Co-expression analysis

Gene ID At3g08000
Gene name RNA-binding protein, putative
Module size 32 genes
NF 0.30
%ile 37.8



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
0.5673.01.00At3g08000819991RNA-binding protein, putativeF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:unknown;MPFOBAO.I.H.G.S.X.
0.5773.80.87At3g18970821430pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFMO.I.H.G.S.X.
0.5166.30.86At1g74600843800pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:chloroplast;POMFBAO.I.H.G.S.X.
0.4862.50.87At1g30550839935-F:molecular_function unknown;P:biological_process unknown;C:unknown;BMFOAPVO.I.H.G.S.X.
0.4761.20.87At2g38570818439-F:molecular_function unknown;P:biological_process unknown;C:unknown;BPOO.I.H.G.S.X.
0.4253.90.86At5g17570831623tatD-related deoxyribonuclease family proteinF:endodeoxyribonuclease activity, producing 5'-phosphomonoesters, deoxyribonuclease activity;P:biological_process unknown;C:cellular_component unknown;BOMFAPO.I.H.G.S.X.
0.4152.40.86At1g270708395965'-AMP-activated protein kinase-relatedF:unknown;P:unknown;C:unknown;MFPOBAO.I.H.G.S.X.
0.4152.40.87At4g39530830107pentatricopeptide (PPR) repeat-containing proteinF:binding;P:biological_process unknown;C:unknown;POMFBAO.I.H.G.S.X.
0.4050.80.88At2g18245816340unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOFO.I.H.G.S.X.
0.3745.00.86At2g19280816445pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:unknown;POMFBAO.I.H.G.S.X.
0.3541.60.86At2g33760817942pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.3439.80.86At1g30010839880intron 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.
0.3439.80.86At1g50260841448NTMC2T5.1 (N-TERMINAL-TRANSMEMBRANE-C2 DOMAIN TYPE 5.1)F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMFOBO.I.H.G.S.X.
0.3235.70.88At2g40720818667pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:unknown;C:cellular_component unknown;POMFBO.I.H.G.S.X.
0.3133.80.86At5g08510830750pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFMABO.I.H.G.S.X.
0.2930.30.86At5g48990834958kelch repeat-containing F-box family proteinencodes an F-box protein that interacts with SKP1 and likely to be involved in ubiquitin-mediated protein degradation.O.I.H.G.S.X.
0.2830.30.86At1g78930844232mitochondrial transcription termination factor-related / mTERF-relatedF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMOO.I.H.G.S.X.
0.2830.30.86At5g53920835475ribosomal protein L11 methyltransferase-relatedF:protein methyltransferase activity;P:protein amino acid methylation;C:cytoplasm;BOAFMPO.I.H.G.S.X.
0.2624.40.87At1g01740839253protein kinase family proteinF:in 6 functions;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:plasma membrane;PMBOFVAO.I.H.G.S.X.
0.2624.40.86At1g66520842970pde194 (pigment defective 194)F:hydroxymethyl-, formyl- and related transferase activity, formyltetrahydrofolate deformylase activity, catalytic activity;P:purine ribonucleotide biosynthetic process, biosynthetic process;C:unknown;BOMFPAVO.I.H.G.S.X.
0.2624.40.86At5g19840832104transcription factor jumonji (jmjC) domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MBOFPVO.I.H.G.S.X.
0.2420.70.86At5g08270830723unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOO.I.H.G.S.X.
0.2319.30.86At4g20740827823pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:unknown;POFMABO.I.H.G.S.X.
0.2217.50.86At5g39710833967EMB2745 (EMBRYO DEFECTIVE 2745)F:unknown;P:embryonic development ending in seed dormancy;C:unknown;POMFBAO.I.H.G.S.X.
0.2217.50.86At1g20230838612pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:cellular_component unknown;POMFBO.I.H.G.S.X.
0.2115.80.86At5g22710832334-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.2014.40.86At4g25270828630pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:chloroplast;POMFBO.I.H.G.S.X.
0.1811.40.87At1g30290839909-unknown proteinO.I.H.G.S.X.
0.1710.20.86At5g55840835678pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.168.80.87At5g25480832623DNMT2 (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.
0.146.80.86At3g22450821816structural constituent of ribosomeF:structural constituent of ribosome;P:translation;C:mitochondrion, ribosome, intracellular;PBOMO.I.H.G.S.X.
0.114.10.87At3g55080824674SET domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOO.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
58.499.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
57.599.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
53.299.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.199.8GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
49.999.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.399.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.299.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.099.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.699.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.299.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.899.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.799.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.599.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.599.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.499.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
42.299.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.699.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.199.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.199.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.099.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.299.7GSM133772Lindsey_1-24_torpedo-apical_Rep6_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
30.099.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
29.699.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
27.499.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
25.899.7GSM133773Lindsey_1-25_torpedo-meristem_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
25.299.6GSM133304RIKEN-NAKABAYASHI1BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
23.699.6GSM133771Lindsey_1-23_torpedo-apical_Rep5_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
23.499.6GSM133767Lindsey_1-19_torpedo-basal_Rep4_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
19.799.6GSM133755Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
17.999.5GSM133303RIKEN-NAKABAYASHI1AGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
17.799.5GSM133117RIKEN-YAMAUCHI1AGSE5687AtGenExpress: Different temperature treatment of seedsLink to GEO
17.499.5GSM133963Fukuda_1-8_6B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
16.799.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
16.399.5GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.299.5GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.899.5GSM133770Lindsey_1-22_torpedo-apical_Rep4_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
15.799.5GSM133962Fukuda_1-7_6A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
15.499.5GSM133769Lindsey_1-21_torpedo-basal_Rep6_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
15.299.4GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.099.4GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.299.3GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.799.3E-ATMX-35-raw-cel-1574334832
10.399.2GSM131706ATGE_84_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.899.1GSM131701ATGE_82_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.699.1GSM131707ATGE_84_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.699.1GSM131702ATGE_82_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.099.1GSM131708ATGE_84_DGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
8.999.0GSM131700ATGE_82_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
8.999.0GSM133961Fukuda_1-6_4B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
8.799.0GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0561GO:0006479The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.Link to AmiGO
0.0511GO:0006278The process whereby new strands of DNA are synthesized, using RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strands.Link to AmiGO
0.0511GO:0009152The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate moiety at either the 3' or 5'-hydroxyl group of its glycose moiety.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.041100670One carbon pool by folateLink to KEGG PATHWAY
0.025100970Aminoacyl-tRNA biosynthesisLink to KEGG PATHWAY
0.021100270Cysteine and methionine 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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