CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g32610

Gene name hydroxyproline-rich glycoprotein family protein

Module size 5 genes

NF 0.49

%ile 69.2

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
0.67 81.6 1.00 At1g32610 840156 hydroxyproline-rich glycoprotein family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOVB O.I. H.G. S.X.
0.67 81.6 0.92 At4g14590 827107 emb2739 (embryo defective 2739) F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;MPO O.I. H.G. S.X.
0.57 73.8 0.92 At4g29560 829077 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM O.I. H.G. S.X.
0.50 65.3 0.91 At2g33760 817942 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:unknown;C:cellular_component unknown;POMFBA O.I. H.G. S.X.
0.32 35.7 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.
0.67	81.6	1.00	At1g32610	840156	hydroxyproline-rich glycoprotein family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOVB	O.I.	H.G.	S.X.
0.67	81.6	0.92	At4g14590	827107	emb2739 (embryo defective 2739)	F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;MPO	O.I.	H.G.	S.X.
0.57	73.8	0.92	At4g29560	829077	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM	O.I.	H.G.	S.X.
0.50	65.3	0.91	At2g33760	817942	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:unknown;C:cellular_component unknown;POMFBA	O.I.	H.G.	S.X.
0.32	35.7	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
22.4 99.6 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
22.2 99.6 E-MEXP-285-raw-cel-440782725
21.2 99.6 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
20.8 99.6 E-MEXP-285-raw-cel-440782791
18.7 99.5 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
17.3 99.5 E-ATMX-35-raw-cel-1574334880
15.9 99.5 GSM239253 CaMV::DME pollen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
15.6 99.5 E-ATMX-35-raw-cel-1574334848
15.4 99.5 GSM239251 Columbia glabrous (C24) wild type pollen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
13.0 99.4 GSM131638 ATGE_73_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
12.7 99.3 GSM131636 ATGE_73_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
11.9 99.3 E-ATMX-1-raw-cel-1112746154
11.4 99.3 GSM131637 ATGE_73_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
10.6 99.2 GSM184906 Arabidopsis, root cells, protophloem, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
10.5 99.2 GSM184904 Arabidopsis, root cells, protophloem, standard conditions, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
9.5 99.1 E-ATMX-35-raw-cel-1574334864
9.5 99.1 GSM131698 ATGE_81_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
9.5 99.1 GSM131699 ATGE_81_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
9.2 99.1 GSM133957 Fukuda_1-2_0B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
8.8 99.0 E-ATMX-1-raw-cel-1112746267

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
22.4	99.6	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
22.2	99.6	E-MEXP-285-raw-cel-440782725
21.2	99.6	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
20.8	99.6	E-MEXP-285-raw-cel-440782791
18.7	99.5	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
17.3	99.5	E-ATMX-35-raw-cel-1574334880
15.9	99.5	GSM239253	CaMV::DME pollen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
15.6	99.5	E-ATMX-35-raw-cel-1574334848
15.4	99.5	GSM239251	Columbia glabrous (C24) wild type pollen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
13.0	99.4	GSM131638	ATGE_73_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
12.7	99.3	GSM131636	ATGE_73_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
11.9	99.3	E-ATMX-1-raw-cel-1112746154
11.4	99.3	GSM131637	ATGE_73_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
10.6	99.2	GSM184906	Arabidopsis, root cells, protophloem, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
10.5	99.2	GSM184904	Arabidopsis, root cells, protophloem, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
9.5	99.1	E-ATMX-35-raw-cel-1574334864
9.5	99.1	GSM131698	ATGE_81_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
9.5	99.1	GSM131699	ATGE_81_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
9.2	99.1	GSM133957	Fukuda_1-2_0B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
8.8	99.0	E-ATMX-1-raw-cel-1112746267

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

A co-expression module including the wheat gene, TaAffx.85758.2.S1_at, orthologous to the query gene, At1g32610

VF %ile Gene ID Repr. ID Gene Name Func. Ev AGI code Arabidopsis gene name O.I. H.G. S.X. Other DB
0.98 99.9 TaAffx.85758.2.S1_at - - - 1e-15 At1g22450 COX6B (CYTOCHROME C OXIDASE 6B) O.I. H.G. S.X.
0.24 30.3 Ta.2592.2.S1_s_at - - - 6e+0 At4g19270 unknown protein O.I. H.G. S.X.
0.22 27.1 Ta.28783.1.S1_x_at - single-stranded nucleic acid binding protein - 5e-4 At4g39260 GR-RBP8 O.I. H.G. S.X.
0.19 22.4 Ta.6335.1.S1_at - - - 3e+0 At3g59680 unknown protein O.I. H.G. S.X.
0.16 18.2 Ta.1078.2.S1_a_at - Cyclophilin - 8e-6 At4g38740 ROC1 (ROTAMASE CYP 1) O.I. H.G. S.X.
0.14 15.8 Ta.28350.1.S1_a_at - 14-3-3 protein - 3e-28 At3g02520 GRF7 (GENERAL REGULATORY FACTOR 7) O.I. H.G. S.X.
0.12 13.3 Ta.659.4.S1_a_at - - - 0 At1g07920 elongation factor 1-alpha / EF-1-alpha O.I. H.G. S.X.
0.11 12.4 TaAffx.12787.1.S1_at - - - 4e+0 At3g16670 unknown protein O.I. H.G. S.X.
0.10 11.3 TaAffx.51434.1.S1_at - - - 1e+1 At5g28919 - O.I. H.G. S.X.
0.10 11.3 Ta.25306.1.S1_at - - - 2e-1 At5g47210 nuclear RNA-binding protein, putative O.I. H.G. S.X.
0.08 9.4 TaAffx.85913.1.S1_at - - - 1e+0 At1g08880 H2AXA O.I. H.G. S.X.
0.08 9.4 TaAffx.86057.1.S1_at - - - 7e-2 At4g29480 mitochondrial ATP synthase g subunit family protein O.I. H.G. S.X.
0.07 8.6 Ta.9084.3.S1_at - - - 1e+1 At5g50050 invertase/pectin methylesterase inhibitor family protein O.I. H.G. S.X.
0.06 7.6 Ta.15782.1.S1_at - - - 8e-1 At5g56190 WD-40 repeat family protein O.I. H.G. S.X.
0.06 7.6 Ta.9784.3.S1_x_at - - - 4e+0 At2g22630 AGL17 (agamous-like 17) O.I. H.G. S.X.
0.06 7.6 TaAffx.5030.1.S1_at - - - 3e+0 At5g14105 unknown protein O.I. H.G. S.X.
0.04 5.8 TaAffx.51864.1.S1_at - - - 4e+0 At2g39410 hydrolase, alpha/beta fold family protein O.I. H.G. S.X.
0.04 5.8 TaAffx.113241.1.S1_at - - - 1e+1 At4g30370 zinc finger (C3HC4-type RING finger) family protein O.I. H.G. S.X.
0.04 5.8 Ta.6231.3.S1_x_at - - - 7e-5 At5g02270 ATNAP9 O.I. H.G. S.X.
0.01 2.4 TaAffx.92487.1.A1_at - - - 8e-1 At5g07475 plastocyanin-like domain-containing protein O.I. H.G. S.X.
0.01 2.4 TaAffx.119239.1.S1_at - - - 3e-7 At2g39480 PGP6 (P-GLYCOPROTEIN 6) O.I. H.G. S.X.
0.01 2.4 Ta.2643.2.S1_x_at - - - 1e-3 At1g71790 F-actin capping protein beta subunit family protein O.I. H.G. S.X.

VF	%ile	Gene ID	Repr. ID	Gene Name	Func.	Ev	AGI code	Arabidopsis gene name	O.I.	H.G.	S.X.
0.98	99.9	TaAffx.85758.2.S1_at	-	-	-	1e-15	At1g22450	COX6B (CYTOCHROME C OXIDASE 6B)	O.I.	H.G.	S.X.
0.24	30.3	Ta.2592.2.S1_s_at	-	-	-	6e+0	At4g19270	unknown protein	O.I.	H.G.	S.X.
0.22	27.1	Ta.28783.1.S1_x_at	-	single-stranded nucleic acid binding protein	-	5e-4	At4g39260	GR-RBP8	O.I.	H.G.	S.X.
0.19	22.4	Ta.6335.1.S1_at	-	-	-	3e+0	At3g59680	unknown protein	O.I.	H.G.	S.X.
0.16	18.2	Ta.1078.2.S1_a_at	-	Cyclophilin	-	8e-6	At4g38740	ROC1 (ROTAMASE CYP 1)	O.I.	H.G.	S.X.
0.14	15.8	Ta.28350.1.S1_a_at	-	14-3-3 protein	-	3e-28	At3g02520	GRF7 (GENERAL REGULATORY FACTOR 7)	O.I.	H.G.	S.X.
0.12	13.3	Ta.659.4.S1_a_at	-	-	-	0	At1g07920	elongation factor 1-alpha / EF-1-alpha	O.I.	H.G.	S.X.
0.11	12.4	TaAffx.12787.1.S1_at	-	-	-	4e+0	At3g16670	unknown protein	O.I.	H.G.	S.X.
0.10	11.3	TaAffx.51434.1.S1_at	-	-	-	1e+1	At5g28919	-	O.I.	H.G.	S.X.
0.10	11.3	Ta.25306.1.S1_at	-	-	-	2e-1	At5g47210	nuclear RNA-binding protein, putative	O.I.	H.G.	S.X.
0.08	9.4	TaAffx.85913.1.S1_at	-	-	-	1e+0	At1g08880	H2AXA	O.I.	H.G.	S.X.
0.08	9.4	TaAffx.86057.1.S1_at	-	-	-	7e-2	At4g29480	mitochondrial ATP synthase g subunit family protein	O.I.	H.G.	S.X.
0.07	8.6	Ta.9084.3.S1_at	-	-	-	1e+1	At5g50050	invertase/pectin methylesterase inhibitor family protein	O.I.	H.G.	S.X.
0.06	7.6	Ta.15782.1.S1_at	-	-	-	8e-1	At5g56190	WD-40 repeat family protein	O.I.	H.G.	S.X.
0.06	7.6	Ta.9784.3.S1_x_at	-	-	-	4e+0	At2g22630	AGL17 (agamous-like 17)	O.I.	H.G.	S.X.
0.06	7.6	TaAffx.5030.1.S1_at	-	-	-	3e+0	At5g14105	unknown protein	O.I.	H.G.	S.X.
0.04	5.8	TaAffx.51864.1.S1_at	-	-	-	4e+0	At2g39410	hydrolase, alpha/beta fold family protein	O.I.	H.G.	S.X.
0.04	5.8	TaAffx.113241.1.S1_at	-	-	-	1e+1	At4g30370	zinc finger (C3HC4-type RING finger) family protein	O.I.	H.G.	S.X.
0.04	5.8	Ta.6231.3.S1_x_at	-	-	-	7e-5	At5g02270	ATNAP9	O.I.	H.G.	S.X.
0.01	2.4	TaAffx.92487.1.A1_at	-	-	-	8e-1	At5g07475	plastocyanin-like domain-containing protein	O.I.	H.G.	S.X.
0.01	2.4	TaAffx.119239.1.S1_at	-	-	-	3e-7	At2g39480	PGP6 (P-GLYCOPROTEIN 6)	O.I.	H.G.	S.X.
0.01	2.4	Ta.2643.2.S1_x_at	-	-	-	1e-3	At1g71790	F-actin capping protein beta subunit family protein	O.I.	H.G.	S.X.

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

Back to the CoP portal site

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Gene ID	At1g32610
Gene name	hydroxyproline-rich glycoprotein family protein
Module size	5 genes
NF	0.49
%ile	69.2

Co-expression analysis

Gene ID At1g32610 Gene name hydroxyproline-rich glycoprotein family protein Module size 5 genes NF 0.49 %ile 69.2

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_trichocarpaVitis_viniferaZea_mays

Gene ID At1g32610

Gene name hydroxyproline-rich glycoprotein family protein

Module size 5 genes

NF 0.49

%ile 69.2

: 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
Vitis_vinifera
Zea_mays