Co-expression analysis

Gene ID At3g44380
Gene name -
Module size 39 genes
NF 0.18
%ile 15.4



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
1.00100.01.00At3g44380823563-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.4558.30.90At3g59840825153unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast, chloroplast envelope;PO.I.H.G.S.X.
0.3439.80.89At5g55210835614unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PO.I.H.G.S.X.
0.3133.80.90At5g63670836487SPT42 (SPT4 HOMOLOG 2)F:positive transcription elongation factor activity, zinc ion binding;P:positive regulation of transcription, N-terminal protein myristoylation;C:nucleus;MFOPO.I.H.G.S.X.
0.3032.10.89At5g01650831707macrophage migration inhibitory factor family protein / MIF family proteinF:molecular_function unknown;P:inflammatory response, response to other organism;C:chloroplast;MOBPFO.I.H.G.S.X.
0.2624.40.89At1g09660837494KH domain-containing quaking protein, putativeF:RNA binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPFOO.I.H.G.S.X.
0.2624.40.89At1g08880837409H2AXAEncodes HTA5, a histone H2A protein. H2AX is a meiosis-specific isoform of histone H2A. Upon DSB formation, rapid accumulation of phosphorylated H2AX (γ-H2AX) occurs around the break site. H2AX foci accumulate in early G2. Immunolocalization studies in spread preparations of wild-type meiocytes at G2/early leptotene revealed the accumulation of numerous rather diffuse γ-H2AX foci throughout the chromatin. However, their accumulation is not contemporaneous with that of AtSPO11-1. At 3 h post-S, no γ-H2AX foci are detected. During the 3- to 5-h window when AtSPO11-1 foci rapidly disappear, there is an equally swift accumulation of γ-H2AX to a maximum of >50 diffuse foci. The level of γH2AX then remains constant for a further 13 h before undergoing a gradual decrease to 1020 foci in the 18- to 24-h post-S period. By 30 h the foci have disappeared from the chromatin.O.I.H.G.S.X.
0.2522.60.89At5g09995830861unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BPOO.I.H.G.S.X.
0.2522.60.89At5g01470831788unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPBOAO.I.H.G.S.X.
0.2420.70.89At5g17070831570unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOO.I.H.G.S.X.
0.2319.30.90At1g71750843505phosphoribosyltransferase family proteinF:transferase activity, hypoxanthine phosphoribosyltransferase activity;P:nucleoside metabolic process, purine ribonucleoside salvage;C:cytoplasm;BOMAPFO.I.H.G.S.X.
0.2319.30.89At5g48630834920cyclin family proteinF:cyclin-dependent protein kinase activity;P:regulation of cell cycle;C:unknown;MFPOO.I.H.G.S.X.
0.2319.30.89At1g06960837206small nuclear ribonucleoprotein U2B, putative / spliceosomal protein, putativeF:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:unknown;MFOPBVO.I.H.G.S.X.
0.2319.30.89At3g49560824118mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23 family proteinF:protein transporter activity, P-P-bond-hydrolysis-driven protein transmembrane transporter activity;P:protein transport;C:in 6 components;PMOO.I.H.G.S.X.
0.2319.30.90At5g63440836463unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOFO.I.H.G.S.X.
0.2217.50.89At4g28440828961DNA-binding protein-relatedF:molecular_function unknown;P:biological_process unknown;C:unknown;PAOO.I.H.G.S.X.
0.2115.80.89At2g11910815665unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast envelope;BMOFPVAO.I.H.G.S.X.
0.2014.40.89At2g43950819000OEP37Constitutes a peptide sensitive ion channel in chloroplast outer membranes. Accumulates in germinating seeds and developing embryos.O.I.H.G.S.X.
0.2014.40.89At2g47580819371U1A (SPLICEOSOMAL PROTEIN U1A)encodes spliceosomal protein U1AO.I.H.G.S.X.
0.2014.40.89At4g32900829426aminoacyl-tRNA hydrolaseF:aminoacyl-tRNA hydrolase activity;P:translation;C:unknown;MOAFPVO.I.H.G.S.X.
0.2014.40.90At2g33255817888catalytic/ hydrolase/ phosphoglycolate phosphataseF:hydrolase activity, catalytic activity, phosphoglycolate phosphatase activity;P:metabolic process;C:chloroplast;BOAFPMO.I.H.G.S.X.
0.1912.70.90At1g43190840918polypyrimidine tract-binding protein, putative / heterogeneous nuclear ribonucleoprotein, putativeF:RNA binding, nucleotide binding, nucleic acid binding;P:mRNA processing;C:nucleus;MPOFO.I.H.G.S.X.
0.1710.20.90At5g20130832135unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PMOBO.I.H.G.S.X.
0.1710.20.89At1g54770841918-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOO.I.H.G.S.X.
0.1710.20.90At3g13570820559SCL30aencodes an SC35-like splicing factor of 30 kD that is localized to the nuclear specks.O.I.H.G.S.X.
0.1710.20.89At3g49470824109NACA2 (NASCENT POLYPEPTIDE-ASSOCIATED COMPLEX SUBUNIT ALPHA-LIKE PROTEIN 2)F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPAVBO.I.H.G.S.X.
0.168.80.89At1g31160840001zinc-binding protein, putative / protein kinase C inhibitor, putativeF:protein kinase C binding, zinc ion binding, catalytic activity;P:biological_process unknown;C:chloroplast;BOMAFPO.I.H.G.S.X.
0.157.80.89At4g25550828660protein bindingF:protein binding;P:biological_process unknown;C:cellular_component unknown;MOFPO.I.H.G.S.X.
0.157.80.90At5g49230834983HRB1 (HYPERSENSITIVE TO RED AND BLUE)Identified in a screen for mutations hypersensitive to red and blue light. Mutants have shorter hypocotyls. Encodes a nuclear localized protein with similarity to drought induced proteins. Contains a ZZ zinc finger domain which is thought to mediate protein-protein interactions.May be involved in red and blue light signal transduction.O.I.H.G.S.X.
0.135.80.89At1g52370841667ribosomal protein L22 family proteinF:structural constituent of ribosome;P:translation;C:ribosome, intracellular, large ribosomal subunit;BOPMFO.I.H.G.S.X.
0.135.80.89At1g17880838367nascent polypeptide-associated complex (NAC) domain-containing protein / BTF3b-like transcription factor, putativeF:transcription factor activity;P:response to salt stress;C:cellular_component unknown;MFPOO.I.H.G.S.X.
0.124.90.90At4g40030830164histone H3.2F:DNA binding;P:nucleosome assembly;C:nucleus, nucleosome;MFPOO.I.H.G.S.X.
0.124.90.89At1g19800838568TGD1 (TRIGALACTOSYLDIACYLGLYCEROL 1)Encodes a permease-Like protein involved in lipid transfer from the ER to the chloroplast, more specifically, transfer of phosphatidate across the chloroplast inner membrane. Mutant leaves accumulate trigalactosyldiacylglycerol, triacylglycerol and phosphatidate. Chloroplast lipids are altered in their fatty acid composition and as a consequence the development of chloroplasts in the mutants are impacted. The mutant seeds has a higher abortion rate.O.I.H.G.S.X.
0.114.10.89At4g33250829461EIF3K (EUKARYOTIC TRANSLATION INITIATION FACTOR 3K)Encodes initiation factor 3k (EIF3k).O.I.H.G.S.X.
0.103.40.89At3g1151082032440S ribosomal protein S14 (RPS14B)F:structural constituent of ribosome;P:translation;C:cytosolic small ribosomal subunit, cytosolic ribosome, nucleolus;BOPMAFO.I.H.G.S.X.
0.103.40.89At3g4503082363840S ribosomal protein S20 (RPS20A)F:structural constituent of ribosome, RNA binding;P:translation;C:cytosolic small ribosomal subunit, small ribosomal subunit;BOMAPFO.I.H.G.S.X.
0.092.80.89At1g53120841746RNA-binding S4 domain-containing proteinF:RNA binding;P:biological_process unknown;C:chloroplast;BOPMO.I.H.G.S.X.
0.092.80.89At2g26770817218plectin-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAVO.I.H.G.S.X.
0.082.30.89At3g12130820388KH domain-containing protein / zinc finger (CCCH type) family proteinF:transcription factor activity, nucleic acid binding;P:regulation of transcription;C:unknown;MPOFBO.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
34.699.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.599.7GSM133778Lindsey_1-2_globular-apical_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
31.699.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
29.799.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.699.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.499.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.499.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.499.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.899.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.899.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.299.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.199.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.999.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.399.6GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.099.6GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
23.199.6GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.299.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
21.299.6GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
21.199.6GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
19.699.6GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
19.499.6GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
17.099.5GSM133776Lindsey_1-1_globular-apical_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
16.599.5GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.599.5GSM133962Fukuda_1-7_6A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
15.599.5GSM133963Fukuda_1-8_6B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
14.299.4GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
13.599.4E-MEXP-1443-raw-cel-1581869515
13.499.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.099.3GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.899.3E-MEXP-1451-raw-cel-1585200362
11.199.2GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.899.2GSM131655ATGE_27_AGSE5633AtGenExpress: Developmental series (shoots and stems)Link to GEO
10.599.2GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
10.099.2GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.799.1GSM184912Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.199.1GSM131656ATGE_27_BGSE5633AtGenExpress: Developmental series (shoots and stems)Link to GEO
8.799.0GSM131657ATGE_27_CGSE5633AtGenExpress: Developmental series (shoots and stems)Link to GEO
8.799.0E-MEXP-1443-raw-cel-1581869573
8.699.0GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
8.699.0GSM133961Fukuda_1-6_4B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
8.699.0GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0542GO:0000398The joining together of exons from one or more primary transcripts of nuclear messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.Link to AmiGO
0.0501GO:0006166Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.Link to AmiGO
0.0471GO:0006954The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.014100230Purine metabolismLink to KEGG PATHWAY
0.007103010RibosomeLink to KEGG PATHWAY
0.002101100Metabolic pathwaysLink 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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