Co-expression analysis

Gene ID At5g11010
Gene name pre-mRNA cleavage complex-related
Module size 56 genes
NF 0.26
%ile 29.7



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
0.9396.41.00At5g11010830968pre-mRNA cleavage complex-relatedF:molecular_function unknown;P:biological_process unknown;C:chloroplast;MFOPABO.I.H.G.S.X.
0.4050.80.90At5g67630836899DNA helicase, putativeF:DNA helicase activity, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:unknown;C:nucleolus, chloroplast;BMOFPAO.I.H.G.S.X.
0.4050.80.90At4g25210828624transcription regulatorF:transcription regulator activity;P:biological_process unknown;C:nucleolus, chloroplast;OMFBPVAO.I.H.G.S.X.
0.3846.70.91At2g36070818180ATTIM44-2One of two genes in Arabidopsis that encode a putative subunit of the mitochondrial inner membrane translocase complex. TIM44 subunit is thought to provide the energy for translocation via hydrolysis of ATP.O.I.H.G.S.X.
0.3643.60.89At1g75670843901DNA-directed RNA polymerase/ RNA bindingF:DNA-directed RNA polymerase activity, RNA binding;P:transcription;C:cellular_component unknown;POFO.I.H.G.S.X.
0.3643.60.89At4g26430828749CSN6Bone of two genes encoding subunit 6 of COP9 signalosome complexO.I.H.G.S.X.
0.3541.60.90At1g36310840538methyltransferaseF:methyltransferase activity;P:metabolic process;C:unknown;BOMAFPO.I.H.G.S.X.
0.3541.60.89At2g19540816473transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFOPBAO.I.H.G.S.X.
0.3541.60.90At3g49990824161-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFPBVAO.I.H.G.S.X.
0.3541.60.89At2g40290818621eukaryotic translation initiation factor 2 subunit 1, putative / eIF-2A, putative / eIF-2-alpha, putativeF:RNA binding, translation initiation factor activity;P:translation;C:nucleus;BOMAFPVO.I.H.G.S.X.
0.3439.80.89At1g14300837991bindingF:binding;P:biological_process unknown;C:cellular_component unknown;FMPOO.I.H.G.S.X.
0.3439.80.89At5g62290836350nucleotide-sensitive chloride conductance regulator (ICln) family proteinF:ion channel activity;P:cell volume homeostasis, chloride transport;C:cellular_component unknown;MPFOO.I.H.G.S.X.
0.3338.10.89At3g49430824105SRp34a (Ser/Arg-rich protein 34a)F:RNA binding, nucleotide binding, nucleic acid binding;P:RNA splicing;C:nucleolus;MOPFBVAO.I.H.G.S.X.
0.3338.10.90At4g31790829307diphthine synthase, putative (DPH5)F:methyltransferase activity, diphthine synthase activity;P:peptidyl-diphthamide biosynthetic process from peptidyl-histidine, metabolic process;C:cellular_component unknown;AOMFBPO.I.H.G.S.X.
0.3235.70.89At3g01800821076ribosome recycling factor family protein / ribosome releasing factor family proteinF:unknown;P:translation;C:mitochondrion;BOMPFO.I.H.G.S.X.
0.3235.70.90At2g38560818438TFIIS (TRANSCRIPT ELONGATION FACTOR IIS)Encodes RNA polymerase II transcript elongation factor TFIIS. Complements yeast TFIIS mutation. Mutant plants display essentially normal development, but they flower slightly earlier than the wild type and show clearly reduced seed dormancy.O.I.H.G.S.X.
0.3235.70.90At5g60990836220DEAD/DEAH box helicase, putative (RH10)F:helicase activity, nucleic acid binding, ATP-dependent helicase activity, ATP binding;P:unknown;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.3235.70.90At5g11170830986ATP binding / ATP-dependent helicase/ helicase/ nucleic acid bindingF:helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding;P:response to cadmium ion;C:nucleolus;BOMFPAVO.I.H.G.S.X.
0.3133.80.90At3g02220821238unknown proteinF:unknown;P:biological_process unknown;C:cellular_component unknown;MOPFBAO.I.H.G.S.X.
0.3133.80.89At4g24940828596SAE1A (SUMO-ACTIVATING ENZYME 1A)Encodes one of the two subunits of the SUMO activation enzyme required during sumolation. Sumolation is a post-translational protein modification process similar to ubiquitination during which a polypeptide (SUMO) is covalently attached to a target protein.O.I.H.G.S.X.
0.3032.10.90At5g17070831570unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOO.I.H.G.S.X.
0.3032.10.89At1g31660840053-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBO.I.H.G.S.X.
0.2930.30.89At1g48920841314ATNUC-L1Encodes the predominant form of the two nucleolin proteins found in Arabidopsis. This protein is involved in rRNA processing, ribosome biosynthesis, and vascular pattern formation. PARL1 localizes to the nucleolus and parl1 mutants accumulate elevated levels of the unspliced 35S pre-rRNA. parl1 mutants also have defects in cotyledon, leaf, sepal, and petal vein patterning and have reduced stature, reduced fertility, increased bushiness, and reduced root length. The sugar-induced expression of ribosome proteins is also reduced in parl1 mutants.O.I.H.G.S.X.
0.2830.30.89At4g39280830084phenylalanyl-tRNA synthetase, putative / phenylalanine--tRNA ligase, putativeF:phenylalanine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:phenylalanyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:cytoplasm;BOMAFPO.I.H.G.S.X.
0.2830.30.89At3g07170819904sterile alpha motif (SAM) domain-containing proteinF:transferase activity, transferring glycosyl groups;P:biological_process unknown;C:cellular_component unknown;MPOBFO.I.H.G.S.X.
0.2830.30.89At3g15010820730RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:nucleolus;MBPOFVAO.I.H.G.S.X.
0.2726.20.89At3g09890820147ankyrin repeat family proteinF:protein binding;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.2726.20.89At1g79650844304RAD23putative DNA repair protein RAD23O.I.H.G.S.X.
0.2726.20.90At1g55900842040TIM50component of a translocase in the mitochondrial inner membraneO.I.H.G.S.X.
0.2624.40.89At4g22720828368glycoprotease M22 family proteinF:endopeptidase activity, metalloendopeptidase activity, zinc ion binding;P:proteolysis;C:cellular_component unknown;OBMFAPO.I.H.G.S.X.
0.2624.40.89At2g35040818069AICARFT/IMPCHase bienzyme family proteinF:phosphoribosylaminoimidazolecarboxamide formyltransferase activity, IMP cyclohydrolase activity, catalytic activity;P:response to cold, purine nucleotide biosynthetic process;C:stromule, chloroplast, chloroplast stroma;OBMFAPVO.I.H.G.S.X.
0.2522.60.89At1g72550843587tRNA synthetase beta subunit family proteinF:phenylalanine-tRNA ligase activity, RNA binding, magnesium ion binding, nucleotide binding, ATP binding;P:phenylalanyl-tRNA aminoacylation, translation;C:phenylalanine-tRNA ligase complex, cytoplasm;BOMAFPO.I.H.G.S.X.
0.2522.60.89At2g34260817987transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MBFOPAO.I.H.G.S.X.
0.2522.60.89At5g10070830871RNase L inhibitor protein-relatedF:molecular_function unknown;P:biological_process unknown;C:cytosol, nucleus;OAMFPO.I.H.G.S.X.
0.2522.60.89At4g19150827653ankyrin repeat family proteinF:protein binding;P:biological_process unknown;C:unknown;MOFBPVAO.I.H.G.S.X.
0.2522.60.89At2g43770818980transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MFOBPAVO.I.H.G.S.X.
0.2522.60.89At5g59460836065scarecrow-like transcription factor 11 (SCL11)F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO.I.H.G.S.X.
0.2522.60.89At1g65650842876UCH2F:ubiquitin-specific protease activity, ubiquitin thiolesterase activity;P:protein deubiquitination, shoot development, shoot morphogenesis, leaf development, ubiquitin-dependent protein catabolic process;C:nucleus, intracellular, cytoplasm;MFOPO.I.H.G.S.X.
0.2522.60.90At5g23880832453CPSF100 (CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 100)Encodes a protein similar to the 100kD subunit of cleavage and polyadenylation specificity factor (CPSF), the factor responsible for the recognition of the AAUAAA motif during mRNA polyadenylation. The protein interacts with a portion of a nuclear poly(A) polymerase. It is likely to be a part of the mRNA 3'end formation apparatus.O.I.H.G.S.X.
0.2319.30.90At5g41970834202-F:molecular_function unknown;P:biological_process unknown;C:mitochondrion;MBOFPO.I.H.G.S.X.
0.2319.30.91At5g56280835727CSN6Aone of two genes encoding subunit 6 of COP9 signalosome complex. Protein contains a MPR1p and PAD1p N-terminal (MPN) domain at the N-terminal region and belongs to the Mov34 superfamily. Mutant and antisense expression result in a number of developmental defects and in ubiquitin/proteasome-mediated protein degradation.O.I.H.G.S.X.
0.2319.30.89At2g44020819007mitochondrial transcription termination factor-related / mTERF-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.2319.30.90At4g28450828962nucleotide binding / protein bindingThis gene is predicted to encode a protein with a DWD motif. It can bind to DDB1a in Y2H assays and may be involved in the formation of a CUL4-based E3 ubiquitin ligaseO.I.H.G.S.X.
0.2217.50.89At5g04280830307glycine-rich RNA-binding proteinF:RNA binding, zinc ion binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:nucleolus;MPFOBVAO.I.H.G.S.X.
0.2217.50.90At5g20920832216EIF2 BETAprotein synthesis initiation factor eIF2 betaO.I.H.G.S.X.
0.2115.80.90At2g46230819231-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPAO.I.H.G.S.X.
0.2115.80.89At5g49510835011PDF3 (PREFOLDIN 3)F:unfolded protein binding;P:protein folding;C:prefoldin complex;MFOPO.I.H.G.S.X.
0.2115.80.89At1g73180843652eukaryotic translation initiation factor-relatedF:molecular_function unknown;P:biological_process unknown;C:plasma membrane;MFOPBO.I.H.G.S.X.
0.2014.40.89At1g09150837434pseudouridine synthase and archaeosine transglycosylase (PUA) domain-containing proteinF:RNA binding;P:biological_process unknown;C:cellular_component unknown;MOFAPO.I.H.G.S.X.
0.2014.40.89At1g74230843763GR-RBP5 (glycine-rich RNA-binding protein 5)encodes a glycine-rich RNA binding protein.O.I.H.G.S.X.
0.2014.40.89At5g06550830543-F:molecular_function unknown;P:cell surface receptor linked signal transduction;C:unknown;MBOFPO.I.H.G.S.X.
0.1710.20.90At5g22370832298QQT1 (QUATRE-QUART 1)Encodes QQT1. Required for early embryo development. qqt1 mutant lines are embryo-defective. Participates in the organization of microtubules during cell division. Interacts with QQT2 (encoded by AT4G21800).O.I.H.G.S.X.
0.1710.20.90At2g39990818587EIF2translation initiation factor eIF2 p47 subunit homologO.I.H.G.S.X.
0.157.80.90At4g34960829648peptidyl-prolyl cis-trans isomerase, putative / cyclophilin, putative / rotamase, putativeF:peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:Golgi apparatus;BOMFPAVO.I.H.G.S.X.
0.146.80.89At3g18210821348oxidoreductase, 2OG-Fe(II) oxygenase family proteinF:oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, oxidoreductase activity, iron ion binding;P:protein metabolic process;C:cellular_component unknown;MPOBVO.I.H.G.S.X.
0.135.80.89At1g10840837627TIF3H1Encodes eukaryotic initiation factor 3H1 subunit (TIF3H1).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
49.999.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
46.799.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
45.299.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
45.199.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.799.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.999.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
39.599.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
39.199.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.499.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.799.7GSM143298Low_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
33.199.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.099.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.999.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.599.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.899.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.899.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.799.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.499.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.099.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
28.399.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.899.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.599.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
25.199.6GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.899.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.199.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
22.099.6E-MEXP-509-raw-cel-829148703
17.599.5GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
17.599.5GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
16.299.5GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
12.899.3GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
12.499.3GSM133758Lindsey_1-11_heart-stage-root_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
11.599.3GSM184477Lateral Root Cap root cells 2hr KCl control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
11.599.3E-MEXP-1138-raw-cel-1432772650
11.499.3GSM154503Arabidopsis desiccated mature pollen grains rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
10.299.2E-MEXP-1138-raw-cel-1432772522
9.499.1GSM154507Arabidopsis growing pollen tubes rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
9.199.1E-MEXP-1138-raw-cel-1432772586
8.999.0GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
8.699.0E-MEXP-1138-raw-cel-1432772682

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0652GO:0010387The aggregation, arrangement and bonding together of a set of components to form a signalosome.Link to AmiGO
0.0632GO:0006432The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.Link to AmiGO
0.0473GO:0006413The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.039200970Aminoacyl-tRNA biosynthesisLink to KEGG PATHWAY
0.027100670One carbon pool by folateLink to KEGG PATHWAY
0.019103018RNA degradationLink 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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