CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g54910

Gene name DEAD/DEAH box helicase, putative

Module size 9 genes

NF 0.35

%ile 46.4

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
0.36 43.6 1.00 At5g54910 835582 DEAD/DEAH box helicase, putative F:helicase activity, nucleic acid binding, ATP binding, ATP-dependent helicase activity;P:biological_process unknown;C:nucleolus;BOMFPAV O.I. H.G. S.X.
0.48 62.5 0.88 At2g21440 816683 RNA recognition motif (RRM)-containing protein F:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:unknown;MOFPBAV O.I. H.G. S.X.
0.36 43.6 0.88 At4g25730 828678 FtsJ-like methyltransferase family protein F:methyltransferase activity;P:rRNA processing, rRNA methylation;C:nucleus;OMBFPVA O.I. H.G. S.X.
0.35 41.6 0.89 At3g12340 820412 FK506 binding / peptidyl-prolyl cis-trans isomerase F:FK506 binding, peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:chloroplast thylakoid lumen;MOBFPAV O.I. H.G. S.X.
0.35 41.6 0.88 At3g24080 821994 KRR1 family protein F:molecular_function unknown;P:response to salt stress;C:cytosol;MOFBPVA O.I. H.G. S.X.
0.33 38.1 0.88 At1g71850 843515 ubiquitin thiolesterase F:ubiquitin thiolesterase activity;P:ubiquitin-dependent protein catabolic process;C:intracellular;POFMVB O.I. H.G. S.X.
0.29 30.3 0.88 At1g11240 837665 unknown protein F:unknown;P:unknown;C:cellular_component unknown;MOFPBV O.I. H.G. S.X.
0.29 30.3 0.87 At5g09840 830844 unknown protein F:unknown;P:unknown;C:mitochondrion;PMFOB O.I. H.G. S.X.
0.25 22.6 0.88 At5g22320 832292 leucine-rich repeat family protein F:protein binding;P:biological_process unknown;C:cellular_component unknown;MOBPFVA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.36	43.6	1.00	At5g54910	835582	DEAD/DEAH box helicase, putative	F:helicase activity, nucleic acid binding, ATP binding, ATP-dependent helicase activity;P:biological_process unknown;C:nucleolus;BOMFPAV	O.I.	H.G.	S.X.
0.48	62.5	0.88	At2g21440	816683	RNA recognition motif (RRM)-containing protein	F:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:unknown;MOFPBAV	O.I.	H.G.	S.X.
0.36	43.6	0.88	At4g25730	828678	FtsJ-like methyltransferase family protein	F:methyltransferase activity;P:rRNA processing, rRNA methylation;C:nucleus;OMBFPVA	O.I.	H.G.	S.X.
0.35	41.6	0.89	At3g12340	820412	FK506 binding / peptidyl-prolyl cis-trans isomerase	F:FK506 binding, peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:chloroplast thylakoid lumen;MOBFPAV	O.I.	H.G.	S.X.
0.35	41.6	0.88	At3g24080	821994	KRR1 family protein	F:molecular_function unknown;P:response to salt stress;C:cytosol;MOFBPVA	O.I.	H.G.	S.X.
0.33	38.1	0.88	At1g71850	843515	ubiquitin thiolesterase	F:ubiquitin thiolesterase activity;P:ubiquitin-dependent protein catabolic process;C:intracellular;POFMVB	O.I.	H.G.	S.X.
0.29	30.3	0.88	At1g11240	837665	unknown protein	F:unknown;P:unknown;C:cellular_component unknown;MOFPBV	O.I.	H.G.	S.X.
0.29	30.3	0.87	At5g09840	830844	unknown protein	F:unknown;P:unknown;C:mitochondrion;PMFOB	O.I.	H.G.	S.X.
0.25	22.6	0.88	At5g22320	832292	leucine-rich repeat family protein	F:protein binding;P:biological_process unknown;C:cellular_component unknown;MOBPFVA	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
138.2 99.9 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
105.8 99.9 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
97.2 99.9 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.9 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.1 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.8 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
44.3 99.8 GSM311291 Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
43.4 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.1 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.9 99.7 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.3 99.7 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.9 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
35.6 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.7 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.3 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.8 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.6 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
30.8 99.7 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
26.2 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.0 99.7 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
25.8 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
23.4 99.6 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
20.2 99.6 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
17.1 99.5 E-MEXP-715-raw-cel-1121836247
16.7 99.5 GSM133763 Lindsey_1-15_torpedo-cotyledon_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.4 99.4 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
12.4 99.3 GSM176880 AWP_Control_2 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
12.2 99.3 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
11.0 99.2 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
10.8 99.2 GSM133303 RIKEN-NAKABAYASHI1A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
10.3 99.2 E-MEXP-509-raw-cel-829148561
10.1 99.2 E-MEXP-715-raw-cel-1121836221
9.6 99.1 GSM133307 RIKEN-NAKABAYASHI3A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
9.3 99.1 E-MEXP-715-raw-cel-1121836196
9.2 99.1 GSM142907 WW002_ATH1_A2-willa-ISOX-REP3 GSE6181 Assembly of the cell wall pectic matrix.
9.1 99.1 GSM142735 DH001_ATH1_A2-BCP1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
8.7 99.0 GSM133951 Murray_2-7_T12-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies
8.7 99.0 E-MEXP-509-raw-cel-829148456
8.6 99.0 GSM133308 RIKEN-NAKABAYASHI4A GSE5700 AtGenExpress: Effect of ABA during seed imbibition

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
138.2	99.9	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
105.8	99.9	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
97.2	99.9	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.9	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.1	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.8	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
44.3	99.8	GSM311291	Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
43.4	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.1	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.9	99.7	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.3	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.9	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.6	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.7	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.3	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.8	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.6	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
30.8	99.7	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
26.2	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.0	99.7	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
25.8	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
23.4	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
20.2	99.6	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
17.1	99.5	E-MEXP-715-raw-cel-1121836247
16.7	99.5	GSM133763	Lindsey_1-15_torpedo-cotyledon_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.4	99.4	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
12.4	99.3	GSM176880	AWP_Control_2	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
12.2	99.3	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
11.0	99.2	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
10.8	99.2	GSM133303	RIKEN-NAKABAYASHI1A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
10.3	99.2	E-MEXP-509-raw-cel-829148561
10.1	99.2	E-MEXP-715-raw-cel-1121836221
9.6	99.1	GSM133307	RIKEN-NAKABAYASHI3A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
9.3	99.1	E-MEXP-715-raw-cel-1121836196
9.2	99.1	GSM142907	WW002_ATH1_A2-willa-ISOX-REP3	GSE6181	Assembly of the cell wall pectic matrix.
9.1	99.1	GSM142735	DH001_ATH1_A2-BCP1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
8.7	99.0	GSM133951	Murray_2-7_T12-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies
8.7	99.0	E-MEXP-509-raw-cel-829148456
8.6	99.0	GSM133308	RIKEN-NAKABAYASHI4A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.105 1 GO:0031167 The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
0.049 1 GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.105	1	GO:0031167	The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
0.049	1	GO:0006364	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.

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	At5g54910
Gene name	DEAD/DEAH box helicase, putative
Module size	9 genes
NF	0.35
%ile	46.4

Co-expression analysis

Gene ID At5g54910 Gene name DEAD/DEAH box helicase, putative Module size 9 genes NF 0.35 %ile 46.4

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

SFGenesGO IDProcess NameLink to AmiGO0.1051GO:0031167The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.0.0491GO:0006364Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.

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 At5g54910

Gene name DEAD/DEAH box helicase, putative

Module size 9 genes

NF 0.35

%ile 46.4

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

SF Genes GO ID Process Name Link to AmiGO
0.105 1 GO:0031167 The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
0.049 1 GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.

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