CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g55550

Gene name RNA recognition motif (RRM)-containing protein

Module size 29 genes

NF 0.53

%ile 73.6

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
0.61 76.7 1.00 At5g55550 835649 RNA recognition motif (RRM)-containing protein F:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:unknown;MPOFBAV O.I. H.G. S.X.
0.69 82.9 0.87 At1g65430 842854 zinc finger protein-related F:ubiquitin-protein ligase activity;P:unknown;C:intracellular;MOPFV O.I. H.G. S.X.
0.69 82.9 0.87 At5g23670 832432 LCB2 Encodes the LCB2 subunit of serine palmitoyltransferase, an enzyme involved in sphingosine biosynthesis. The protein is localized to the endoplasmic reticulum. O.I. H.G. S.X.
0.67 81.6 0.88 At5g54310 835519 AGD5 (ARF-GAP domain 5) A member of ARF GAP domain (AGD), A thaliana has 15 members, grouped into four classes. O.I. H.G. S.X.
0.63 78.1 0.88 At1g71410 843482 protein kinase family protein F:binding, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:membrane;MOFPBVA O.I. H.G. S.X.
0.63 78.1 0.88 At4g38260 829983 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BOMFPAV O.I. H.G. S.X.
0.61 76.7 0.86 At5g64920 836616 CIP8 (COP1-INTERACTING PROTEIN 8) Encodes a RING-H2 protein that interacts with the RING finger domain of COP1. CIP8 exhibits a strong interaction with the E2 ubiquitin conjugating enzyme AtUBC8 through its N-terminal domain and promotes ubiquitination in an E2-dependent fashion in vitro. It is possible that the AtUBC8-CIP8 module might interact with COP1 in vivo, thereby participating in proteasome-mediated degradation of HY5. O.I. H.G. S.X.
0.60 75.7 0.87 At1g06890 837199 transporter-related F:unknown;P:unknown;C:Golgi apparatus, membrane;PMFOBA O.I. H.G. S.X.
0.59 74.7 0.88 At4g19110 827649 protein kinase, putative F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MOPFBVA O.I. H.G. S.X.
0.59 74.7 0.88 At1g49340 841357 ATPI4K ALPHA Encodes a phosphatidylinositol 4-kinase that is expressed in inflorescences and shoots. O.I. H.G. S.X.
0.58 73.8 0.86 At4g00720 828023 ATSK32 (SHAGGY-LIKE PROTEIN KINASE 32) F:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cytosol;MOPFBVA O.I. H.G. S.X.
0.56 73.0 0.87 At1g33250 840219 fringe-related protein F:transferase activity, transferring glycosyl groups;P:unknown;C:chloroplast, membrane;MPFO O.I. H.G. S.X.
0.55 70.6 0.86 At5g32440 833203 - F:unknown;P:unknown;C:chloroplast;OPMFB O.I. H.G. S.X.
0.54 69.5 0.86 At2g31350 817693 GLX2-5 (GLYOXALASE 2-5) Encodes a mitochondrial glyoxalase 2 that can accommodate a number of different metal centers and with the predominant metal center being Fe(III)Zn(II). O.I. H.G. S.X.
0.54 69.5 0.88 At2g44090 819015 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOV O.I. H.G. S.X.
0.53 68.6 0.89 At1g15490 838119 hydrolase, alpha/beta fold family protein F:hydrolase activity;P:unknown;C:unknown;BOPMFA O.I. H.G. S.X.
0.53 68.6 0.89 At1g13900 837949 calcineurin-like phosphoesterase family protein F:hydrolase activity, protein serine/threonine phosphatase activity, metal ion binding, acid phosphatase activity;P:biological_process unknown;C:chloroplast;PBMOF O.I. H.G. S.X.
0.53 68.6 0.87 At1g55520 841999 TBP2 (TATA BINDING PROTEIN 2) TATA-box binding protein. Required for basal transcription. Acts facilitating the recruitment of TFIID to the promoter, which together with the RNA polymerase form the preinitiation complex. O.I. H.G. S.X.
0.53 68.6 0.86 At1g69330 843265 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:unknown;MPO O.I. H.G. S.X.
0.48 62.5 0.86 At1g61770 842474 DNAJ heat shock N-terminal domain-containing protein J domain protein. O.I. H.G. S.X.
0.47 61.2 0.86 At4g35790 829733 ATPLDDELTA Encodes a protein with phospholipase D activity. Involved in phospolipase metabolism. Mutants are affected in hydrogen peroxide mediated cell death. O.I. H.G. S.X.
0.45 58.3 0.87 At5g43930 834415 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:biological_process unknown;C:chloroplast;MBFOPA O.I. H.G. S.X.
0.44 57.2 0.88 At3g07330 819921 ATCSLC6 (CELLULOSE-SYNTHASE LIKE C6) encodes a gene similar to cellulose synthase O.I. H.G. S.X.
0.43 55.3 0.88 At3g15290 820760 3-hydroxybutyryl-CoA dehydrogenase, putative F:coenzyme binding, oxidoreductase activity, 3-hydroxybutyryl-CoA dehydrogenase activity, binding, catalytic activity;P:fatty acid metabolic process, metabolic process;C:peroxisome;BOMAFP O.I. H.G. S.X.
0.41 52.4 0.86 At3g50000 824162 CKA2 (CASEIN KINASE II, ALPHA CHAIN 2) casein kinase II catalytic subunit alpha O.I. H.G. S.X.
0.40 50.8 0.86 At3g03720 821176 CAT4 (CATIONIC AMINO ACID TRANSPORTER 4) Encodes a member of the cationic amino acid transporter (CAT) subfamily of amino acid polyamine choline transporters. O.I. H.G. S.X.
0.38 46.7 0.87 At1g11480 837691 eukaryotic translation initiation factor-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPB O.I. H.G. S.X.
0.38 46.7 0.87 At2g42780 818878 - F:molecular_function unknown;P:regulation of transcription;C:integral to membrane, nucleus;MFPO O.I. H.G. S.X.
0.31 33.8 0.89 At3g58040 824973 SINAT2 (SEVEN IN ABSENTIA OF ARABIDOPSIS 2) Encodes a RING finger domain containing protein that interacts with AtRAP2.2. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.61	76.7	1.00	At5g55550	835649	RNA recognition motif (RRM)-containing protein	F:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:unknown;MPOFBAV	O.I.	H.G.	S.X.
0.69	82.9	0.87	At1g65430	842854	zinc finger protein-related	F:ubiquitin-protein ligase activity;P:unknown;C:intracellular;MOPFV	O.I.	H.G.	S.X.
0.69	82.9	0.87	At5g23670	832432	LCB2	Encodes the LCB2 subunit of serine palmitoyltransferase, an enzyme involved in sphingosine biosynthesis. The protein is localized to the endoplasmic reticulum.	O.I.	H.G.	S.X.
0.67	81.6	0.88	At5g54310	835519	AGD5 (ARF-GAP domain 5)	A member of ARF GAP domain (AGD), A thaliana has 15 members, grouped into four classes.	O.I.	H.G.	S.X.
0.63	78.1	0.88	At1g71410	843482	protein kinase family protein	F:binding, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:membrane;MOFPBVA	O.I.	H.G.	S.X.
0.63	78.1	0.88	At4g38260	829983	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BOMFPAV	O.I.	H.G.	S.X.
0.61	76.7	0.86	At5g64920	836616	CIP8 (COP1-INTERACTING PROTEIN 8)	Encodes a RING-H2 protein that interacts with the RING finger domain of COP1. CIP8 exhibits a strong interaction with the E2 ubiquitin conjugating enzyme AtUBC8 through its N-terminal domain and promotes ubiquitination in an E2-dependent fashion in vitro. It is possible that the AtUBC8-CIP8 module might interact with COP1 in vivo, thereby participating in proteasome-mediated degradation of HY5.	O.I.	H.G.	S.X.
0.60	75.7	0.87	At1g06890	837199	transporter-related	F:unknown;P:unknown;C:Golgi apparatus, membrane;PMFOBA	O.I.	H.G.	S.X.
0.59	74.7	0.88	At4g19110	827649	protein kinase, putative	F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MOPFBVA	O.I.	H.G.	S.X.
0.59	74.7	0.88	At1g49340	841357	ATPI4K ALPHA	Encodes a phosphatidylinositol 4-kinase that is expressed in inflorescences and shoots.	O.I.	H.G.	S.X.
0.58	73.8	0.86	At4g00720	828023	ATSK32 (SHAGGY-LIKE PROTEIN KINASE 32)	F:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cytosol;MOPFBVA	O.I.	H.G.	S.X.
0.56	73.0	0.87	At1g33250	840219	fringe-related protein	F:transferase activity, transferring glycosyl groups;P:unknown;C:chloroplast, membrane;MPFO	O.I.	H.G.	S.X.
0.55	70.6	0.86	At5g32440	833203	-	F:unknown;P:unknown;C:chloroplast;OPMFB	O.I.	H.G.	S.X.
0.54	69.5	0.86	At2g31350	817693	GLX2-5 (GLYOXALASE 2-5)	Encodes a mitochondrial glyoxalase 2 that can accommodate a number of different metal centers and with the predominant metal center being Fe(III)Zn(II).	O.I.	H.G.	S.X.
0.54	69.5	0.88	At2g44090	819015	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOV	O.I.	H.G.	S.X.
0.53	68.6	0.89	At1g15490	838119	hydrolase, alpha/beta fold family protein	F:hydrolase activity;P:unknown;C:unknown;BOPMFA	O.I.	H.G.	S.X.
0.53	68.6	0.89	At1g13900	837949	calcineurin-like phosphoesterase family protein	F:hydrolase activity, protein serine/threonine phosphatase activity, metal ion binding, acid phosphatase activity;P:biological_process unknown;C:chloroplast;PBMOF	O.I.	H.G.	S.X.
0.53	68.6	0.87	At1g55520	841999	TBP2 (TATA BINDING PROTEIN 2)	TATA-box binding protein. Required for basal transcription. Acts facilitating the recruitment of TFIID to the promoter, which together with the RNA polymerase form the preinitiation complex.	O.I.	H.G.	S.X.
0.53	68.6	0.86	At1g69330	843265	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:unknown;MPO	O.I.	H.G.	S.X.
0.48	62.5	0.86	At1g61770	842474	DNAJ heat shock N-terminal domain-containing protein	J domain protein.	O.I.	H.G.	S.X.
0.47	61.2	0.86	At4g35790	829733	ATPLDDELTA	Encodes a protein with phospholipase D activity. Involved in phospolipase metabolism. Mutants are affected in hydrogen peroxide mediated cell death.	O.I.	H.G.	S.X.
0.45	58.3	0.87	At5g43930	834415	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:biological_process unknown;C:chloroplast;MBFOPA	O.I.	H.G.	S.X.
0.44	57.2	0.88	At3g07330	819921	ATCSLC6 (CELLULOSE-SYNTHASE LIKE C6)	encodes a gene similar to cellulose synthase	O.I.	H.G.	S.X.
0.43	55.3	0.88	At3g15290	820760	3-hydroxybutyryl-CoA dehydrogenase, putative	F:coenzyme binding, oxidoreductase activity, 3-hydroxybutyryl-CoA dehydrogenase activity, binding, catalytic activity;P:fatty acid metabolic process, metabolic process;C:peroxisome;BOMAFP	O.I.	H.G.	S.X.
0.41	52.4	0.86	At3g50000	824162	CKA2 (CASEIN KINASE II, ALPHA CHAIN 2)	casein kinase II catalytic subunit alpha	O.I.	H.G.	S.X.
0.40	50.8	0.86	At3g03720	821176	CAT4 (CATIONIC AMINO ACID TRANSPORTER 4)	Encodes a member of the cationic amino acid transporter (CAT) subfamily of amino acid polyamine choline transporters.	O.I.	H.G.	S.X.
0.38	46.7	0.87	At1g11480	837691	eukaryotic translation initiation factor-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPB	O.I.	H.G.	S.X.
0.38	46.7	0.87	At2g42780	818878	-	F:molecular_function unknown;P:regulation of transcription;C:integral to membrane, nucleus;MFPO	O.I.	H.G.	S.X.
0.31	33.8	0.89	At3g58040	824973	SINAT2 (SEVEN IN ABSENTIA OF ARABIDOPSIS 2)	Encodes a RING finger domain containing protein that interacts with AtRAP2.2.	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
64.4 99.8 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
50.1 99.8 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
50.0 99.8 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
46.0 99.8 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
45.7 99.8 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
43.8 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
40.5 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.8 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
38.2 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
37.9 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.1 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.7 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.3 99.7 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.1 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.8 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.7 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.4 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.1 99.7 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
31.6 99.7 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.4 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.5 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.0 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
30.0 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.8 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.3 99.7 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
25.9 99.7 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.0 99.6 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
18.4 99.5 GSM154508 Arabidopsis growing pollen tubes rep2 GSE6696 Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
18.3 99.5 GSM106833 opr3_JA_0.5 hr_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
16.7 99.5 GSM158702 HY213-ESTRADIOL-REP1 GSE6954 Identification of AGL24 downstream genes by using XVE inducible system
15.7 99.5 GSM106913 opr3_JA_8 hrs_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
14.6 99.4 GSM106912 opr3_JA 8hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
13.8 99.4 GSM106911 opr2_JA_2 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
13.2 99.4 GSM106909 opr3-JA_2 hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
13.1 99.4 GSM106914 opr3_JA_8 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
12.1 99.3 GSM106827 opr3_0 hr_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
12.0 99.3 GSM106825 opr3_0 hr_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.8 99.3 GSM106921 opr3_OPDA_0.5 hr_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.7 99.3 GSM106910 opr3_JA_2 hrs_rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.7 99.3 GSM106908 opr3_JA_0.5 hr_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.3 99.3 GSM106919 opr3_OPDA_0.5 hr_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.1 99.2 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
10.9 99.2 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
10.7 99.2 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.5 99.2 GSM106920 opr3_OPDA_0.5 hr_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
10.4 99.2 GSM106934 opr3_OPDA_8 hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
10.2 99.2 GSM154507 Arabidopsis growing pollen tubes rep1 GSE6696 Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
9.8 99.1 GSM106924 opr3_OPDA_2 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.7 99.1 GSM142735 DH001_ATH1_A2-BCP1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
9.7 99.1 GSM133117 RIKEN-YAMAUCHI1A GSE5687 AtGenExpress: Different temperature treatment of seeds
9.5 99.1 GSM142734 DH001_ATH1_A1-UNM1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
9.5 99.1 GSM142624 MC002_ATH1_A1.2-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.4 99.1 GSM106973 ws_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.1 99.1 GSM106966 opr3_OPDA_8 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.0 99.1 GSM106922 opr3_OPDA_2 hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
8.9 99.0 GSM133777 Lindsey_1-4_globular-basal_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
8.8 99.0 GSM142631 MC002_ATH1_A3.3-dubos-6kx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.6 99.0 GSM142625 MC002_ATH1_A1.3-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
64.4	99.8	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
50.1	99.8	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
50.0	99.8	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
46.0	99.8	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
45.7	99.8	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
43.8	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
40.5	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.8	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
38.2	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
37.9	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.1	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.7	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.3	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.1	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.8	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.7	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.4	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.1	99.7	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
31.6	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.4	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.5	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.0	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
30.0	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.8	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.3	99.7	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
25.9	99.7	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.0	99.6	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
18.4	99.5	GSM154508	Arabidopsis growing pollen tubes rep2	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
18.3	99.5	GSM106833	opr3_JA_0.5 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
16.7	99.5	GSM158702	HY213-ESTRADIOL-REP1	GSE6954	Identification of AGL24 downstream genes by using XVE inducible system
15.7	99.5	GSM106913	opr3_JA_8 hrs_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
14.6	99.4	GSM106912	opr3_JA 8hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
13.8	99.4	GSM106911	opr2_JA_2 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
13.2	99.4	GSM106909	opr3-JA_2 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
13.1	99.4	GSM106914	opr3_JA_8 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
12.1	99.3	GSM106827	opr3_0 hr_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
12.0	99.3	GSM106825	opr3_0 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.8	99.3	GSM106921	opr3_OPDA_0.5 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.7	99.3	GSM106910	opr3_JA_2 hrs_rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.7	99.3	GSM106908	opr3_JA_0.5 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.3	99.3	GSM106919	opr3_OPDA_0.5 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.1	99.2	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
10.9	99.2	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
10.7	99.2	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.5	99.2	GSM106920	opr3_OPDA_0.5 hr_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
10.4	99.2	GSM106934	opr3_OPDA_8 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
10.2	99.2	GSM154507	Arabidopsis growing pollen tubes rep1	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
9.8	99.1	GSM106924	opr3_OPDA_2 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.7	99.1	GSM142735	DH001_ATH1_A2-BCP1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
9.7	99.1	GSM133117	RIKEN-YAMAUCHI1A	GSE5687	AtGenExpress: Different temperature treatment of seeds
9.5	99.1	GSM142734	DH001_ATH1_A1-UNM1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
9.5	99.1	GSM142624	MC002_ATH1_A1.2-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.4	99.1	GSM106973	ws_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.1	99.1	GSM106966	opr3_OPDA_8 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.0	99.1	GSM106922	opr3_OPDA_2 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
8.9	99.0	GSM133777	Lindsey_1-4_globular-basal_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
8.8	99.0	GSM142631	MC002_ATH1_A3.3-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.6	99.0	GSM142625	MC002_ATH1_A1.3-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.067 1 GO:0032857 Any process that initiates the activity of the inactive enzyme ARF GTPase through the replacement of GDP by GTP.
0.067 1 GO:0046473 The chemical reactions and pathways involving phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
0.067 1 GO:0046512 The chemical reactions and pathways resulting in the formation of sphingosine (sphing-4-enine), trans-D-erytho-2-amino-octadec-4-ene-1,3-diol, a long chain amino diol sphingoid base that occurs in most sphingolipids in animal tissues.

SF	Genes	GO ID	Process Name
0.067	1	GO:0032857	Any process that initiates the activity of the inactive enzyme ARF GTPase through the replacement of GDP by GTP.
0.067	1	GO:0046473	The chemical reactions and pathways involving phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
0.067	1	GO:0046512	The chemical reactions and pathways resulting in the formation of sphingosine (sphing-4-enine), trans-D-erytho-2-amino-octadec-4-ene-1,3-diol, a long chain amino diol sphingoid base that occurs in most sphingolipids in animal tissues.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.051 1 00600 Sphingolipid metabolism
0.039 1 00650 Butanoate metabolism
0.034 1 04712 Circadian rhythm - plant

SF	Genes	KEGG ID	Pathway name
0.051	1	00600	Sphingolipid metabolism
0.039	1	00650	Butanoate metabolism
0.034	1	04712	Circadian rhythm - plant

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

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Gene ID	At5g55550
Gene name	RNA recognition motif (RRM)-containing protein
Module size	29 genes
NF	0.53
%ile	73.6

Co-expression analysis

Gene ID At5g55550 Gene name RNA recognition motif (RRM)-containing protein Module size 29 genes NF 0.53 %ile 73.6

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 KEGG0.051100600Sphingolipid metabolism0.039100650Butanoate metabolism0.034104712Circadian rhythm - plant

Inter-species module comparison

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

Gene ID At5g55550

Gene name RNA recognition motif (RRM)-containing protein

Module size 29 genes

NF 0.53

%ile 73.6

: 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
0.051 1 00600 Sphingolipid metabolism
0.039 1 00650 Butanoate metabolism
0.034 1 04712 Circadian rhythm - plant

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