Co-expression analysis

Gene ID At5g63660
Gene name PDF2.5
Module size 7 genes
NF 0.52
%ile 72.8



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
0.7586.91.00At5g63660836486PDF2.5Predicted to encode a PR (pathogenesis-related) protein. Belongs to the plant defensin (PDF) family with the following members: At1g75830/PDF1.1, At5g44420/PDF1.2a, At2g26020/PDF1.2b, At5g44430/PDF1.2c, At2g26010/PDF1.3, At1g19610/PDF1.4, At1g55010/PDF1.5, At2g02120/PDF2.1, At2g02100/PDF2.2, At2g02130/PDF2.3, At1g61070/PDF2.4, At5g63660/PDF2.5, At2g02140/PDF2.6, At5g38330/PDF3.1 and At4g30070/PDF3.2.O.I.H.G.S.X.
0.6075.70.63At2g23050816835NPY4 (NAKED PINS IN YUC MUTANTS 4)A member of the NPY gene family (NPY1/AT4G31820, NPY2/AT2G14820, NPY3/AT5G67440, NPY4/AT2G23050, NPY5/AT4G37590). Involved in auxin-mediated organogenesis.O.I.H.G.S.X.
0.5065.30.68At1g74500843791bHLH family proteinF:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;PO.I.H.G.S.X.
0.5065.30.65At5g48940834952leucine-rich repeat transmembrane protein kinase, putativeF:protein binding, protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:unknown;MPOBFVAO.I.H.G.S.X.
0.4457.20.72At3g15240820755--O.I.H.G.S.X.
0.4457.20.63At5g62340836355invertase/pectin methylesterase inhibitor family proteinF:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:endomembrane system;PO.I.H.G.S.X.
0.3338.10.63At1g31950840085terpene synthase/cyclase family proteinF:lyase activity, magnesium ion binding;P:metabolic process;C:membrane;POO.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
205.2100.0GSM311291Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
177.4100.0GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
159.399.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
115.199.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
85.499.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
79.299.9GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
77.099.9GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
76.499.9GSM311292Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
76.499.9GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
73.999.9GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
73.999.9GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
72.299.9GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
69.999.9GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
69.399.9GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
68.899.9GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
68.499.9GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
66.599.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
66.199.8E-ATMX-35-raw-cel-1574334816
62.499.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
61.099.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
61.099.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
56.499.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
53.299.8E-ATMX-35-raw-cel-1574334832
52.199.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.299.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
48.299.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.499.8E-ATMX-35-raw-cel-1574334800
40.299.8GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
35.799.7GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
33.399.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
21.199.6GSM205185protoplast_KIN10_rep2GSE8257Identification of KIN10-target genes in Arabidopsis mesophyll cellsLink to GEO
20.799.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.399.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.399.6GSM128654Underwood_1-7_DC3000-10e6-24h_Rep1_ATH1GSE5520Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interactionLink to GEO
18.299.5GSM205160protoplast_controlDNA_rep2GSE8257Identification of KIN10-target genes in Arabidopsis mesophyll cellsLink to GEO
17.199.5GSM128675Underwood_1-28_DC3000-10e8-7h_Rep1_ATH1GSE5520Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interactionLink to GEO
16.599.5GSM133029BC482-1GSE5684AtGenExpress: Pathogen Series: Response to Botrytis cinerea infectionLink to GEO
16.399.5GSM131603ATGE_41_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
15.099.4GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
14.299.4GSM205156protoplast_controlDNA_rep1GSE8257Identification of KIN10-target genes in Arabidopsis mesophyll cellsLink to GEO
14.199.4GSM128655Underwood_1-8_DC3000-10e6-24h_Rep2_ATH1GSE5520Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interactionLink to GEO
13.799.4GSM204026protoplast_control_rep1GSE8248Identification of hypoxia-inducible genes in Arabidopsis mesophyll cellsLink to GEO
12.899.3GSM128676Underwood_1-29_DC3000-10e8-7h_Rep2_ATH1GSE5520Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interactionLink to GEO
12.599.3E-MEXP-1451-raw-cel-1585200330
11.799.3GSM131604ATGE_41_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
11.599.3GSM131605ATGE_41_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.899.1GSM205159protoplast_KIN10_rep1GSE8257Identification of KIN10-target genes in Arabidopsis mesophyll cellsLink to GEO
9.799.1E-MEXP-449-raw-cel-676423362
9.599.1GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
8.999.0GSM142846MG001_ATH1_A27-Torres-9N1GSE6176Impact of Type III effectors on plant defense responsesLink to GEO
8.899.0E-MEXP-711-raw-cel-1563002768
8.799.0E-MEXP-711-raw-cel-1563002839
8.799.0E-MEXP-1451-raw-cel-1585200298
8.799.0GSM176879AWP_Control_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
8.699.0GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0161GO:0009416A 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 light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.Link to AmiGO
0.0151GO:0007169The series of molecular signals generated as a consequence of a transmembrane receptor tyrosine kinase binding to its physiological ligand.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



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