CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g04190

Gene name tetratricopeptide repeat (TPR)-containing protein

Module size 5 genes

NF 0.53

%ile 73.8

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
0.47 61.2 1.00 At1g04190 839442 tetratricopeptide repeat (TPR)-containing protein F:binding;P:biological_process unknown;C:cellular_component unknown;OBMPFA O.I. H.G. S.X.
0.89 94.6 0.95 At3g61620 825335 RRP41 exonuclease RRP41 (RRP41) O.I. H.G. S.X.
0.50 65.3 0.95 At4g23620 828462 50S ribosomal protein-related F:structural constituent of ribosome, 5S rRNA binding;P:translation;C:ribosome, intracellular;OBP O.I. H.G. S.X.
0.44 57.2 0.95 At3g62940 825469 OTU-like cysteine protease family protein F:cysteine-type peptidase activity;P:biological_process unknown;C:cellular_component unknown;OMFBPVA O.I. H.G. S.X.
0.43 55.3 0.95 At2g37990 818377 ribosome biogenesis regulatory protein (RRS1) family protein F:unknown;P:ribosome biogenesis;C:nucleolus;MFOPB O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.47	61.2	1.00	At1g04190	839442	tetratricopeptide repeat (TPR)-containing protein	F:binding;P:biological_process unknown;C:cellular_component unknown;OBMPFA	O.I.	H.G.	S.X.
0.89	94.6	0.95	At3g61620	825335	RRP41	exonuclease RRP41 (RRP41)	O.I.	H.G.	S.X.
0.50	65.3	0.95	At4g23620	828462	50S ribosomal protein-related	F:structural constituent of ribosome, 5S rRNA binding;P:translation;C:ribosome, intracellular;OBP	O.I.	H.G.	S.X.
0.44	57.2	0.95	At3g62940	825469	OTU-like cysteine protease family protein	F:cysteine-type peptidase activity;P:biological_process unknown;C:cellular_component unknown;OMFBPVA	O.I.	H.G.	S.X.
0.43	55.3	0.95	At2g37990	818377	ribosome biogenesis regulatory protein (RRS1) family protein	F:unknown;P:ribosome biogenesis;C:nucleolus;MFOPB	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
19.1 99.6 E-MEXP-1443-raw-cel-1581869632
18.4 99.5 E-MEXP-1443-raw-cel-1581869803
17.7 99.5 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.2 99.5 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.0 99.5 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.8 99.5 E-MEXP-1443-raw-cel-1581869745
15.5 99.5 GSM205156 protoplast_controlDNA_rep1 GSE8257 Identification of KIN10-target genes in Arabidopsis mesophyll cells
14.5 99.4 GSM133968 Birnbaum_1-19_LRC-1_Rep1_ATH1 GSE5749 A gene expression map of the Arabidopsis root
14.5 99.4 E-MEXP-1443-raw-cel-1581869921
14.0 99.4 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.0 99.4 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.5 99.4 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.4 99.4 E-MEXP-1443-raw-cel-1581869688
13.1 99.4 E-ATMX-6-raw-cel-1308219081
12.5 99.3 GSM133991 Birnbaum_1-24_gl2-3_Rep3_ATH1 GSE5749 A gene expression map of the Arabidopsis root
12.5 99.3 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.5 99.3 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.5 99.3 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.4 99.3 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.2 99.2 GSM205160 protoplast_controlDNA_rep2 GSE8257 Identification of KIN10-target genes in Arabidopsis mesophyll cells
10.3 99.2 GSM133969 Birnbaum_1-20_LRC-2_Rep2_ATH1 GSE5749 A gene expression map of the Arabidopsis root
9.5 99.1 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.6 99.0 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
19.1	99.6	E-MEXP-1443-raw-cel-1581869632
18.4	99.5	E-MEXP-1443-raw-cel-1581869803
17.7	99.5	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.2	99.5	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.0	99.5	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.8	99.5	E-MEXP-1443-raw-cel-1581869745
15.5	99.5	GSM205156	protoplast_controlDNA_rep1	GSE8257	Identification of KIN10-target genes in Arabidopsis mesophyll cells
14.5	99.4	GSM133968	Birnbaum_1-19_LRC-1_Rep1_ATH1	GSE5749	A gene expression map of the Arabidopsis root
14.5	99.4	E-MEXP-1443-raw-cel-1581869921
14.0	99.4	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.0	99.4	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.5	99.4	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.4	99.4	E-MEXP-1443-raw-cel-1581869688
13.1	99.4	E-ATMX-6-raw-cel-1308219081
12.5	99.3	GSM133991	Birnbaum_1-24_gl2-3_Rep3_ATH1	GSE5749	A gene expression map of the Arabidopsis root
12.5	99.3	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.5	99.3	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.5	99.3	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.4	99.3	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.2	99.2	GSM205160	protoplast_controlDNA_rep2	GSE8257	Identification of KIN10-target genes in Arabidopsis mesophyll cells
10.3	99.2	GSM133969	Birnbaum_1-20_LRC-2_Rep2_ATH1	GSE5749	A gene expression map of the Arabidopsis root
9.5	99.1	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.6	99.0	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.024 1 GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
0.018 1 GO:0042254 The process of the formation of the constituents of the ribosome subunits, their assembly, and their transport to the sites of protein synthesis.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.024	1	GO:0006396	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
0.018	1	GO:0042254	The process of the formation of the constituents of the ribosome subunits, their assembly, and their transport to the sites of protein synthesis.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.038 1 03018 RNA degradation

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.038	1	03018	RNA degradation

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

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Gene ID	At1g04190
Gene name	tetratricopeptide repeat (TPR)-containing protein
Module size	5 genes
NF	0.53
%ile	73.8

Co-expression analysis

Gene ID At1g04190 Gene name tetratricopeptide repeat (TPR)-containing protein Module size 5 genes NF 0.53 %ile 73.8

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 KEGG0.038103018RNA degradation

Inter-species module comparison

Select a plant to compare co-expressed genes between species.Glycine_maxHordeum_vulgareOryza_sativaPopulus_trichocarpaTriticum_aestivumVitis_viniferaZea_mays

Gene ID At1g04190

Gene name tetratricopeptide repeat (TPR)-containing protein

Module size 5 genes

NF 0.53

%ile 73.8

: 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
0.038 1 03018 RNA degradation

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