Co-expression analysis

Gene ID At2g21170
Gene name TIM (TRIOSEPHOSPHATE ISOMERASE)
Module size 25 genes
NF 0.72
%ile 90.3



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
0.4457.21.00At2g21170816652TIM (TRIOSEPHOSPHATE ISOMERASE)Encodes triosephosphate isomerase.O.I.H.G.S.X.
0.8290.90.95At1g05190839273emb2394 (embryo defective 2394)F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation;C:chloroplast stroma, chloroplast, large ribosomal subunit, membrane, chloroplast envelope;BOAFPMO.I.H.G.S.X.
0.8190.40.94At3g52150824379RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast stroma, chloroplast, chloroplast envelope;MPOFBAO.I.H.G.S.X.
0.8089.80.95At2g43030818905ribosomal protein L3 family proteinF:structural constituent of ribosome;P:translation;C:ribosome, chloroplast stroma, chloroplast, membrane;BOAMFPO.I.H.G.S.X.
0.7989.10.95At1g78630844199emb1473 (embryo defective 1473)F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation;C:thylakoid, ribosome, chloroplast, chloroplast stroma;BOMFAPO.I.H.G.S.X.
0.7788.00.96At3g54210824588ribosomal protein L17 family proteinF:structural constituent of ribosome;P:translation;C:ribosome, chloroplast;BOMFPO.I.H.G.S.X.
0.7788.00.95At1g07320837243RPL4encodes a plastid ribosomal protein L4O.I.H.G.S.X.
0.7788.00.95At3g1312082050030S ribosomal protein S10, chloroplast, putativeF:structural constituent of ribosome, RNA binding;P:translation;C:small ribosomal subunit, chloroplast;BOMAPFO.I.H.G.S.X.
0.7788.00.95At4g01310827947ribosomal protein L5 family proteinF:structural constituent of ribosome;P:translation;C:in 6 components;BOPAFMO.I.H.G.S.X.
0.7687.40.94At1g3568084047250S ribosomal protein L21, chloroplast / CL21 (RPL21)F:structural constituent of ribosome, RNA binding;P:response to cold, translation;C:ribosome, chloroplast stroma, nucleus, chloroplast, chloroplast envelope;BOPMFO.I.H.G.S.X.
0.7687.40.95At4g24770828579RBP31 (31-KDA RNA BINDING PROTEIN)Encodes a chloroplast RNA-binding protein. A substrate of the type III effector HopU1 (mono-ADP-ribosyltransferase).O.I.H.G.S.X.
0.7687.40.94At1g64510842759ribosomal protein S6 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:thylakoid, chloroplast thylakoid membrane, ribosome, chloroplast;BOPO.I.H.G.S.X.
0.7687.40.94At2g3345081791050S ribosomal protein L28, chloroplast (CL28)F:structural constituent of ribosome;P:translation;C:ribosome, chloroplast, membrane;BOPFO.I.H.G.S.X.
0.7586.90.94At1g29070839781ribosomal protein L34 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:ribosome, intracellular, chloroplast;BPOFO.I.H.G.S.X.
0.7486.10.94At5g08280830724HEMC (HYDROXYMETHYLBILANE SYNTHASE)Encodes a protein with porphobilinogen deaminase activity. This protein is targeted to the chloroplast.O.I.H.G.S.X.
0.7486.10.94At1g50900841512-F:molecular_function unknown;P:biological_process unknown;C:chloroplast, chloroplast stroma;POO.I.H.G.S.X.
0.7486.10.94At2g33800817947ribosomal protein S5 family proteinF:structural constituent of ribosome, RNA binding;P:response to cadmium ion, response to cold, translation;C:in 8 components;BOMAFPO.I.H.G.S.X.
0.7385.50.95At3g08740820021elongation factor P (EF-P) family proteinF:translation elongation factor activity;P:translational elongation;C:chloroplast, chloroplast stroma;BOPAO.I.H.G.S.X.
0.7385.50.95At5g1432083128230S ribosomal protein S13, chloroplast (CS13)F:structural constituent of ribosome, RNA binding, nucleic acid binding;P:translation;C:small ribosomal subunit, chloroplast, chloroplast envelope;BOPMFAO.I.H.G.S.X.
0.7385.50.94At5g14910831343heavy-metal-associated domain-containing proteinF:metal ion binding;P:metal ion transport;C:thylakoid, chloroplast thylakoid membrane, chloroplast stroma, chloroplast;PO.I.H.G.S.X.
0.7385.50.95At5g13510831195ribosomal protein L10 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic ribosome, ribosome, chloroplast, chloroplast stroma;BOAPMFO.I.H.G.S.X.
0.7083.50.94At1g32990840194PRPL11 (PLASTID RIBOSOMAL PROTEIN L11)mutant has Decreased effective quantum yield of photosystem II; Pale green plants; Reduced growth rate; Plastid Ribosomal Protein L11O.I.H.G.S.X.
0.6982.90.94At4g18480827580CHLI1Encodes the CHLI subunit of magnesium chelatase which is required for chlorophyll biosynthesis. All four cysteine residues of the protein form two disulfide bonds (Cys102-Cys193 and Cys354-Cys396) under oxidized conditions but are fully reduced by reduction. It was suggested that the redox state of CHLI is regulated in vivo by the change of the redox environment in the chloroplasts probably via the Trx system.O.I.H.G.S.X.
0.6882.20.96At5g45390834575CLPP4 (CLP PROTEASE P4)One of several nuclear-encoded ClpPs (caseinolytic protease). Contains a highly conserved catalytic triad of Ser-type proteases (Ser-His-Asp). The name reflects nomenclature described in Adam et. al (2001).O.I.H.G.S.X.
0.6781.60.95At1g75350843871emb2184 (embryo defective 2184)F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation, ribosome biogenesis;C:ribosome, chloroplast, chloroplast stroma, chloroplast envelope;BOPO.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
66.099.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
62.499.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
61.999.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.899.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.599.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.599.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.399.8GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
45.399.8GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
41.599.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.999.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.899.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.799.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.999.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.299.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.899.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.799.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.899.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.099.7GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
30.499.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
29.199.7GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
28.599.7GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
25.199.6GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
24.799.6GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.899.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.699.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.599.6GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
21.899.6E-MEXP-1443-raw-cel-1581869745
21.699.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.499.6GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.199.6GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
17.199.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.599.4GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.499.3GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
12.099.3GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.599.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
11.499.3E-MEXP-1443-raw-cel-1581869803
11.299.2E-MEXP-1138-raw-cel-1432773322
10.699.2GSM184922Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
10.099.2GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.099.2GSM269825T8 leaf-drought-rep2GSE10670Global expression profiling of wild type and transgenic Arabidopsis plants in response to water stressLink to GEO
9.899.1GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.699.1E-MEXP-1138-raw-cel-1432773258
9.599.1GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.599.1GSM269821WT leaf-drought-rep2GSE10670Global expression profiling of wild type and transgenic Arabidopsis plants in response to water stressLink to GEO
9.599.1E-MEXP-1138-raw-cel-1432773066
9.599.1E-MEXP-285-raw-cel-440782725
9.299.1GSM311291Laser 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
8.899.0E-MEXP-285-raw-cel-440782791

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0782GO:0015995The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, from less complex precursors.Link to AmiGO
0.0755GO:0042254The process of the formation of the constituents of the ribosome subunits, their assembly, and their transport to the sites of protein synthesis.Link to AmiGO
0.0651GO:0019253The fixation of carbon dioxide (CO2) as glucose in the chloroplasts of C3 plants; uses ATP and NADPH formed in the light reactions of photosynthesis; carbon dioxide reacts with ribulose 1,5-bisphosphate (catalyzed by the function of ribulose-bisphosphate carboxylase) to yield two molecules of 3-phosphoglycerate; these are then phosphorylated by ATP to 1,3-bisphosphateglyceraldehyde which, in turn, is then reduced by NADPH to glyceraldehyde 3-phosphate. The glyceraldehyde 3-phosphate is converted to fructose 5-phosphate and ribulose 5-phosphate by aldolase and other enzymes; the ribulose 5-phosphate is phosphorylated by ATP to ribulose 1,5-bisphosphate.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.078200860Porphyrin and chlorophyll metabolismLink to KEGG PATHWAY
0.062803010RibosomeLink to KEGG PATHWAY
0.032100562Inositol phosphate 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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