Co-expression analysis

Gene ID At5g39980
Gene name pentatricopeptide (PPR) repeat-containing protein
Module size 11 genes
NF 0.27
%ile 30.1



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
1.00100.01.00At5g39980833995pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:chloroplast;POMFBAO.I.H.G.S.X.
0.3846.70.89At1g74850843824PTAC2 (PLASTID TRANSCRIPTIONALLY ACTIVE2)Present in transcriptionally active plastid chromosomes. Involved in plastid gene expression.O.I.H.G.S.X.
0.3338.10.90At1g17850838364-F:molecular_function unknown;P:biological_process unknown;C:chloroplast;OBPMFO.I.H.G.S.X.
0.3032.10.89At5g54180835506PTAC15 (PLASTID TRANSCRIPTIONALLY ACTIVE15)F:molecular_function unknown;P:biological_process unknown;C:plastid chromosome, chloroplast, nucleoid;PMOO.I.H.G.S.X.
0.2930.30.92At5g50280835093EMB1006 (embryo defective 1006)F:unknown;P:embryonic development ending in seed dormancy;C:chloroplast;POMFBAO.I.H.G.S.X.
0.2522.60.89At1g79080844249pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:chloroplast;POMFBAO.I.H.G.S.X.
0.2420.70.90At1g63680842672MUREEncodes AtMurE, a homolog of the bacterial MurE that catalyze the ATP-dependent formation of UDP-N-acetylmuramic acid-tripeptide in bacterial peptidoglycan biosynthesis. Localized to plastids. AtMurE is involved in chloroplast biogenesis.O.I.H.G.S.X.
0.2217.50.89At1g71460843487pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFO.I.H.G.S.X.
0.2217.50.89At2g20020816521CAF1Promotes the splicing of chloroplast group II introns. Splices clpP-1 and ropC1 introns.O.I.H.G.S.X.
0.1912.70.89At3g61780825351emb1703 (embryo defective 1703)F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:chloroplast;OMFBPAVO.I.H.G.S.X.
0.103.40.90At3g02660821282emb2768 (EMBRYO DEFECTIVE 2768)F:RNA binding, tyrosine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:embryonic development ending in seed dormancy, tRNA aminoacylation for protein translation;C:mitochondrion, chloroplast;OBFMPAO.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
86.499.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
67.399.8GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
54.699.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
41.599.8GSM133761Lindsey_1-13_torpedo-cotyledon_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
32.899.7GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
21.599.6GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.599.6GSM133759Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
20.399.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
19.899.6GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
19.699.6GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.699.5GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.599.5GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.299.5GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.199.5GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
17.699.5GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
17.599.5GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
17.499.5GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
17.199.5GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
16.799.5GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
15.899.5GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
15.099.4GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
15.099.4GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.799.4GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
14.699.4GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
14.299.4GSM265411Arabidopsis, whole roots, -Fe, replicate 1GSE10496Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)Link to GEO
14.099.4GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.099.4GSM39209RRE2_C3GSE2169rre1 and rre2 mutantsLink to GEO
13.699.4GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
12.999.3GSM231201chl1 at T0, biological rep3GSE9148Expression data of 10-day-old wild-type and chl1-5 plants exposed to 25 mM nitrate for 0h or 0.5hLink to GEO
12.499.3GSM39192RRE1_C2GSE2169rre1 and rre2 mutantsLink to GEO
12.299.3GSM176879AWP_Control_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
12.099.3GSM39210RRE2_C4GSE2169rre1 and rre2 mutantsLink to GEO
11.699.3GSM39193RRE1_C3GSE2169rre1 and rre2 mutantsLink to GEO
11.499.3GSM231198wild-type at T0.5, biological rep3GSE9148Expression data of 10-day-old wild-type and chl1-5 plants exposed to 25 mM nitrate for 0h or 0.5hLink to GEO
11.299.2GSM265433Arabidopsis, root, longitudinal zone 4, -Fe conditions, rep 2GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
11.199.2GSM231204chl1 at T0.5, biological rep3GSE9148Expression data of 10-day-old wild-type and chl1-5 plants exposed to 25 mM nitrate for 0h or 0.5hLink to GEO
11.099.2GSM265413Arabidopsis, whole roots, -Fe, replicate 3GSE10496Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)Link to GEO
10.499.2GSM231195wild-type at T0, biological rep3GSE9148Expression data of 10-day-old wild-type and chl1-5 plants exposed to 25 mM nitrate for 0h or 0.5hLink to GEO
10.299.2GSM133773Lindsey_1-25_torpedo-meristem_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.999.1GSM142752MJ001_ATH1_A3-jones-rh1GSE6165The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.Link to GEO
9.699.1GSM176878AWP_AL_Txed_2GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
9.499.1GSM39213RRE2_Chitin3GSE2169rre1 and rre2 mutantsLink to GEO
9.399.1GSM39197RRE1_Chitin3GSE2169rre1 and rre2 mutantsLink to GEO
9.299.1GSM39201Col_C3GSE2169rre1 and rre2 mutantsLink to GEO
9.299.1GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
9.299.1GSM39194RRE1_C4GSE2169rre1 and rre2 mutantsLink to GEO
8.799.0GSM266671Arabidopsis, root cells, cortex, -Fe, replicate 3GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
8.699.0GSM39207RRE2_C1GSE2169rre1 and rre2 mutantsLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1431GO:0042793The synthesis of RNA from a plastid DNA template, usually by a specific plastid RNA polymerase.Link to AmiGO
0.1181GO:0000373The splicing of Group II introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group II introns and containing splice site consensus sequences, that is involved in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions (mechanistically similar to those for splicing of nuclear mRNAs) initiated by a bulged adenosine residue within the intron sequence as the initiating nucleophile. The intron is excised as a lariat.Link to AmiGO
0.1111GO:0045893Any process that activates or increases the frequency, rate or extent of DNA-dependent transcription.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.034100970Aminoacyl-tRNA biosynthesisLink 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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