Co-expression analysis

Gene ID At5g04480
Gene name -
Module size 27 genes
NF 0.34
%ile 45.4



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
1.00100.01.00At5g04480830327-F:molecular_function unknown;P:biosynthetic process;C:Golgi apparatus;BOPAO.I.H.G.S.X.
0.5166.30.91At1g71820843512SEC6F:molecular_function unknown;P:pollen germination, pollen tube growth;C:plasma membrane, exocyst;MFOPBAO.I.H.G.S.X.
0.5065.30.91At1g77140844050VPS45 (VACUOLAR PROTEIN SORTING 45)A peripheral membrane protein that associates with microsomal membranes, likely to function in the transport of proteins to the vacuole. It is a member of Sec1p protein family. It may be involved in the regulation of vesicle fusion reactions through interaction with t-SNAREs at the Golgi trans face.O.I.H.G.S.X.
0.4963.50.90At1g27850839678unknown proteinF:molecular_function unknown;P:biological_process unknown;C:plasma membrane;MOFBPVAO.I.H.G.S.X.
0.4862.50.91At2g05170815065ATVPS11Homologous to yeast VPS11. Forms a complex with VCL1 and AtVPS33. Involved in vacuolar biogenesis.O.I.H.G.S.X.
0.4761.20.91At5g39500833946pattern formation protein, putativeF:ARF guanyl-nucleotide exchange factor activity;P:regulation of ARF protein signal transduction;C:intracellular;MFOPBO.I.H.G.S.X.
0.4659.80.92At1g73200843654phosphoinositide bindingF:phosphoinositide binding;P:signal transduction;C:vacuole;FMPOO.I.H.G.S.X.
0.4457.20.90At3g03810821131EDA30 (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.
0.3948.40.91At4g00570828222malate oxidoreductase, putativeF:oxidoreductase activity, acting on NADH or NADPH, NAD or NADP as acceptor, malic enzyme activity, ATP binding;P:oxidation reduction, malate metabolic process, metabolic process;C:mitochondrion, chloroplast;BOMPFAO.I.H.G.S.X.
0.3948.40.91At3g58050824974unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.3846.70.90At1g19430838527dehydration-responsive protein-relatedF:unknown;P:biological_process unknown;C:Golgi apparatus;MOFPBVAO.I.H.G.S.X.
0.3745.00.90At3g10380820201SEC8 (SUBUNIT OF EXOCYST COMPLEX 8)Subunit of the Putative Arabidopsis Exocyst ComplexO.I.H.G.S.X.
0.3643.60.91At3g50590824223nucleotide bindingF:nucleotide binding;P:biological_process unknown;C:plasma membrane;MBFOPVO.I.H.G.S.X.
0.3643.60.91At5g22770832340alpha-ADR (alpha-adaptin)F:protein transporter activity, protein binding, binding;P:intracellular protein transport, vesicle-mediated transport, protein transport;C:plasma membrane, membrane;MOFPO.I.H.G.S.X.
0.3541.60.91At5g18190831937protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MBOPFVAO.I.H.G.S.X.
0.3541.60.90At1g21630838765calcium-binding EF hand family proteinF:calcium ion binding;P:unknown;C:cytosol, plasma membrane;BMOFPVAO.I.H.G.S.X.
0.3439.80.90At1g27600839652glycosyl transferase family 43 proteinF:transferase activity, transferring glycosyl groups;P:protein amino acid glycosylation;C:membrane;MPOO.I.H.G.S.X.
0.3338.10.90At1g34550840358EMB2756 (EMBRYO DEFECTIVE 2756)F:unknown;P:embryonic development ending in seed dormancy, response to cadmium ion;C:unknown;OPMFBAO.I.H.G.S.X.
0.3338.10.91At2g27900817335unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOO.I.H.G.S.X.
0.2930.30.90At5g16280831488unknown proteinF:unknown;P:biological_process unknown;C:endomembrane system;MFOPVO.I.H.G.S.X.
0.2624.40.90At2g29510817500unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPFBVO.I.H.G.S.X.
0.2522.60.90At4g38200829976guanine nucleotide exchange family proteinF:binding, ARF guanyl-nucleotide exchange factor activity, guanyl-nucleotide exchange factor activity;P:regulation of ARF protein signal transduction;C:chloroplast;MFOPBO.I.H.G.S.X.
0.2420.70.90At5g64813836603LIP1 (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.
0.2217.50.90At3g17750821043protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cytosol, plasma membrane;MOPFBVAO.I.H.G.S.X.
0.2217.50.90At5g63870836507PP7 (SERINE/THREONINE PHOSPHATASE 7)Encodes a nuclear localized serine/threonine phosphatase that appears to be regulated by redox activity and is a positive regulator of cryptochrome mediated blue light signalling.O.I.H.G.S.X.
0.1710.20.90At3g24350822024SYP32 (SYNTAXIN OF PLANTS 32)member of Glycoside Hydrolase Family 17O.I.H.G.S.X.
0.146.80.90At1g67930843121Golgi transport complex protein-relatedF:unknown;P:unknown;C:chloroplast;OMFBPVO.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
69.599.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
58.399.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
53.899.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
42.599.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
38.299.8GSM311290Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
32.199.7GSM131325AtGen_6-3521_Saltstress-Roots-12.0h_Rep1GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
29.299.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.999.7E-MEXP-1725-raw-cel-1669614623
25.899.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
25.299.6E-MEXP-1725-raw-cel-1669614634
22.199.6GSM311289Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
21.199.6GSM131329AtGen_6-3621_Saltstress-Roots-24.0h_Rep1GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
20.999.6E-MEXP-98-raw-cel-320188914
20.399.6E-MEXP-1725-raw-cel-1669614562
18.799.5GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.199.5GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.199.5GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
18.099.5GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
16.699.5GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
16.699.5GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
16.299.5GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
16.299.5GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
15.999.5GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
15.499.5E-MEXP-1725-raw-cel-1669614582
15.499.5GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
15.299.4GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
15.199.4GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
14.899.4GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.699.4GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.399.4GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.099.4GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.999.4GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
13.899.4GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
13.799.4GSM131330AtGen_6-3622_Saltstress-Roots-24.0h_Rep2GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
13.299.4E-MEXP-98-raw-cel-320188969
11.199.2GSM131322AtGen_6-3422_Saltstress-Roots-6.0h_Rep2GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
9.199.1GSM133767Lindsey_1-19_torpedo-basal_Rep4_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
8.899.0GSM133303RIKEN-NAKABAYASHI1AGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1292GO:0032012Any process that modulates the frequency, rate or extent of ARF protein signal transduction.Link to AmiGO
0.0712GO:0009846The physiological and developmental changes that occur in a heterosporous plant pollen grain, beginning with hydration and terminating with the emergence of the pollen tube through the aperture.Link 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

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.027104130SNARE interactions in vesicular transportLink to KEGG PATHWAY
0.022100620Pyruvate metabolismLink to KEGG PATHWAY
0.022104144EndocytosisLink 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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