Co-expression analysis

Gene ID At4g29820
Gene name CFIM-25
Module size 39 genes
NF 0.20
%ile 17.9



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
1.00100.01.00At4g29820829104CFIM-25Encodes a homolog of the protein CFI-25, a polyadenylation factor subunit.O.I.H.G.S.X.
0.4355.30.86At1g10210837559ATMPK1 (MITOGEN-ACTIVATED PROTEIN KINASE 1)Encodes ATMPK1.O.I.H.G.S.X.
0.3541.60.87At1g36070840511WD-40 repeat family proteinF:molecular_function unknown;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MBFOPAO.I.H.G.S.X.
0.3439.80.87At4g00335828093RHB1AF:protein binding, zinc ion binding;P:N-terminal protein myristoylation;C:unknown;PMOFVO.I.H.G.S.X.
0.3338.10.86At1g51550841580F-box family proteinF:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:chloroplast;MOPFBAO.I.H.G.S.X.
0.3133.80.86At5g46760834719basic helix-loop-helix (bHLH) family proteinF:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;POMFBVO.I.H.G.S.X.
0.2830.30.88At1g07530837267SCL14 (SCARECROW-LIKE 14)Encodes a member of the GRAS family of transcription factors. The protein interacts with the TGA2 transcription factor and affects the transcription of stress-responsive genes. The protein is found in the nucleus and is also exported to the cytoplasm.O.I.H.G.S.X.
0.2726.20.87At4g25970828703PSD3 (phosphatidylserine decarboxylase 3)Encodes the major form of the two non-mitochondrail phosphatidylserine decarboxylase. Located at the ER.O.I.H.G.S.X.
0.2624.40.86At1g15740838143leucine-rich repeat family proteinF:protein binding;P:unknown;C:cellular_component unknown;MPBOFVAO.I.H.G.S.X.
0.2624.40.88At5g02800831285protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:unknown;MPOBFVAO.I.H.G.S.X.
0.2522.60.87At5g35330833487MBD02 (METHYL-CPG-BINDING DOMAIN PROTEIN 02)Protein containing methyl-CpG-binding domain.Has sequence similarity to human MBD proteins.O.I.H.G.S.X.
0.2420.70.86At3g52240824389unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPFBO.I.H.G.S.X.
0.2115.80.85At1g43700840957VIP1 (VIRE2-INTERACTING PROTEIN 1)Encodes a VirE2-interacting protein. VIP1 mediates nuclear translocation of VirE2 via its amino half, and interacts with histone H2A via it carboxyl half.O.I.H.G.S.X.
0.2115.80.88At3g09880820146ATB' BETAEncodes B' regulatory subunit of PP2A (AtB'beta).O.I.H.G.S.X.
0.2014.40.87At5g05110830393cysteine protease inhibitor, putative / cystatin, putativeF:cysteine-type endopeptidase inhibitor activity;P:biological_process unknown;C:endomembrane system;PMOO.I.H.G.S.X.
0.1912.70.85At1g01730839260unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMBFO.I.H.G.S.X.
0.1912.70.85At3g09030820055potassium channel tetramerisation domain-containing proteinF:protein binding, voltage-gated potassium channel activity;P:potassium ion transport;C:voltage-gated potassium channel complex, membrane;MPOO.I.H.G.S.X.
0.1811.40.87At5g51170835191unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOO.I.H.G.S.X.
0.1811.40.87At5g16380831499unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;POO.I.H.G.S.X.
0.1811.40.86At1g07230837234hydrolase, acting on ester bondsF:hydrolase activity, acting on ester bonds;P:unknown;C:endomembrane system;BFPOAO.I.H.G.S.X.
0.1710.20.86At1g17530838327ATTIM23-1 (TRANSLOCASE OF INNER MITOCHONDRIAL MEMBRANE 23)Encodes a translocase of inner mitochondrial membrane.O.I.H.G.S.X.
0.168.80.87At1g49850841408zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVBO.I.H.G.S.X.
0.168.80.89At5g41350834137zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:mitochondrion;PMOFVO.I.H.G.S.X.
0.168.80.87At1g01820839257PEX11C (PEROXIN 11C)member of the peroxin11 (PEX11) gene family, integral to peroxisome membrane, controls peroxisome proliferation.O.I.H.G.S.X.
0.157.80.86At4g12570826870UPL5 (UBIQUITIN PROTEIN LIGASE 5)F:ubiquitin-protein ligase activity, binding, acid-amino acid ligase activity;P:protein modification process;C:intracellular;MOPFVBO.I.H.G.S.X.
0.157.80.86At2g45910819199protein kinase family protein / U-box domain-containing proteinF:ubiquitin-protein ligase activity, protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation, protein ubiquitination;C:ubiquitin ligase complex;MPOBFVAO.I.H.G.S.X.
0.146.80.87At1g56610842116syntaxin-related family proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO.I.H.G.S.X.
0.146.80.85At1g76185843951unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.146.80.85At2g33740817940CUTAencodes a copper binding protein that forms tetramers in vitro. Gene is expressed in all tissues examined and protein is localized to the chloroplast.O.I.H.G.S.X.
0.135.80.85At1g73950843732zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:biological_process unknown;C:vacuole;MPOVFO.I.H.G.S.X.
0.135.80.86At3g06170819791TMS membrane family protein / tumour differentially expressed (TDE) family proteinF:unknown;P:unknown;C:endomembrane system, membrane;MFPOBO.I.H.G.S.X.
0.135.80.86At4g39100830065SHL1 (short life)Putative transcription factor containing a PHD finger and BAH motif, required for normal developmentO.I.H.G.S.X.
0.124.90.86At5g14680831320universal stress protein (USP) family proteinF:molecular_function unknown;P:response to stress;C:cellular_component unknown;BPAMOFO.I.H.G.S.X.
0.114.10.85At5g13570831201DCP2 (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.
0.114.10.85At5g59950836117RNA and export factor-binding protein, putativeF:nucleotide binding, nucleic acid binding;P:biological_process unknown;C:chloroplast;MPFOBVAO.I.H.G.S.X.
0.092.80.87At3g29270822584ubiquitin-protein ligaseF:ubiquitin-protein ligase activity;P:unknown;C:unknown;MPOO.I.H.G.S.X.
0.092.80.86At3g55530824718SDIR1 (SALT- AND DROUGHT-INDUCED RING FINGER1)Encodes an intracellular membrane localized protein with E3 ligase activity that is involved in regulation of ABA signaling. Loss of function alleles show decreased sensitivity to ABA. Overexpression results in increased sensitivity to ABA.O.I.H.G.S.X.
0.082.30.86At3g48750824036CDC2 (CELL DIVISION CONTROL 2)A-type cyclin-dependent kinase. Together with its specific inhibitor, the Kip-related protein, KRP2 they regulate the mitosis-to-endocycle transition during leaf development. Dominant negative mutations abolish cell division. Loss of function phenotype has reduced fertility with failure to transmit via pollen. Pollen development is arrested at the second mitotic division. Expression is regulated by environmental and chemical signals. Part of the promoter is responsible for expression in trichomes. Functions as a positive regulator of cell proliferation during development of the male gametophyte, embryo and endosperm. Phosphorylation of threonine 161 is required for activation of its associated kinase.O.I.H.G.S.X.
0.071.90.86At5g35560833521DENN (AEX-3) domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;MOFPO.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
68.299.9GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
60.399.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
48.399.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
46.399.8GSM133774Lindsey_1-26_torpedo-meristem_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
43.299.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
41.099.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.899.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.599.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.799.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.599.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.699.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
36.599.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
35.399.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.099.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.199.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.099.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.699.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.599.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.399.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.199.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.999.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.099.7GSM142735DH001_ATH1_A2-BCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
28.299.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
26.799.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.599.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.499.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.899.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.399.6GSM142734DH001_ATH1_A1-UNM1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
24.299.6GSM142736DH001_ATH1_A3-TCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
23.999.6E-MEXP-1138-raw-cel-1432773258
23.199.6GSM133755Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
21.699.6E-MEXP-1138-raw-cel-1432773322
20.099.6E-MEXP-1138-raw-cel-1432773290
17.599.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
17.399.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
15.899.5GSM226548Slice6JWGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
15.699.5E-ATMX-35-raw-cel-1574334800
15.099.4GSM142738DH001_ATH1_A5-BCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
14.599.4GSM142739DH001_ATH1_A6-TCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
13.199.4GSM106916opr3_JA_22 hrs_Rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
11.999.3GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
11.199.2GSM226547Slice5JWGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
11.099.2GSM142737DH001_ATH1_A4-UNM2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
9.799.1GSM305282estradiol induced, biological replicate 1GSE12137LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis thalianaLink to GEO
9.599.1E-ATMX-35-raw-cel-1574334816
9.299.1GSM133773Lindsey_1-25_torpedo-meristem_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.299.1GSM106917opr3_JA_22 hrs_Rep3GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
8.999.0E-MEXP-1138-raw-cel-1432773066
8.699.0E-MEXP-1138-raw-cel-1432773034

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0491GO:0051170The directed movement of substances into the nucleus.Link to AmiGO
0.0481GO:0006402The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.Link to AmiGO
0.0471GO:0009410A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a xenobiotic compound stimulus. Xenobiotic compounds are compounds foreign to living organisms.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.038100565Ether lipid metabolismLink to KEGG PATHWAY
0.036104650Natural killer cell mediated cytotoxicityLink to KEGG PATHWAY
0.029100564Glycerophospholipid 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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