Co-expression analysis

Gene ID At4g35130
Gene name pentatricopeptide (PPR) repeat-containing protein
Module size 7 genes
NF 0.47
%ile 66.4



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
0.4050.81.00At4g35130829665pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:unknown;POFMBO.I.H.G.S.X.
0.7184.20.84At2g33290817892SUVH2 (SU(VAR)3-9 HOMOLOG 2)Encodes a SU(VAR)3-9 homolog, a SET domain protein. Known SET domain proteins are involved in epigenetic control of gene expression and act as histone methyltransferases. There are 10 SUVH genes in Arabidopsis and members of this subfamily of the SET proteins have an additional conserved SRA domain. Gene is expressed in rosettes, stems, floral buds, and flowers by RT-PCR.O.I.H.G.S.X.
0.5065.30.85At5g37570833735pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFMO.I.H.G.S.X.
0.4355.30.82At4g07400826171VFB3 (VIER F-BOX PROTEINE 3)Encodes an F-box protein. Based on genetic analysis appears to be functionally redundant with VFB1,2,and 4. When levels of all 4 genes are reduced plants show defects in growth and reduced levels of auxin response genes.O.I.H.G.S.X.
0.4355.30.82At4g20090827754EMB1025 (embryo defective 1025)F:unknown;P:embryonic development ending in seed dormancy;C:unknown;POMFBAO.I.H.G.S.X.
0.4355.30.86At5g46400834683PRP39-2F:unknown;P:RNA processing;C:intracellular;OMFPBVAO.I.H.G.S.X.
0.4050.80.86At4g38010829957pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFMBO.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
54.799.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
40.899.8GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
37.599.7GSM318345ML_35DAS_2GSE12676Arabidopsis thaliana Ler developmental seriesLink to GEO
34.999.7GSM318332ML_35DAS_1GSE12676Arabidopsis thaliana Ler developmental seriesLink to GEO
34.499.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
31.599.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.599.6GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
22.899.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.299.6GSM38668NSNPGSE2268Arabidopsis polysome microarrayLink to GEO
16.599.5GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.799.4GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
10.999.2E-MEXP-828-raw-cel-1156922923
10.799.2GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
10.699.2E-MEXP-828-raw-cel-1156922485
10.599.2GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
10.399.2E-MEXP-828-raw-cel-1156922987
10.399.2GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
10.399.2E-MEXP-828-raw-cel-1156922891
10.299.2GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
9.899.1GSM284384Arabidopsis GEP5GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.899.1GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
9.799.1E-MEXP-828-raw-cel-1156922809
9.699.1GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
9.099.1E-MEXP-828-raw-cel-1156922509
9.099.1E-MEXP-828-raw-cel-1156922905
8.899.0E-MEXP-828-raw-cel-1156922368
8.899.0GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
8.899.0GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
8.699.0GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1181GO:0016571The modification of histones by addition of methyl groups.Link to AmiGO
0.1111GO:0040029Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence.Link to AmiGO
0.0231GO:0006396Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG

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