Co-expression analysis

Gene ID At4g18375
Gene name KH domain-containing protein
Module size 46 genes
NF 0.25
%ile 26.6



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
0.8089.81.00At4g18375827566KH domain-containing proteinF:RNA binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPFOO.I.H.G.S.X.
0.5673.00.84At5g08070830701TCP17 (TCP DOMAIN PROTEIN 17)TCP gene involved in heterochronic control of leaf differentiation.O.I.H.G.S.X.
0.4963.50.86At2g38570818439-F:molecular_function unknown;P:biological_process unknown;C:unknown;BPOO.I.H.G.S.X.
0.4253.90.86At2g19280816445pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:unknown;POMFBAO.I.H.G.S.X.
0.4152.40.85At4g39530830107pentatricopeptide (PPR) repeat-containing proteinF:binding;P:biological_process unknown;C:unknown;POMFBAO.I.H.G.S.X.
0.4050.80.84At5g49390834999-F:unknown;P:unknown;C:endomembrane system;MOFBPVO.I.H.G.S.X.
0.3948.40.86At2g20210816540leucine-rich repeat family proteinF:protein binding;P:unknown;C:endomembrane system;MOPBFO.I.H.G.S.X.
0.3745.00.85At5g39710833967EMB2745 (EMBRYO DEFECTIVE 2745)F:unknown;P:embryonic development ending in seed dormancy;C:unknown;POMFBAO.I.H.G.S.X.
0.3745.00.84At2g18245816340unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOFO.I.H.G.S.X.
0.3541.60.85At1g270708395965'-AMP-activated protein kinase-relatedF:unknown;P:unknown;C:unknown;MFPOBAO.I.H.G.S.X.
0.3439.80.85At4g21890828278unknown proteinF:molecular_function unknown;P:biological_process unknown;C:nucleus;PO.I.H.G.S.X.
0.3338.10.84At1g09820837514pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.3338.10.84At2g46380819246unknown proteinF:unknown;P:unknown;C:cellular_component unknown;POMBO.I.H.G.S.X.
0.3133.80.84At2g20400816559myb family transcription factorF:transcription factor activity, DNA binding;P:regulation of transcription;C:unknown;POO.I.H.G.S.X.
0.2830.30.85At4g20740827823pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:unknown;POFMABO.I.H.G.S.X.
0.2830.30.85At1g26190839160phosphoribulokinase/uridine kinase family proteinF:adenylate cyclase activity, kinase activity, phosphotransferase activity, alcohol group as acceptor, ATP binding;P:biosynthetic process, cAMP biosynthetic process, metabolic process;C:cellular_component unknown;BOMPFAVO.I.H.G.S.X.
0.2830.30.84At2g14050815890MCM9F:nucleoside-triphosphatase activity, DNA-dependent ATPase activity, DNA binding, nucleotide binding, ATP binding;P:DNA replication initiation, DNA replication;C:cellular_component unknown;MOBFAPVO.I.H.G.S.X.
0.2830.30.86At1g63130842617pentatricopeptide (PPR) repeat-containing proteinTransacting siRNA generating locus. Its derived siR9as targets AT1G62930 for cleavage. Itself is targeted by TAS2-derived ta-siR2140 for cleavage.O.I.H.G.S.X.
0.2726.20.85At1g52630841695unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO.I.H.G.S.X.
0.2726.20.86At1g32610840156hydroxyproline-rich glycoprotein family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOVBO.I.H.G.S.X.
0.2624.40.84At1g50260841448NTMC2T5.1 (N-TERMINAL-TRANSMEMBRANE-C2 DOMAIN TYPE 5.1)F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMFOBO.I.H.G.S.X.
0.2624.40.84At1g30010839880intron maturase, type II family proteinF:RNA binding, RNA-directed DNA polymerase activity;P:RNA-dependent DNA replication, RNA splicing;C:unknown;BPOFAMVO.I.H.G.S.X.
0.2624.40.84At1g62130842509AAA-type ATPase family proteinF:nucleoside-triphosphatase activity, ATPase activity, nucleotide binding, ATP binding;P:biological_process unknown;C:chloroplast;OBMFPAVO.I.H.G.S.X.
0.2522.60.86At1g30290839909-unknown proteinO.I.H.G.S.X.
0.2319.30.84At5g28530832948FRS10 (FAR1-related sequence 10)F:zinc ion binding;P:response to red or far red light;C:unknown;PFMO.I.H.G.S.X.
0.2319.30.84At4g02485827953oxidoreductase, 2OG-Fe(II) oxygenase family proteinF:oxidoreductase activity;P:unknown;C:cellular_component unknown;MOBPFVO.I.H.G.S.X.
0.2217.50.84At2g40720818667pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:unknown;C:cellular_component unknown;POMFBO.I.H.G.S.X.
0.2217.50.85At3g06910819876ULP1A (UB-LIKE PROTEASE 1A)Encodes a deSUMOylating enzyme. In vitro it has both peptidase activity and isopeptidase activity: it can cleave the C-terminal residues from SUMO to activate it for attachment to a target protein and it can also act on the isopeptide bond between SUMO and another protein. In vitro assays suggest that this enzyme is active against SUMO1 and SUMO2. It has weak activity with SUMO3 and cannot act on SUMO5. The N-terminal regulatory region of this protein is required for full activity.O.I.H.G.S.X.
0.2217.50.84At2g23740816905nucleic acid binding / transcription factor/ zinc ion bindingF:transcription factor activity, zinc ion binding, nucleic acid binding;P:chromatin modification;C:nucleus, intracellular;MOPFBO.I.H.G.S.X.
0.2115.80.84At2g41080818707pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFMBO.I.H.G.S.X.
0.2014.40.85At1g17850838364-F:molecular_function unknown;P:biological_process unknown;C:chloroplast;OBPMFO.I.H.G.S.X.
0.1912.70.85At5g22710832334-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.1811.40.84At4g24900828592unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO.I.H.G.S.X.
0.1710.20.86At3g580903769734-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknownO.I.H.G.S.X.
0.1710.20.84At1g01740839253protein kinase family proteinF:in 6 functions;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:plasma membrane;PMBOFVAO.I.H.G.S.X.
0.1710.20.84At4g11970826804YT521-B-like family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOO.I.H.G.S.X.
0.1710.20.86At1g74390843780exonuclease family proteinF:exonuclease activity, nucleic acid binding;P:unknown;C:intracellular;BOPO.I.H.G.S.X.
0.1710.20.87At3g10070820168TAF12 (TBP-ASSOCIATED FACTOR 12)Encodes one of two Arabidopsis proteins with similarity to the TBP-associated factor TAF12.O.I.H.G.S.X.
0.157.80.86At2g44440819051emsy N terminus domain-containing protein / ENT domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMFOBO.I.H.G.S.X.
0.146.80.85At5g01510831819-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOBO.I.H.G.S.X.
0.146.80.84At3g46610823814pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.146.80.85At4g10470826639unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.135.80.85At5g25480832623DNMT2 (DNA METHYLTRANSFERASE-2)Encodes a DNA methyltransferase homolog. Human Dnmt2 methylates tRNA-Asp and can methylate Arabidopsis tRNA-Asp in vitro.O.I.H.G.S.X.
0.114.10.84At3g60400825211mitochondrial transcription termination factor-related / mTERF-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.103.40.85At5g03415831847DPBEncodes a homolog of the animal DP protein. DP, in animals, forms a heterodimer with E2F and plays a central role in G1/S transition in the cell division cycle. DPB has been shown to interact with non phosphorylated E2Fc; when E2Fc is phosphorylated, the formation of the E2Fc/DPB heterodimer is lost.O.I.H.G.S.X.
0.092.80.84At2g05210815069AtPOT1a (Protection of Telomeres 1a)Encodes AtPOT1a, an accessory factor for telomerase required for positive telomere length regulation. Note on nomenclature: different names have been given to Arabidopsis POT-like genes (Kuchar and Fajkus, 2004; Shakirov et al, 2005; Tani and Murata, 2005). According to a unifying nomenclature (Surovtseva et al, 2007), At2g05210 (previously named AtPOT1) is designated AtPOT1a, while At5g06310 (previously named AtPOT2) is designated AtPOT1b.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
49.699.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
48.299.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.299.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.099.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.799.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.599.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.399.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.399.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.699.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.599.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.199.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.699.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.999.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.699.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.399.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
39.999.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.999.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.799.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.099.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
35.899.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.299.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.299.6GSM284386Arabidopsis GSUS3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
21.199.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
21.099.6GSM284387Arabidopsis GSUS4bGSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
15.599.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.499.5GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.599.4GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.599.4GSM133963Fukuda_1-8_6B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
13.299.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.699.3GSM133773Lindsey_1-25_torpedo-meristem_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.299.3GSM133962Fukuda_1-7_6A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
12.099.3E-ATMX-35-raw-cel-1574334832
10.899.2GSM142751MJ001_ATH1_A2-jones-WT2GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
10.099.2GSM311296Laser 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
9.999.1GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
9.899.1GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
9.599.1GSM265423Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
9.399.1GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
8.899.0E-ATMX-35-raw-cel-1574334816
8.799.0GSM106913opr3_JA_8 hrs_Rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0411GO:0006171The chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).Link to AmiGO
0.0411GO:0016926The process by which a SUMO protein (small ubiquitin-related modifier) is cleaved from its target protein.Link to AmiGO
0.0401GO:0000082Progression from G1 phase to S phase of the mitotic cell cycle.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.025103022Basal transcription factorsLink to KEGG PATHWAY
0.018100270Cysteine and methionine metabolismLink 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



Back to the CoP portal site

Back to the KAGIANA project homepage