CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At2g40720

Gene name pentatricopeptide (PPR) repeat-containing protein

Module size 5 genes

NF 0.43

%ile 60.6

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
0.55 70.6 1.00 At2g40720 818667 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:unknown;C:cellular_component unknown;POMFB O.I. H.G. S.X.
0.55 70.6 0.92 At2g33760 817942 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:unknown;C:cellular_component unknown;POMFBA O.I. H.G. S.X.
0.44 57.2 0.89 At3g06600 819839 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.43 55.3 0.91 At4g25270 828630 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:biological_process unknown;C:chloroplast;POMFB O.I. H.G. S.X.
0.30 32.1 0.91 At1g30010 839880 intron maturase, type II family protein F:RNA binding, RNA-directed DNA polymerase activity;P:RNA-dependent DNA replication, RNA splicing;C:unknown;BPOFAMV O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.55	70.6	1.00	At2g40720	818667	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:unknown;C:cellular_component unknown;POMFB	O.I.	H.G.	S.X.
0.55	70.6	0.92	At2g33760	817942	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:unknown;C:cellular_component unknown;POMFBA	O.I.	H.G.	S.X.
0.44	57.2	0.89	At3g06600	819839	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.43	55.3	0.91	At4g25270	828630	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:biological_process unknown;C:chloroplast;POMFB	O.I.	H.G.	S.X.
0.30	32.1	0.91	At1g30010	839880	intron maturase, type II family protein	F:RNA binding, RNA-directed DNA polymerase activity;P:RNA-dependent DNA replication, RNA splicing;C:unknown;BPOFAMV	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
19.6 99.6 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
18.6 99.5 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.0 99.5 E-ATMX-13-raw-cel-1556149775
16.0 99.5 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.0 99.5 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.2 99.4 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.0 99.4 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.5 99.4 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.3 99.4 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.1 99.4 E-ATMX-13-raw-cel-1556149935
13.7 99.4 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.6 99.4 E-ATMX-13-raw-cel-1556149839
13.4 99.4 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.1 99.4 GSM268249 dor-drought-2, biological rep 2 GSE10643 Transcription profiling of Arabidopsis dor mutant and wild-type plants in response to drought stress.
13.0 99.4 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.9 99.3 GSM134204 Murray_3-2_D3-GROWTH_Rep1_ATH1 GSE5750 Growth of suspension-cultured cells
12.9 99.3 E-ATMX-13-raw-cel-1556149743
12.7 99.3 E-ATMX-13-raw-cel-1556149727
12.7 99.3 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.7 99.3 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.5 99.3 E-ATMX-13-raw-cel-1556149903
12.5 99.3 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.4 99.3 E-ATMX-13-raw-cel-1556149823
11.9 99.3 E-ATMX-13-raw-cel-1556149855
11.7 99.3 Evans_2-10_col-aeq-cold_ATH1
11.5 99.3 E-ATMX-13-raw-cel-1556149807
11.4 99.3 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.9 99.2 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.8 99.2 E-ATMX-13-raw-cel-1556149791
10.8 99.2 GSM297392 At.StarchSD.WTSS3.WTR1L1 GSE11708 Global gene expression in Atss3 mutant and WT over short day diurnal cycle
10.7 99.2 Evans_2-8_35s-FAD3-cold_ATH1
10.6 99.2 E-ATMX-13-raw-cel-1556149759
10.5 99.2 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.4 99.2 E-MEXP-449-raw-cel-676423218
9.8 99.1 Evans_2-12_fab3-7-8-mut-aeq-cold_ATH1
9.5 99.1 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4 99.1 Evans_2-2_col-WT-cold_ATH1
9.3 99.1 GSM133951 Murray_2-7_T12-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies
9.2 99.1 GSM131608 ATGE_42_D GSE5632 AtGenExpress: Developmental series (flowers and pollen)
9.1 99.1 E-ATMX-13-raw-cel-1556149871
9.1 99.1 Evans_2-4_fab1-mut-cold_ATH1
9.0 99.1 E-ATMX-13-raw-cel-1556149887
8.9 99.0 GSM133952 Murray_2-8_T14-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies
8.7 99.0 GSM297382 At.StarchSD.WTSS3.SS3R1L1 GSE11708 Global gene expression in Atss3 mutant and WT over short day diurnal cycle
8.7 99.0 GSM131606 ATGE_42_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
8.7 99.0 GSM131304 AtGen_6-2612_Osmoticstress-Shoots-24.0h_Rep2 GSE5622 AtGenExpress: Stress Treatments (Osmotic stress)
8.6 99.0 GSM133950 Murray_2-6_T10-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies
8.6 99.0 GSM131303 AtGen_6-2611_Osmoticstress-Shoots-24.0h_Rep1 GSE5622 AtGenExpress: Stress Treatments (Osmotic stress)

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
19.6	99.6	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
18.6	99.5	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.0	99.5	E-ATMX-13-raw-cel-1556149775
16.0	99.5	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.0	99.5	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.2	99.4	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.0	99.4	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.5	99.4	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.3	99.4	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.1	99.4	E-ATMX-13-raw-cel-1556149935
13.7	99.4	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.6	99.4	E-ATMX-13-raw-cel-1556149839
13.4	99.4	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.1	99.4	GSM268249	dor-drought-2, biological rep 2	GSE10643	Transcription profiling of Arabidopsis dor mutant and wild-type plants in response to drought stress.
13.0	99.4	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.9	99.3	GSM134204	Murray_3-2_D3-GROWTH_Rep1_ATH1	GSE5750	Growth of suspension-cultured cells
12.9	99.3	E-ATMX-13-raw-cel-1556149743
12.7	99.3	E-ATMX-13-raw-cel-1556149727
12.7	99.3	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.7	99.3	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.5	99.3	E-ATMX-13-raw-cel-1556149903
12.5	99.3	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.4	99.3	E-ATMX-13-raw-cel-1556149823
11.9	99.3	E-ATMX-13-raw-cel-1556149855
11.7	99.3	Evans_2-10_col-aeq-cold_ATH1
11.5	99.3	E-ATMX-13-raw-cel-1556149807
11.4	99.3	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.9	99.2	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.8	99.2	E-ATMX-13-raw-cel-1556149791
10.8	99.2	GSM297392	At.StarchSD.WTSS3.WTR1L1	GSE11708	Global gene expression in Atss3 mutant and WT over short day diurnal cycle
10.7	99.2	Evans_2-8_35s-FAD3-cold_ATH1
10.6	99.2	E-ATMX-13-raw-cel-1556149759
10.5	99.2	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.4	99.2	E-MEXP-449-raw-cel-676423218
9.8	99.1	Evans_2-12_fab3-7-8-mut-aeq-cold_ATH1
9.5	99.1	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4	99.1	Evans_2-2_col-WT-cold_ATH1
9.3	99.1	GSM133951	Murray_2-7_T12-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies
9.2	99.1	GSM131608	ATGE_42_D	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.1	99.1	E-ATMX-13-raw-cel-1556149871
9.1	99.1	Evans_2-4_fab1-mut-cold_ATH1
9.0	99.1	E-ATMX-13-raw-cel-1556149887
8.9	99.0	GSM133952	Murray_2-8_T14-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies
8.7	99.0	GSM297382	At.StarchSD.WTSS3.SS3R1L1	GSE11708	Global gene expression in Atss3 mutant and WT over short day diurnal cycle
8.7	99.0	GSM131606	ATGE_42_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
8.7	99.0	GSM131304	AtGen_6-2612_Osmoticstress-Shoots-24.0h_Rep2	GSE5622	AtGenExpress: Stress Treatments (Osmotic stress)
8.6	99.0	GSM133950	Murray_2-6_T10-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies
8.6	99.0	GSM131303	AtGen_6-2611_Osmoticstress-Shoots-24.0h_Rep1	GSE5622	AtGenExpress: Stress Treatments (Osmotic stress)

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.167 1 GO:0006278 The process whereby new strands of DNA are synthesized, using RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strands.
0.045 1 GO:0008380 The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.167	1	GO:0006278	The process whereby new strands of DNA are synthesized, using RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strands.
0.045	1	GO:0008380	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.

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	At2g40720
Gene name	pentatricopeptide (PPR) repeat-containing protein
Module size	5 genes
NF	0.43
%ile	60.6

Co-expression analysis

Gene ID At2g40720 Gene name pentatricopeptide (PPR) repeat-containing protein Module size 5 genes NF 0.43 %ile 60.6

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

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 At2g40720

Gene name pentatricopeptide (PPR) repeat-containing protein

Module size 5 genes

NF 0.43

%ile 60.6

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

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