protein	F:calcium ion binding;P:biological_process unknown;C:endomembrane system;MOPF	O.I.	H.G.	S.X.
0.28	30.3	0.89	At1g61010	842393	CPSF73-I (CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 73-I)	F:protein binding;P:mRNA polyadenylation;C:mRNA cleavage and polyadenylation specificity factor complex, nucleus;BOMAFPV	O.I.	H.G.	S.X.
0.27	26.2	0.89	At1g54390	841881	PHD finger protein-related	ING2 encodes a member of the Inhibitor of Growth family of nuclear-localized PhD domain containing homeodomain proteins. Binds to H3K4 di or trimethylated DNA.	O.I.	H.G.	S.X.
0.27	26.2	0.89	At5g21160	832242	La domain-containing protein / proline-rich family protein	F:molecular_function unknown;P:biological_process unknown;C:cytosol, nucleus;MFPBOVA	O.I.	H.G.	S.X.
0.27	26.2	0.90	At2g05230	815071	DNAJ heat shock N-terminal domain-containing protein	F:heat shock protein binding;P:protein folding;C:cellular_component unknown;BOMPFAV	O.I.	H.G.	S.X.
0.27	26.2	0.89	At2g25740	817117	ATP-dependent protease La (LON) domain-containing protein	F:ATP-dependent peptidase activity;P:N-terminal protein myristoylation, ATP-dependent proteolysis;C:cellular_component unknown;BOMPF	O.I.	H.G.	S.X.
0.27	26.2	0.90	At3g22170	821781	FHY3 (FAR-RED ELONGATED HYPOCOTYLS 3)	A component of the PHYA signaling network, mediates the FR-HIR response to far-red light in concert with FAR1.	O.I.	H.G.	S.X.
0.26	24.4	0.89	At4g22140	828303	DNA binding / protein binding / zinc ion binding	F:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:cellular_component unknown;MPFO	O.I.	H.G.	S.X.
0.26	24.4	0.89	At2g29080	817456	ftsh3 (FtsH protease 3)	encodes an FtsH protease that is localized to the mitochondrion	O.I.	H.G.	S.X.
0.26	24.4	0.89	At1g73840	843720	ESP1 (ENHANCED SILENCING PHENOTYPE 1)	Resembles the CstF64 family of RNA processing factors that are conserved between yeast and mammals. In mammals, CstF64 is a component of the CstF complex which is required for mRNA 3'end formation along with other factors.	O.I.	H.G.	S.X.
0.26	24.4	0.89	At1g11930	837744	alanine racemase family protein	F:pyridoxal phosphate binding;P:biological_process unknown;C:cellular_component unknown;OBMFPA	O.I.	H.G.	S.X.
0.25	22.6	0.90	At2g38560	818438	TFIIS (TRANSCRIPT ELONGATION FACTOR IIS)	Encodes RNA polymerase II transcript elongation factor TFIIS. Complements yeast TFIIS mutation. Mutant plants display essentially normal development, but they flower slightly earlier than the wild type and show clearly reduced seed dormancy.	O.I.	H.G.	S.X.
0.25	22.6	0.90	At4g19150	827653	ankyrin repeat family protein	F:protein binding;P:biological_process unknown;C:unknown;MOFBPVA	O.I.	H.G.	S.X.
0.25	22.6	0.91	At2g30620	817612	histone H1.2	F:DNA binding;P:nucleosome assembly;C:nucleolus, nucleus, nucleosome;BMOFPVA	O.I.	H.G.	S.X.
0.25	22.6	0.89	At3g06670	819852	binding	F:binding;P:biological_process unknown;C:cellular_component unknown;MOFPBV	O.I.	H.G.	S.X.
0.25	22.6	0.89	At2g28390	817387	SAND family protein	F:unknown;P:unknown;C:chloroplast;MFOBPAV	O.I.	H.G.	S.X.
0.25	22.6	0.89	At2g36720	818244	PHD finger transcription factor, putative	F:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:nucleus;MPFO	O.I.	H.G.	S.X.
0.25	22.6	0.89	At3g51310	824294	VPS35C (VPS35 HOMOLOG C)	Homolog of yeast retromer subunit VPS35. Part of a retromer-like protein complex involved in endosome to lysosome protein transport.	O.I.	H.G.	S.X.
0.25	22.6	0.89	At3g12130	820388	KH domain-containing protein / zinc finger (CCCH type) family protein	F:transcription factor activity, nucleic acid binding;P:regulation of transcription;C:unknown;MPOFB	O.I.	H.G.	S.X.
0.24	20.7	0.89	At1g02080	839244	transcriptional regulator-related	F:transcription regulator activity;P:unknown;C:membrane;MOFBP	O.I.	H.G.	S.X.
0.24	20.7	0.89	At4g20280	827775	TAF11 (TBP-ASSOCIATED FACTOR 11)	Encodes TAF11, a putative TBP-associated factor (TBP: TATA binding protein).	O.I.	H.G.	S.X.
0.24	20.7	0.90	At3g55460	824712	SCL30	encodes an SC35-like splicing factor that is localized to nuclear specks.	O.I.	H.G.	S.X.
0.24	20.7	0.89	At2g21230	816660	bZIP family transcription factor	F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus, chloroplast;OPMBFAV	O.I.	H.G.	S.X.
0.24	20.7	0.89	At4g27690	828883	VPS26B (VACUOLAR PROTEIN SORTING 26B)	F:molecular_function unknown;P:intracellular protein transport, vacuolar transport, retrograde transport, endosome to Golgi;C:retromer complex;MOFP	O.I.	H.G.	S.X.
0.23	19.3	0.89	At4g15415	827211	ATB' GAMMA	B' regulatory subunit of PP2A (AtB'gamma)	O.I.	H.G.	S.X.
0.23	19.3	0.89	At1g43190	840918	polypyrimidine tract-binding protein, putative / heterogeneous nuclear ribonucleoprotein, putative	F:RNA binding, nucleotide binding, nucleic acid binding;P:mRNA processing;C:nucleus;MPOF	O.I.	H.G.	S.X.
0.23	19.3	0.89	At5g04240	830303	ELF6 (EARLY FLOWERING 6)	Early Flowering 6 (ELF6) encodes a Jumonji N/C and zinc finger domain-containing protein that acts as a repressor in the photoperiod pathway. ELF6 interacts with BES1 in a Y2H assay, in vitro, and in Arabidosis protoplasts (based on BiFC). ELF6 may play a role in brassinosteroid signaling by affecting histone methylation in the promoters of BR-responsive genes.	O.I.	H.G.	S.X.
0.23	19.3	0.89	At5g46210	834663	CUL4 (CULLIN4)	Arabidopsis CULLIN4 (CUL4) forms an E3 ubiquitin ligase with the CDD complex and a common catalytic subunit RBX1 in mediating light control of development. This CUL4-based E3 ligase is essential for the repression of photomorphogenesis. The partial loss of CUL4 function resulted in a constitutive photomorphogenic phenotype with respect to morphogenesis and light-regulated gene expression. CUL4 exhibits a synergistic genetic interaction with COP10 and DET1.	O.I.	H.G.	S.X.
0.23	19.3	0.89	At3g05530	819718	RPT5A (REGULATORY PARTICLE TRIPLE-A ATPASE 5A)	Encodes RPT5a (Regulatory Particle 5a), one of the six AAA-ATPases of the proteasome regulatory particle. Essential for gametophyte development. In Arabidopsis, the RPT5 subunit is encoded by two highly homologous genes, RPT5a and RPT5b. RPT5a and RPT5b show accession-dependent functional redundancy. In Wassilewskija (Ws) accession: mutant alleles of RPT5a displayed 50% pollen lethality, indicating that RPT5a is essential for male gametophyte development. In the Columbia (Col) accession, a rpt5a mutant allele did not display such a phenotype because the RPT5b Col allele complements the rpt5a defect in the male gametophyte, whereas the RPT5b Ws allele does not. Double rpt5a rpt5b mutants in Col background showed a complete male and female gametophyte lethal phenotype.	O.I.	H.G.	S.X.
0.23	19.3	0.89	At3g61600	825333	ATPOB1	POZ/BTB containing-protein AtPOB1	O.I.	H.G.	S.X.
0.23	19.3	0.89	At5g17070	831570	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFO	O.I.	H.G.	S.X.
0.23	19.3	0.89	At5g63110	836431	HDA6 (HISTONE DEACETYLASE 6)	RPD3-like histone deacetylase. HDA6 mutations specifically increase the expression of auxin-responsive transgenes, suggesting a role in transgene silencing.	O.I.	H.G.	S.X.
0.23	19.3	0.89	At4g05420	825890	DDB1A (DAMAGED DNA BINDING PROTEIN 1A)	Structurally similar to damaged DNA binding proteins.DDB1a is part of a 350 KDa nuclear localized DET1 protein complex. This complex may physically interact with histone tails and while bound to chromatin- repress transcription of genes involved in photomorphogenesis.	O.I.	H.G.	S.X.
0.22	17.5	0.89	At5g19330	832053	armadillo/beta-catenin repeat family protein / BTB/POZ domain-containing protein	F:protein binding, binding;P:unknown;C:plasma membrane;MPOFVBA	O.I.	H.G.	S.X.
0.21	15.8	0.89	At5g13570	831201	DCP2 (DECAPPING 2)	Encodes DCP2 with mRNA decapping activity. DCP2 forms a mRNA decapping complex with DCP1 (At1g08370) and VCS (VARICOSE) (At3g13300). Recombinant DCP2 is enzymatically active in vitro, generating from capped mRNAs m7GDP, and 5�-phosphorylated mRNAs. DCP1, DCP2 and VCS colocalize in cytoplasmic loci, which are putative Arabidopsis mRNA processing bodies. Null mutants of DCP1, DCP2, and VCS accumulate capped mRNAs with a reduced degradation rate. These mutants also share a similar lethal phenotype at the seedling cotyledon stage, with disorganized veins, swollen root hairs, and altered epidermal cell morphology. The protein was shown by immunoprecipitation not to interact with DCP1.	O.I.	H.G.	S.X.
0.21	15.8	0.89	At1g04950	839370	TAF6 (TBP-ASSOCIATED FACTOR 6)	Encodes one of two Arabidopsis proteins with significant similarity to the histone fold TBP-associated factor TAF6. Mutants are embryo lethal and transmission of the mutant allele through the male gametophyte is significantly reduced. This is due to reduced pollen tube growth of the mutant.	O.I.	H.G.	S.X.
0.20	14.4	0.89	At5g55230	835616	ATMAP65-1 (MICROTUBULE-ASSOCIATED PROTEINS 65-1)	Binds and bundles microtubules. Plays a role in stabilizing anti-parallel microtubules in the central spindle at anaphase to early cytokinesis but is not essential at the midline of the phragmoplast at later stages. The timing with which the MAP65-1 was targeted to the spindle appears to be regulated by a phosphorylation sensitive switch. Enhances microtubule polymerization, promotes nucleation and stabilizes microtubules against cold treatment and dilution.	O.I.	H.G.	S.X.
0.20	14.4	0.89	At1g52740	841707	HTA9 (HISTONE H2A PROTEIN 9)	Encodes HTA9, a histone H2A protein.	O.I.	H.G.	S.X.
0.19	12.7	0.89	At3g05090	819671	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFOBPAV	O.I.	H.G.	S.X.
0.19	12.7	0.89	At4g40030	830164	histone H3.2	F:DNA binding;P:nucleosome assembly;C:nucleus, nucleosome;MFPO	O.I.	H.G.	S.X.
0.18	11.4	0.89	At2g45810	819189	DEAD/DEAH box helicase, putative	F:helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding;P:unknown;C:cellular_component unknown;OMBFPAV	O.I.	H.G.	S.X.
0.18	11.4	0.89	At2g43770	818980	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MFOBPAV	O.I.	H.G.	S.X.
0.17	10.2	0.89	At5g65960	836726	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOF	O.I.	H.G.	S.X.
0.17	10.2	0.89	At5g42560	834262	abscisic acid-responsive HVA22 family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOBV	O.I.	H.G.	S.X.
0.17	10.2	0.89	At1g72550	843587	tRNA synthetase beta subunit family protein	F:phenylalanine-tRNA ligase activity, RNA binding, magnesium ion binding, nucleotide binding, ATP binding;P:phenylalanyl-tRNA aminoacylation, translation;C:phenylalanine-tRNA ligase complex, cytoplasm;BOMAFP	O.I.	H.G.	S.X.
0.16	8.8	0.89	At2g30980	817649	ASKdZeta (Arabidopsis SHAGGY-related protein kinase dZeta)	Encodes a GSK3-like protein kinase. This protein can interact with the BZR1 protein involved in brassinosteroid-mediated signaling in a Y2H assay and promotes BZR1 phosphorylation in protoplasts.	O.I.	H.G.	S.X.
0.16	8.8	0.90	At2g21240	816663	BPC4 (BASIC PENTACYSTEINE 4)	F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;PMB	O.I.	H.G.	S.X.
0.16	8.8	0.89	At4g29870	829109	-	F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;MPO	O.I.	H.G.	S.X.
0.15	7.8	0.89	At1g27600	839652	glycosyl transferase family 43 protein	F:transferase activity, transferring glycosyl groups;P:protein amino acid glycosylation;C:membrane;MPO	O.I.	H.G.	S.X.
0.14	6.8	0.89	At3g10850	820255	GLY2	glyoxalase II cytoplasmic isozyme (Glx2-2) mRNA, complete	O.I.	H.G.	S.X.

Click More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
48.0 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.4 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.2 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
46.9 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.0 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.9 99.8 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
43.8 99.8 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
43.4 99.8 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
42.1 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.0 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
41.6 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
41.4 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
41.3 99.8 GSM184556 Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
40.9 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.4 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.6 99.7 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
36.4 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
35.5 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.8 99.7 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.6 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.8 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.2 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
31.2 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
28.8 99.7 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
28.3 99.7 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
25.8 99.7 GSM184551 Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
17.0 99.5 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
11.7 99.3 GSM133775 Lindsey_1-27_torpedo-meristem_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.5 99.3 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.4 99.2 GSM133957 Fukuda_1-2_0B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.3 99.1 E-MEXP-1474-raw-cel-1593932929
9.3 99.1 E-MEXP-1474-raw-cel-1593932801
9.1 99.1 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
48.0	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.4	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.2	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
46.9	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.0	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.9	99.8	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
43.8	99.8	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
43.4	99.8	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
42.1	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.0	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
41.6	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
41.4	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
41.3	99.8	GSM184556	Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
40.9	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.4	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.6	99.7	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
36.4	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.5	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.8	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.6	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.8	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.2	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
31.2	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
28.8	99.7	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
28.3	99.7	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
25.8	99.7	GSM184551	Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
17.0	99.5	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
11.7	99.3	GSM133775	Lindsey_1-27_torpedo-meristem_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.5	99.3	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.4	99.2	GSM133957	Fukuda_1-2_0B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.3	99.1	E-MEXP-1474-raw-cel-1593932929
9.3	99.1	E-MEXP-1474-raw-cel-1593932801
9.1	99.1	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.067 5 GO:0006334 The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
0.047 4 GO:0009908 The process whose specific outcome is the progression of the flower over time, from its formation to the mature structure. The flower is the reproductive structure in a plant, and its development begins with the transition of the vegetative or inflorescence meristem into a floral meristem.
0.045 4 GO:0048366 The process whose specific outcome is the progression of the leaf over time, from its formation to the mature structure.

SF	Genes	GO ID	Process Name
0.067	5	GO:0006334	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
0.047	4	GO:0009908	The process whose specific outcome is the progression of the flower over time, from its formation to the mature structure. The flower is the reproductive structure in a plant, and its development begins with the transition of the vegetative or inflorescence meristem into a floral meristem.
0.045	4	GO:0048366	The process whose specific outcome is the progression of the leaf over time, from its formation to the mature structure.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.032 2 03022 Basal transcription factors
0.031 3 04120 Ubiquitin mediated proteolysis
0.029 2 03018 RNA degradation

SF	Genes	KEGG ID	Pathway name
0.032	2	03022	Basal transcription factors
0.031	3	04120	Ubiquitin mediated proteolysis
0.029	2	03018	RNA degradation

Inter-species module comparison

Select a plant to compare co-expressed genes between species.
Glycine_max
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays

Back to the CoP portal site

Back to the KAGIANA project homepage

Gene ID	At3g18035
Gene name	HON4
Module size	92 genes
NF	0.27
%ile	31.1

Co-expression analysis

Gene ID At3g18035 Gene name HON4 Module size 92 genes NF 0.27 %ile 31.1

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein: VF over 0.50, : over 0.25, : below 0.25

Co-expressed genes

Click More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Biological processes inferred to relate to the module

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG0.032203022Basal transcription factors0.031304120Ubiquitin mediated proteolysis0.029203018RNA degradation

Inter-species module comparison

Select a plant to compare co-expressed genes between species.Glycine_maxHordeum_vulgareOryza_sativaPopulus_trichocarpaTriticum_aestivumVitis_viniferaZea_mays

Gene ID At3g18035

Gene name HON4

Module size 92 genes

NF 0.27

%ile 31.1

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

SF Genes KEGG ID Pathway name Link to KEGG
0.032 2 03022 Basal transcription factors
0.031 3 04120 Ubiquitin mediated proteolysis
0.029 2 03018 RNA degradation

Select a plant to compare co-expressed genes between species.
Glycine_max
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays