CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g02420

Gene name pentatricopeptide (PPR) repeat-containing protein

Module size 16 genes

NF 0.61

%ile 82.7

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
0.44 57.2 1.00 At1g02420 837779 pentatricopeptide (PPR) repeat-containing protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;POMFBA O.I. H.G. S.X.
0.74 86.1 0.88 At3g45120 823648 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.73 85.5 0.87 At2g19300 816447 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. H.G. S.X.
0.73 85.5 0.84 At3g14670 820695 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPVA O.I. H.G. S.X.
0.71 84.2 0.88 At5g35290 833483 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown O.I. H.G. S.X.
0.69 82.9 0.88 At3g50320 824194 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.68 82.2 0.87 At2g04870 815034 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POM O.I. H.G. S.X.
0.67 81.6 0.88 At1g17275 3766742 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.63 78.1 0.87 At1g44990 841064 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system O.I. H.G. S.X.
0.61 76.7 0.90 At5g27340 832792 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown O.I. H.G. S.X.
0.61 76.7 0.85 At5g27190 3770742 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.59 74.7 0.84 At5g37880 833767 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.56 73.0 0.84 At3g43150 823381 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.53 68.6 0.86 At4g08890 3769919 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.49 63.5 0.84 At2g10780 3767798 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.47 61.2 0.85 At3g46380 823785 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.44	57.2	1.00	At1g02420	837779	pentatricopeptide (PPR) repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;POMFBA	O.I.	H.G.	S.X.
0.74	86.1	0.88	At3g45120	823648	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.73	85.5	0.87	At2g19300	816447	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	H.G.	S.X.
0.73	85.5	0.84	At3g14670	820695	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPVA	O.I.	H.G.	S.X.
0.71	84.2	0.88	At5g35290	833483	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown	O.I.	H.G.	S.X.
0.69	82.9	0.88	At3g50320	824194	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.68	82.2	0.87	At2g04870	815034	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POM	O.I.	H.G.	S.X.
0.67	81.6	0.88	At1g17275	3766742	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.63	78.1	0.87	At1g44990	841064	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system	O.I.	H.G.	S.X.
0.61	76.7	0.90	At5g27340	832792	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown	O.I.	H.G.	S.X.
0.61	76.7	0.85	At5g27190	3770742	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.59	74.7	0.84	At5g37880	833767	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.56	73.0	0.84	At3g43150	823381	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.53	68.6	0.86	At4g08890	3769919	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.49	63.5	0.84	At2g10780	3767798	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.47	61.2	0.85	At3g46380	823785	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	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
49.0 99.8 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
45.5 99.8 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
41.9 99.8 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
38.6 99.8 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
33.3 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
31.9 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
31.0 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.0 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
30.7 99.7 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
30.5 99.7 GSM284386 Arabidopsis GSUS3 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
30.0 99.7 E-MEXP-1443-raw-cel-1581869573
29.8 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
29.4 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.2 99.7 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.6 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.9 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.8 99.7 GSM184900 Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
26.4 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
26.3 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.6 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.3 99.6 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.3 99.6 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.4 99.6 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.5 99.6 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.5 99.6 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
22.2 99.6 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.6 99.6 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
21.5 99.6 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
20.6 99.6 GSM284387 Arabidopsis GSUS4b GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
18.9 99.5 GSM184918 Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
18.2 99.5 GSM131699 ATGE_81_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
15.6 99.5 GSM131698 ATGE_81_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
14.0 99.4 E-ATMX-35-raw-cel-1574334832
13.8 99.4 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
12.7 99.3 GSM131695 ATGE_79_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
12.5 99.3 E-MEXP-1443-raw-cel-1581869515
12.1 99.3 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
11.3 99.3 GSM131694 ATGE_79_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
11.3 99.3 GSM184899 Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
11.1 99.2 GSM131697 ATGE_81_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
10.8 99.2 E-ATMX-1-raw-cel-1112746095
10.2 99.2 GSM131702 ATGE_82_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
9.7 99.1 GSM184551 Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.3 99.1 GSM131696 ATGE_79_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
9.2 99.1 GSM133755 Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.1 99.1 GSM311292 Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
9.0 99.1 GSM10453 WT Mature Green Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
8.9 99.0 GSM311282 Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
8.9 99.0 GSM133774 Lindsey_1-26_torpedo-meristem_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
49.0	99.8	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
45.5	99.8	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
41.9	99.8	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
38.6	99.8	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
33.3	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
31.9	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
31.0	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.0	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
30.7	99.7	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
30.5	99.7	GSM284386	Arabidopsis GSUS3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
30.0	99.7	E-MEXP-1443-raw-cel-1581869573
29.8	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
29.4	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.2	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.6	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.9	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.8	99.7	GSM184900	Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
26.4	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
26.3	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.6	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.3	99.6	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.3	99.6	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.4	99.6	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.5	99.6	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.5	99.6	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
22.2	99.6	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.6	99.6	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
21.5	99.6	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
20.6	99.6	GSM284387	Arabidopsis GSUS4b	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
18.9	99.5	GSM184918	Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
18.2	99.5	GSM131699	ATGE_81_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
15.6	99.5	GSM131698	ATGE_81_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
14.0	99.4	E-ATMX-35-raw-cel-1574334832
13.8	99.4	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
12.7	99.3	GSM131695	ATGE_79_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
12.5	99.3	E-MEXP-1443-raw-cel-1581869515
12.1	99.3	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
11.3	99.3	GSM131694	ATGE_79_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
11.3	99.3	GSM184899	Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
11.1	99.2	GSM131697	ATGE_81_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
10.8	99.2	E-ATMX-1-raw-cel-1112746095
10.2	99.2	GSM131702	ATGE_82_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
9.7	99.1	GSM184551	Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.3	99.1	GSM131696	ATGE_79_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
9.2	99.1	GSM133755	Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.1	99.1	GSM311292	Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
9.0	99.1	GSM10453	WT Mature Green Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
8.9	99.0	GSM311282	Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
8.9	99.0	GSM133774	Lindsey_1-26_torpedo-meristem_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues

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	At1g02420
Gene name	pentatricopeptide (PPR) repeat-containing protein
Module size	16 genes
NF	0.61
%ile	82.7

Co-expression analysis

Gene ID At1g02420 Gene name pentatricopeptide (PPR) repeat-containing protein Module size 16 genes NF 0.61 %ile 82.7

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 At1g02420

Gene name pentatricopeptide (PPR) repeat-containing protein

Module size 16 genes

NF 0.61

%ile 82.7

: 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