Co-expression analysis

Gene ID At4g35740
Gene name RecQl3
Module size 42 genes
NF 0.24
%ile 25.8



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
1.00100.01.00At4g35740829727RecQl3F:helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding;P:DNA recombination;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.4355.30.87At2g31970817756RAD50F:zinc ion binding, ATP binding, nuclease activity;P:DNA repair;C:chromosome, Mre11 complex;MOBFPAVO.I.H.G.S.X.
0.4253.90.88At2g06510815209RPA1A (REPLICATION PROTEIN A 1A)Encodes a homolog of Replication Protein A that is involved in meiosis I in pollen mother cells. rpa1a mutants have a reduced number of class I crossovers. The protein is located in chromatin-associated foci in early leptotene and can be detected in these foci until late pachytene of meiosis I.O.I.H.G.S.X.
0.4050.80.87At4g09140826493MLH1 (MUTL-HOMOLOGUE 1)Encodes a protein with similarity to Mut1 DNA mismatch repair protein, from E.coli. The protein is expressed during prophase I of meiosis, colocalizes with MLH3 throughout pachytene and is dependent on MLH3 for proper localization.O.I.H.G.S.X.
0.3541.60.90At5g20930832217TSL (TOUSLED)Nuclear serine/threonine protein kinase that requires a coiled-coil region for oligomerization and catalytic activity. Required for leaf and flower development. Expression localized to the developing style by stage 13.O.I.H.G.S.X.
0.3439.80.87At2g39090818495tetratricopeptide repeat (TPR)-containing proteinF:binding;P:biological_process unknown;C:cellular_component unknown;BOMAFPO.I.H.G.S.X.
0.3338.10.86At3g43590823456zinc knuckle (CCHC-type) family proteinF:zinc ion binding, nucleic acid binding;P:unknown;C:unknown;VMOFPBO.I.H.G.S.X.
0.3338.10.87At3g17450821009hAT dimerisation domain-containing proteinF:protein dimerization activity, DNA binding;P:biological_process unknown;C:cellular_component unknown;POMVFBO.I.H.G.S.X.
0.3235.70.87At1g01920839313SET domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;FMPOO.I.H.G.S.X.
0.3133.80.90At2g31320817690PARP2 (POLY(ADP-RIBOSE) POLYMERASE 2)Abiotic Stress-inducible gene.O.I.H.G.S.X.
0.2930.30.87At1g22660838872tRNA-nucleotidyltransferase, putative / tRNA adenylyltransferase, putativeF:tRNA adenylyltransferase activity, RNA binding, nucleotidyltransferase activity;P:tRNA processing, RNA processing;C:mitochondrion;BOFMPVAO.I.H.G.S.X.
0.2930.30.87At5g38840833875forkhead-associated domain-containing protein / FHA domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:membrane;MOBFPAVO.I.H.G.S.X.
0.2830.30.87At1g48950841317zinc ion bindingF:zinc ion binding;P:biological_process unknown;C:nucleus, chloroplast;MFPOO.I.H.G.S.X.
0.2830.30.87At4g15570827233MAA3 (MAGATAMA 3)Similar to yeast Sen1 (splicing endonuclease 1)helicase protein. Involved in female gametophyte development.O.I.H.G.S.X.
0.2726.20.86At5g58130835925RNA recognition motif (RRM)-containing proteinF:nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.2624.40.86At5g13480831191FYEncodes a protein with similarity to yeast Pfs2p, an mRNA processing factor. Involved in regulation of flowering time; affects FCA mRNA processing. Homozygous mutants are late flowering, null alleles are embryo lethal.O.I.H.G.S.X.
0.2522.60.87At1g73450843680protein kinase, putativeF:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cytosol, plasma membrane;MOPFBVAO.I.H.G.S.X.
0.2522.60.87At3g60740825245TTN1 (TITAN 1)Encodes tubulin-folding cofactor D. Mutants arrest during embryogenesis with embryos that are small, mushroom-shaped ('pilz') and consist of only one or few large cells each containing one or more variably enlarged nuclei and often cell wall stubs. Gene product necessary for continuous microtubule organization.O.I.H.G.S.X.
0.2522.60.88At2g46180819225GC4 (golgin candidate 4)This gene is predicted to encode a protein that functions as a Golgi apparatus structural component known as a golgin in mammals and yeast. A fluorescently-tagged version of GC4 co-localizes with Golgi markers, and this localization appears to be replicated using the C-terminal (169 aa) portion of the protein.O.I.H.G.S.X.
0.2420.70.89At1g33400840233tetratricopeptide repeat (TPR)-containing proteinF:binding;P:biological_process unknown;C:cellular_component unknown;MOPBFAO.I.H.G.S.X.
0.2319.30.86At4g28470828964RPN1B (26S PROTEASOME REGULATORY SUBUNIT S2 1B)encoding the RPN subunits of the 26S proteasomeO.I.H.G.S.X.
0.2319.30.87At5g20170832140unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFO.I.H.G.S.X.
0.2319.30.88At5g65180836642-F:molecular_function unknown;P:biological_process unknown;C:unknown;MOFBPAVO.I.H.G.S.X.
0.2319.30.86At3g19840821521FF domain-containing protein / WW domain-containing proteinF:protein binding;P:biological_process unknown;C:cellular_component unknown;MOFPBAVO.I.H.G.S.X.
0.2217.50.86At4g32420829377peptidyl-prolyl cis-trans isomerase cyclophilin-type family proteinF:peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:unknown;MOBFPVAO.I.H.G.S.X.
0.2115.80.87At5g42920834304unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOO.I.H.G.S.X.
0.2115.80.88At1g33410840234SAR1 (suppressor of auxin resistance1)F:unknown;P:response to auxin stimulus, mRNA export from nucleus, developmental process;C:nuclear membrane;MPFOO.I.H.G.S.X.
0.2115.80.87At3g62620825436sucrose-phosphatase-relatedF:unknown;P:biological_process unknown;C:unknown;OMFBPVO.I.H.G.S.X.
0.2014.40.87At2g46020819210transcription regulatory protein SNF2, putativeEncodes a SWI/SNF chromatin remodeling ATPase that upregulates transcription of all three CUC genes and is involved in the formation and/or maintenance of boundary cells during embryogenesis. Also mediates repression of expression of seed storage proteins in vegetative tissues. Interacts strongly with AtSWI3C, also with AtSWI3B, but not with AtSWI3A or AtSWI3D.O.I.H.G.S.X.
0.2014.40.87At4g31200829247SWAP (Suppressor-of-White-APricot)/surp domain-containing proteinF:RNA binding;P:RNA processing;C:cellular_component unknown;MPFOBVAO.I.H.G.S.X.
0.1912.70.87At4g10760826670MTA (MRNA ADENOSINE METHYLASE)F:S-adenosylmethionine-dependent methyltransferase activity, methyltransferase activity;P:embryonic development ending in seed dormancy, mRNA methylation;C:nuclear speck, chloroplast;MOBPFAVO.I.H.G.S.X.
0.1710.20.87At3g62310825404RNA helicase, putativeF:RNA helicase activity, helicase activity, ATP binding, nucleic acid binding;P:unknown;C:nucleolus;MBOFVPAO.I.H.G.S.X.
0.1710.20.86At4g32620829397nucleic acid bindingF:nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;OPMFBO.I.H.G.S.X.
0.1710.20.87At1g52380841668Ran-binding protein 1 domain-containing protein / RanBP1 domain-containing proteinF:molecular_function unknown;P:intracellular transport;C:cytosol, nucleus;MFOPBVO.I.H.G.S.X.
0.1710.20.86At5g63110836431HDA6 (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.
0.168.80.88At1g26170839158binding / protein transporterF:protein transporter activity, binding;P:intracellular protein transport, protein import into nucleus, docking;C:nucleus, nuclear pore, cytoplasm;MFPOO.I.H.G.S.X.
0.168.80.87At1g32490840143ESP3 (ENHANCED SILENCING PHENOTYPE 3)Encodes a homolog of the yeast PRP2 protein, one of four related DEAH RNA helicases identified as essential cofactors for RNA splicing.O.I.H.G.S.X.
0.168.80.86At2g35630818131MOR1 (MICROTUBULE ORGANIZATION 1)Member of the MAP215 family of microtubule-associated proteins required to establish interphase arrays of cortical microtubules.Mutants have defects in cytokinesis during pollen development. Vegetative phenotypes observed in temperature sensitive mutants include left-handed organ twisting, isotropic cell expansion and impairment of root hair polarity.O.I.H.G.S.X.
0.157.80.87At3g56120824778Met-10+ like family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;AMOFBPO.I.H.G.S.X.
0.114.10.86At2g15530816045zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MPOFBVO.I.H.G.S.X.
0.092.80.87At2g25570817096bindingF:binding;P:biological_process unknown;C:unknown;BOMPVFO.I.H.G.S.X.
0.082.30.86At3g51310824294VPS35C (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.

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
87.799.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
77.699.9GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
52.399.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
52.199.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.999.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.999.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
49.799.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.599.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.099.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.699.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.699.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.199.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.799.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.699.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
41.399.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.199.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.599.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.099.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.099.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.299.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.099.7GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
30.799.7GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
30.499.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.399.7GSM311279Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
28.899.7GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
28.599.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.799.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
22.599.6GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
20.799.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.399.6GSM311280Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
16.999.5GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.399.4GSM311291Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
15.299.4GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
14.299.4GSM142737DH001_ATH1_A4-UNM2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
14.299.4GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.099.4GSM142734DH001_ATH1_A1-UNM1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
13.799.4E-ATMX-35-raw-cel-1574334832
13.599.4E-ATMX-35-raw-cel-1574334816
12.099.3GSM142738DH001_ATH1_A5-BCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
11.499.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
10.099.2E-ATMX-1-raw-cel-1112746154
9.499.1GSM142735DH001_ATH1_A2-BCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
9.099.1E-ATMX-1-raw-cel-1112746267
8.699.0GSM290758root - 01% oxygen - 48h - AGSE11558transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plantsLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0822GO:0016458Any transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.Link to AmiGO
0.0632GO:0000910A cellular process resulting in the division of the cytoplasm of a cell and its separation into two daughter cells. Cytokinesis usually occurs after growth, replication, and segregation of cellular components.Link to AmiGO
0.0492GO:0008380The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.060203440Homologous recombinationLink to KEGG PATHWAY
0.059203430Mismatch repairLink to KEGG PATHWAY
0.040103450Non-homologous end-joiningLink 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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