CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g13880

Gene name pentatricopeptide (PPR) repeat-containing protein

Module size 5 genes

NF 0.22

%ile 21.1

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : 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
0.13 5.8 1.00 At3g13880 820601 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:biological_process unknown;C:unknown;POMFB O.I. H.G. S.X.
0.29 30.3 0.85 At4g19190 827658 zinc knuckle (CCHC-type) family protein F:zinc ion binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MOFBPVA O.I. H.G. S.X.
0.29 30.3 0.84 At5g39680 833964 EMB2744 (EMBRYO DEFECTIVE 2744) F:unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;POMF O.I. H.G. S.X.
0.24 20.7 0.86 At1g77010 844037 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:biological_process unknown;C:unknown;POMF O.I. H.G. S.X.
0.21 15.8 0.85 At4g13650 826999 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:biological_process unknown;C:cellular_component unknown;POMFBA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.13	5.8	1.00	At3g13880	820601	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:biological_process unknown;C:unknown;POMFB	O.I.	H.G.	S.X.
0.29	30.3	0.85	At4g19190	827658	zinc knuckle (CCHC-type) family protein	F:zinc ion binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MOFBPVA	O.I.	H.G.	S.X.
0.29	30.3	0.84	At5g39680	833964	EMB2744 (EMBRYO DEFECTIVE 2744)	F:unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;POMF	O.I.	H.G.	S.X.
0.24	20.7	0.86	At1g77010	844037	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:biological_process unknown;C:unknown;POMF	O.I.	H.G.	S.X.
0.21	15.8	0.85	At4g13650	826999	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:biological_process unknown;C:cellular_component unknown;POMFBA	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
121.0 99.9 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
70.7 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
62.9 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
56.7 99.8 GSM133761 Lindsey_1-13_torpedo-cotyledon_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
54.7 99.8 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
48.3 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
48.1 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
47.3 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
45.4 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.4 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
42.3 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.7 99.7 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.2 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
37.2 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.8 99.7 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
33.3 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.3 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.5 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
29.8 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.4 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.6 99.7 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.5 99.6 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.5 99.6 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.3 99.6 GSM184556 Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
19.0 99.5 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.5 99.1 E-MEXP-739-raw-cel-1099467384
9.4 99.1 GSM133773 Lindsey_1-25_torpedo-meristem_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.4 99.1 E-MEXP-739-raw-cel-1099467393
8.7 99.0 E-MEXP-739-raw-cel-1099467375

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
121.0	99.9	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
70.7	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
62.9	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
56.7	99.8	GSM133761	Lindsey_1-13_torpedo-cotyledon_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
54.7	99.8	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
48.3	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
48.1	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
47.3	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
45.4	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.4	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
42.3	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.7	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.2	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
37.2	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.8	99.7	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
33.3	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.3	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.5	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
29.8	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.4	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.6	99.7	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.5	99.6	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.5	99.6	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.3	99.6	GSM184556	Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
19.0	99.5	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.5	99.1	E-MEXP-739-raw-cel-1099467384
9.4	99.1	GSM133773	Lindsey_1-25_torpedo-meristem_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.4	99.1	E-MEXP-739-raw-cel-1099467393
8.7	99.0	E-MEXP-739-raw-cel-1099467375

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link 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

Gene ID	At3g13880
Gene name	pentatricopeptide (PPR) repeat-containing protein
Module size	5 genes
NF	0.22
%ile	21.1

Co-expression analysis

Gene ID At3g13880 Gene name pentatricopeptide (PPR) repeat-containing protein Module size 5 genes NF 0.22 %ile 21.1

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein: VF over 0.50, : over 0.25, : below 0.25

Co-expressed genes

Click More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink 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_maxHordeum_vulgareOryza_sativaPopulus_trichocarpaTriticum_aestivumVitis_viniferaZea_mays

Gene ID At3g13880

Gene name pentatricopeptide (PPR) repeat-containing protein

Module size 5 genes

NF 0.22

%ile 21.1

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

SF Genes GO ID Process Name Link to AmiGO

SF Genes KEGG ID Pathway name Link to KEGG

Select a plant to compare co-expressed genes between species.
Glycine_max
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays