Co-expression analysis

Gene ID	At5g20220
Gene name	zinc knuckle (CCHC-type) family protein
Module size	5 genes
NF	0.42
%ile	58.7

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
0.50	65.3	1.00	At5g20220	832144	zinc knuckle (CCHC-type) family protein	F:unfolded protein binding, heat shock protein binding, zinc ion binding, nucleic acid binding;P:protein folding;C:unknown;VMFOPB	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.60	75.7	0.89	At1g76570	843990	chlorophyll A-B binding family protein	F:chlorophyll binding;P:response to blue light, response to far red light, photosynthesis;C:light-harvesting complex, chloroplast, membrane;POM	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.40	50.8	0.92	At5g19850	832105	hydrolase, alpha/beta fold family protein	F:hydrolase activity;P:unknown;C:unknown;BOMPFA	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.38	46.7	0.90	At1g66330	842950	senescence-associated family protein	F:unknown;P:senescence;C:unknown;PB	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.31	33.8	0.88	At1g53090	841743	SPA4 (SPA1-RELATED 4)	Encodes a member of the SPA (suppressor of phyA-105) protein family (SPA1-SPA4). SPA proteins contain an N-terminal serine/threonine kinase-like motif followed by a coiled-coil structure and a C-terminal WD-repeat domain. SPA proteins function redundantly in suppressing photomorphogenesis in dark- and light-grown seedlings. SPA4 (and SPA3) predominantly regulates elongation growth in adult plants.	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)

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Link to AtGenExpress Visualization Tool

Specific experiments for the module

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title	Link to GEO
93.1	99.9	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
80.5	99.9	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
76.7	99.9	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
76.5	99.9	GSM106833	opr3_JA_0.5 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
76.2	99.9	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
74.8	99.9	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
72.4	99.9	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
71.7	99.9	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
70.3	99.9	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.2	99.9	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
66.6	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
66.4	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
63.8	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
59.6	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.4	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
54.7	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
54.0	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
50.9	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.9	99.8	GSM106919	opr3_OPDA_0.5 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
43.1	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.2	99.7	GSM106825	opr3_0 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
31.2	99.7	GSM106920	opr3_OPDA_0.5 hr_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
30.2	99.7	GSM106934	opr3_OPDA_8 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
27.0	99.7	GSM106908	opr3_JA_0.5 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
26.6	99.7	GSM106922	opr3_OPDA_2 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
26.0	99.7	GSM106921	opr3_OPDA_0.5 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
24.7	99.6	GSM106827	opr3_0 hr_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
23.7	99.6	GSM106909	opr3-JA_2 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
23.7	99.6	GSM131592	ATGE_36_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
22.7	99.6	GSM131591	ATGE_36_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
20.8	99.6	GSM106907	opr3_JA_0.5 hr_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
20.1	99.6	GSM106924	opr3_OPDA_2 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
19.9	99.6	GSM239254	CaMV::DME stamen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
19.1	99.6	GSM131593	ATGE_36_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
19.0	99.5	GSM131617	ATGE_53_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
18.7	99.5	E-MEXP-1592-raw-cel-1617526864
17.9	99.5	GSM106966	opr3_OPDA_8 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
17.1	99.5	GSM131615	ATGE_53_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
16.9	99.5	GSM131616	ATGE_53_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
16.8	99.5	E-MEXP-1592-raw-cel-1617526968
15.8	99.5	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
15.6	99.5	GSM106973	ws_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
14.5	99.4	GSM106910	opr3_JA_2 hrs_rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
14.2	99.4	GSM106911	opr2_JA_2 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
13.6	99.4	E-MEXP-849-raw-cel-1181980966
13.3	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
12.7	99.3	GSM133966	Fukuda_1-11_10A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
12.4	99.3	GSM134206	Murray_3-3_D5-GROWTH_Rep1_ATH1	GSE5750	Growth of suspension-cultured cells
12.2	99.3	GSM131582	ATGE_33_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
11.9	99.3	GSM133967	Fukuda_1-12_10B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
11.7	99.3	GSM134208	Murray_3-4_D7-GROWTH_Rep1_ATH1	GSE5750	Growth of suspension-cultured cells
11.6	99.3	GSM106912	opr3_JA 8hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.5	99.3	GSM131583	ATGE_33_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
11.5	99.3	GSM131584	ATGE_33_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
11.5	99.3	GSM128729	Hennig_1-1_flower-buds-CK_021114_1_A_Rep1_ATH1	GSE5526	Transcriptional Programs of Early Reproductive Stages in Arabidopsis
11.3	99.3	GSM106923	opr3_OPDA_2 hrs_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.1	99.2	E-MEXP-1592-raw-cel-1617526872
11.1	99.2	E-MEXP-1592-raw-cel-1617526896
10.6	99.2	E-MEXP-1592-raw-cel-1617526992
10.4	99.2	E-MEXP-849-raw-cel-1181980942
9.7	99.1	E-MEXP-849-raw-cel-1181980974
9.6	99.1	E-MEXP-1592-raw-cel-1617526936
9.3	99.1	E-MEXP-849-raw-cel-1181980958
9.1	99.1	GSM133965	Fukuda_1-10_8B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.0	99.1	E-MEXP-849-raw-cel-1181980902
8.6	99.0	GSM106828	opr3_0 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling

Biological processes inferred to relate to the module

SF	Genes	GO ID	Process Name	Link to AmiGO
0.154	1	GO:0010149	A preprogrammed process associated with the dismantling of an anatomical structure and an overall decline in metabolism. This may include the breakdown of organelles, membranes and other cellular components. An example of this process is found in Arabidopsis thaliana, when older leaves or floral organs are shed.
0.051	1	GO:0009637	A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a blue light stimulus. Blue light is electromagnetic radiation with a wavelength of between 440 and 500nm.
0.044	1	GO:0010218	A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of far red light stimulus. Far red light is electromagnetic radiation of wavelength 700-800nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.

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

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