Co-expression analysis

Gene ID At2g35230
Gene name VQ motif-containing protein
Module size 27 genes
NF 0.41
%ile 57.9



Co-expression network

pink confeito: Transcription factor, green bicone: Binding protein, red cone: Enzyme protein, blue sphere: Other protein
large node: VF over 0.50, middle node: over 0.25, small node: 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
1.00100.01.00At2g35230818090VQ motif-containing proteinF:unknown;P:unknown;C:unknown;MFPOBVAO.I.H.G.S.X.
0.6075.70.93At1g22020838807SHM6 (serine hydroxymethyltransferase 6)Encodes a putative serine hydroxymethyltransferase.O.I.H.G.S.X.
0.5267.40.92At4g15180827183SDG2 (SET DOMAIN-CONTAINING PROTEIN 2)F:unknown;P:unknown;C:unknown;MOPFBVO.I.H.G.S.X.
0.5166.30.92At5g19420832062Ran GTPase binding / chromatin binding / zinc ion bindingF:chromatin binding, zinc ion binding, Ran GTPase binding;P:unknown;C:unknown;MOPBFAVO.I.H.G.S.X.
0.5166.30.92At3g03810821131EDA30 (embryo sac development arrest 30)F:molecular_function unknown;P:N-terminal protein myristoylation, polar nucleus fusion, pollen tube development;C:chloroplast;PO.I.H.G.S.X.
0.5065.30.92At1g24190839032SNL3 (SIN3-LIKE 3)Enhances AtERF7-mediated transcriptional repression. RNAi lines show ABA hypersensitivity. Interacts with ERF7 and HDA19.O.I.H.G.S.X.
0.4862.50.93At2g22090816744UBP1 interacting protein 1a (UBA1a)encodes a nuclear protein that binds to RNA with a specificity for oligouridylates in vitro. As with UBP1, transient overexpression of UBA1a in protoplasts increases the steady-state levels of reporter mRNAs in a promoter-dependent manner. Along with UBP1 and UBA2a, 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.
0.4761.20.92At1g73200843654phosphoinositide bindingF:phosphoinositide binding;P:signal transduction;C:vacuole;FMPOO.I.H.G.S.X.
0.4761.20.92At1g28320839726DEG15Mutants in this gene are defective in the processing of pre-glyoxysomal malate dehydrogenase (pre-gMDH) to gMDH.O.I.H.G.S.X.
0.4659.80.93At1g30970839984SUF4 (suppressor of FRIGIDA4)Encodes SUF4 (SUPPRESSOR of FRI 4), a putative zinc-finger-containing transcription factor that is required for delayed flowering in winter-annual Arabidopsis. suf4 mutations strongly suppress the late-flowering phenotype of FRI (FRIGIDA) mutants. suf4 mutants also show reduced H3K4 trimethylation at FLC (FLOWERING LOCUS C), a floral inhibitor. SUF4 may act to specifically recruit a putative histone H3 methyltransferase EFS (EARLY FLOWERING IN SHORT DAYS) and the PAF1-like complex to the FLC locus.O.I.H.G.S.X.
0.4659.80.92At3g58050824974unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.4659.80.92At1g11060837647unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MBPOFO.I.H.G.S.X.
0.4457.20.92At3g44530823578HIRA (Arabidopsis homolog of histone chaperone HIRA)Encodes a nuclear localized WD-repeat containing protein involved in negative regulation of knox gene expression via epigenetic mechanism of chromatin re-organization. Interacts physically and genetically with AS1. Expressed in meristem and leaf primordia. Homozygous mutants are embryo lethal. Phenotype of cosuppressed lines is variable but show effects on leaf development similar to as1/as2.O.I.H.G.S.X.
0.4152.40.92At3g27320822351hydrolaseF:hydrolase activity;P:metabolic process;C:unknown;BOPFMAVO.I.H.G.S.X.
0.4152.40.92At5g46190834661KH domain-containing proteinF:RNA binding, nucleic acid binding;P:biological_process unknown;C:unknown;MPFOBO.I.H.G.S.X.
0.4050.80.92At4g00450827954CRP (CRYPTIC PRECOCIOUS)A genetic locus involved in flowering time. The mutant enhances the expression of the flowering time (FT) gene. A knockout mutant of this gene showed late-flowering phenotype.O.I.H.G.S.X.
0.3948.40.91At5g07270830618ankyrin repeat family proteinF:ubiquitin-protein ligase activity, protein binding;P:N-terminal protein myristoylation;C:unknown;MOFBPVAO.I.H.G.S.X.
0.3745.00.93At1g21630838765calcium-binding EF hand family proteinF:calcium ion binding;P:unknown;C:cytosol, plasma membrane;BMOFPVAO.I.H.G.S.X.
0.3541.60.93At5g35980833590protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cytosol;MOPFBVAO.I.H.G.S.X.
0.3541.60.92At2g44900819099armadillo/beta-catenin repeat family protein / F-box family proteinARABIDILLO-1 and its homolog, ARABIDILLO -2, are unique among Arabidopsis Arm-repeat proteins in having an F-box motif and fall into a phylogenetically distinct subgroup from other plant Arm-repeat proteins Similar to arm repeat protein in rice and armadillo/beta-catenin repeat family protein / F-box family protein in Dictyostelium. ARABIDILLO-1 promote lateral root development. Mutant plants form fewer lateral roots, while ARABIDILLO-1-overexpressing lines produce more lateral roots than wild-type seedlings.O.I.H.G.S.X.
0.3541.60.92At5g21040832228FBX2 (F-BOX PROTEIN 2)Encodes an F-box containing protein that interacts physically with BHLH32 and appears to be involved in mediating phosphate starvation responses.O.I.H.G.S.X.
0.3439.80.92At2g05170815065ATVPS11Homologous to yeast VPS11. Forms a complex with VCL1 and AtVPS33. Involved in vacuolar biogenesis.O.I.H.G.S.X.
0.3338.10.91At1g55325841978-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MBPOFO.I.H.G.S.X.
0.3235.70.92At3g08850820032RAPTOR1Encodes one of two Arabidopsis RAPTOR/KOG1 homologs. RAPTOR proteins are binding partners of the target of rapamycin kinase that is present in all eukaryotes and play a central role in the stimulation of cell growth and metabolism in response to nutrients. Mutants show embryo lethal phenotype which occurs at pre-globular stage. May interact with TOR kinase in a rapamycin like signaling pathway. Interacts with TOR and S6K1 in vivo. Overexpression of RAPTOR1 rendered the S6K1 osmotic stress insensitive.O.I.H.G.S.X.
0.3133.80.92At5g64813836603LIP1 (Light Insensitive Period1)The LIP1 gene encodes a small GTPase that influences the light input pathway of the plant circadian network. An MBP:LIP1 fusion protein has GTP hydrolyzing abilities in vitro. In plants, LIP1 seems to play a negative role in regulating circadian period that can be suppressed by light. LIP1 also seems to negatively affect light-pulse-dependent resetting of the clock, especially during the first portion of the subjective evening. LIP1 expression levels are not significantly affected by the circadian clock in seedlings grown under LL conditions. The levels of the YFP:LIP1 protein expressed under the control of the 35S promoter, shows a low amplitude variation, with protein levels peaking near the beginning of subjective night under LL conditions. In hypocotyl epidermal cells of dark and light-grown seedlings, a YFP:LIP1 fusion protein can be seen in the cytoplasm and the nucleus, and does not cluster in nuclear speckles. LIP1 may also be involved in photomorphogenesis.O.I.H.G.S.X.
0.2115.80.92At5g35430833507bindingF:binding;P:biological_process unknown;C:cellular_component unknown;MPOBFO.I.H.G.S.X.
0.1811.40.91At2g27900817335unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOO.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
74.199.9GSM311296Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
55.099.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
53.899.8GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
52.199.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
50.699.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.499.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
49.499.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
48.499.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.399.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
48.199.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
48.099.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.899.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.799.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.199.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.499.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
42.399.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.299.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.499.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.499.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.099.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.599.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.999.7GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
35.499.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
22.399.6GSM311274Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
22.199.6GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
19.699.6E-MEXP-1725-raw-cel-1669614623
18.999.5GSM311295Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
17.199.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
16.599.5E-MEXP-1725-raw-cel-1669614634
15.999.5GSM311273Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
15.099.4GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.499.4GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.499.4GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.199.4E-MEXP-807-raw-cel-1173273170
12.899.3GSM133759Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.499.3GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.899.3E-MEXP-1725-raw-cel-1669614582
11.799.3E-MEXP-1725-raw-cel-1669614562
11.699.3GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.499.3GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.199.2GSM131303AtGen_6-2611_Osmoticstress-Shoots-24.0h_Rep1GSE5622AtGenExpress: Stress Treatments (Osmotic stress)Link to GEO
10.699.2GSM131692ATGE_78_EGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
10.599.2GSM131693ATGE_78_FGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
10.199.2GSM131691ATGE_78_DGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.899.1E-MEXP-807-raw-cel-1173273196
9.399.1E-MEXP-98-raw-cel-320188914
9.199.1GSM284395Arabidopsis GPSc1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.099.1GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.099.1E-MEXP-807-raw-cel-1173273088
8.799.0GSM284396Arabidopsis GPSc2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0691GO:0032922Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.Link to AmiGO
0.0691GO:0048255Prevention of degradation of mRNA molecules. In the absence of compensating changes in other processes, the slowing of mRNA degradation can result in an overall increase in the population of active mRNA molecules.Link to AmiGO
0.0591GO:0006563The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.045100670One carbon pool by folateLink to KEGG PATHWAY
0.040100460Cyanoamino acid metabolismLink to KEGG PATHWAY
0.028100260Glycine, serine and threonine metabolismLink to KEGG PATHWAY

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



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