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.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.67	81.6	0.90	At3g06600	819839	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.67	81.6	0.87	At3g45440	823682	lectin protein kinase family protein	F:carbohydrate binding, kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVA	O.I.	H.G.	S.X.
0.67	81.6	0.85	At1g12630	837819	DNA binding / transcription activator/ transcription factor	encodes a member of the DREB subfamily A-4 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 17 members in this subfamily including TINY.	O.I.	H.G.	S.X.
0.61	76.7	0.86	At3g05480	819713	RAD9	Involved in the regulation of DNA damage repair and homologous recombination.	O.I.	H.G.	S.X.
0.60	75.7	0.85	At1g31840	840074	-	F:unknown;P:unknown;C:endomembrane system;POFMBA	O.I.	H.G.	S.X.
0.60	75.7	0.85	At1g31240	840012	DNA binding	F:DNA binding;P:biological_process unknown;C:cellular_component unknown;MPO	O.I.	H.G.	S.X.
0.57	73.8	0.88	At4g39440	830099	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PM	O.I.	H.G.	S.X.
0.57	73.8	0.87	At1g64250	3767631	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.56	73.0	0.89	At1g74350	843776	intron maturase, type II family protein	F:RNA binding, RNA-directed DNA polymerase activity;P:RNA-dependent DNA replication, RNA splicing;C:cellular_component unknown;BPOFAM	O.I.	H.G.	S.X.
0.55	70.6	0.91	At1g55970	842048	HAC4 (HISTONE ACETYLTRANSFERASE OF THE CBP FAMILY 4)	HAC4 is most likely to be an expressed pseudogene that lacks HAT function. there is a single nucleotide deletion in both the HAC4 genomic and cDNA sequences relative to its homologs. The resulting frameshift within the open reading frame causes a stop codon to occur within the predicted acetyltransferase catalytic domain.	O.I.	H.G.	S.X.
0.55	70.6	0.87	At5g12280	831103	RNA binding	F:RNA binding;P:protein modification process, RNA processing;C:cellular_component unknown;MPOF	O.I.	H.G.	S.X.
0.53	68.6	0.90	At4g13330	826963	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMBO	O.I.	H.G.	S.X.
0.50	65.3	0.88	At4g25270	828630	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:biological_process unknown;C:chloroplast;POMFB	O.I.	H.G.	S.X.
0.50	65.3	0.89	At2g47820	819394	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMBFPV	O.I.	H.G.	S.X.
0.50	65.3	0.89	At4g21880	828277	-	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;POMFBA	O.I.	H.G.	S.X.
0.50	65.3	0.84	At5g29040	3770873	-	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.46	59.8	0.90	At1g25360	839121	pentatricopeptide (PPR) repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFA	O.I.	H.G.	S.X.
0.46	59.8	0.89	At5g05350	830417	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PF	O.I.	H.G.	S.X.
0.46	59.8	0.87	At4g08840	826455	APUM11 (Arabidopsis Pumilio 11)	F:RNA binding, binding;P:biological_process unknown;C:cellular_component unknown;FMOP	O.I.	H.G.	S.X.
0.44	57.2	0.86	At4g25540	828659	MSH3 (Arabidopsis homolog of DNA mismatch repair protein MSH3)	encodes a DNA mismatch repair homolog of human MutS gene, MSH6. There are four MutS genes in Arabidopsis, MSH2, MSH3, MSH6, and MSH7, which all act as heterodimers and bind to 51-mer duplexes. MSH2*MSH3 heterodimers bound 'insertion-deletion' DNA with three nucleotides (+AAG) or one nucleotide (+T) looped out much better than they bound DNA with a base/base mispair (T/G).	O.I.	H.G.	S.X.
0.44	57.2	0.87	At3g18840	821417	-	-	O.I.	H.G.	S.X.
0.44	57.2	0.84	At3g14640	820692	CYP72A10	putative cytochrome P450	O.I.	H.G.	S.X.
0.44	57.2	0.84	At5g28310	832915	oxidoreductase-related	F:oxidoreductase activity, binding, oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, catalytic activity, cofactor binding;P:metabolic process;C:cellular_component unknown;BOPFAM	O.I.	H.G.	S.X.
0.43	55.3	0.90	At3g49740	824136	pentatricopeptide (PPR) repeat-containing protein	F:binding;P:biological_process unknown;C:unknown;POFMB	O.I.	H.G.	S.X.
0.43	55.3	0.88	At2g16260	816122	-	pseudogene of glycine-rich RNA-binding protein	O.I.	H.G.	S.X.
0.42	53.9	0.90	At5g08230	830719	PWWP domain-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOBFVA	O.I.	H.G.	S.X.
0.42	53.9	0.89	At1g61210	842414	WD-40 repeat family protein / katanin p80 subunit, putative	F:nucleotide binding;P:unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MFOPBVA	O.I.	H.G.	S.X.
0.40	50.8	0.91	At1g63730	842677	disease resistance protein (TIR-NBS-LRR class), putative	F:protein binding, transmembrane receptor activity, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:defense response;C:intrinsic to membrane;PMBOAF	O.I.	H.G.	S.X.
0.40	50.8	0.92	At2g20210	816540	leucine-rich repeat family protein	F:protein binding;P:unknown;C:endomembrane system;MOPBF	O.I.	H.G.	S.X.
0.40	50.8	0.90	At1g52620	841694	pentatricopeptide (PPR) repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBA	O.I.	H.G.	S.X.
0.40	50.8	0.88	At5g24980	832568	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	H.G.	S.X.
0.40	50.8	0.88	At4g19650	827709	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMB	O.I.	H.G.	S.X.
0.40	50.8	0.84	At1g25250	839108	AtIDD16 (Arabidopsis thaliana Indeterminate(ID)-Domain 16)	F:transcription factor activity, zinc ion binding, nucleic acid binding;P:regulation of transcription;C:intracellular;MOPFBVA	O.I.	H.G.	S.X.
0.40	50.8	0.85	At3g53840	824551	protein kinase family protein	F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVA	O.I.	H.G.	S.X.
0.38	46.7	0.84	At1g74200	843760	AtRLP16 (Receptor Like Protein 16)	F:protein binding;P:signal transduction;C:cellular_component unknown;PMOBFA	O.I.	H.G.	S.X.
0.38	46.7	0.92	At1g50260	841448	NTMC2T5.1 (N-TERMINAL-TRANSMEMBRANE-C2 DOMAIN TYPE 5.1)	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMFOB	O.I.	H.G.	S.X.
0.36	43.6	0.90	At5g19830	832103	aminoacyl-tRNA hydrolase	F:aminoacyl-tRNA hydrolase activity;P:translation;C:mitochondrion;BOPFM	O.I.	H.G.	S.X.
0.36	43.6	0.88	At5g16420	831503	pentatricopeptide (PPR) repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBA	O.I.	H.G.	S.X.
0.36	43.6	0.85	At5g04610	830338	spermidine synthase-related / putrescine aminopropyltransferase-related	F:catalytic activity;P:unknown;C:unknown;BPMOFA	O.I.	H.G.	S.X.
0.35	41.6	0.89	At4g39380	830093	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.35	41.6	0.84	At1g31430	840033	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:unknown;C:unknown;POMFB	O.I.	H.G.	S.X.
0.35	41.6	0.90	At1g23980	839010	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVB	O.I.	H.G.	S.X.
0.35	41.6	0.89	At1g50910	841513	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVA	O.I.	H.G.	S.X.
0.33	38.1	0.89	At2g40720	818667	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:unknown;C:cellular_component unknown;POMFB	O.I.	H.G.	S.X.
0.33	38.1	0.88	At4g16570	827358	PRMT7 (PROTEIN ARGININE METHYLTRANSFERASE 7)	F:methyltransferase activity;P:protein amino acid methylation;C:chloroplast;MFOPBA	O.I.	H.G.	S.X.
0.33	38.1	0.90	At4g30700	829193	pentatricopeptide (PPR) repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMF	O.I.	H.G.	S.X.
0.33	38.1	0.89	At1g74400	843781	pentatricopeptide (PPR) repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFMB	O.I.	H.G.	S.X.
0.33	38.1	0.89	At3g20730	821621	pentatricopeptide (PPR) repeat-containing protein	F:binding;P:biological_process unknown;C:endomembrane system;POMFB	O.I.	H.G.	S.X.
0.33	38.1	0.85	At5g41710	3771395	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.33	38.1	0.85	At2g36980	818272	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:biological_process unknown;C:unknown;POMFAB	O.I.	H.G.	S.X.

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

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	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

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 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
Triticum_aestivum
Vitis_vinifera
Zea_mays