CoP: Co-expressed Biological Processes

Gene omics information

Query gene ID At4g28520

Gene name CRU3 (CRUCIFERIN 3)

Organism Arabidopsis thaliana

Co-expressed genes

As this page just shows up to 10 genes to the query, if you wish to have the complete list of co-expressed genes, click Gene/Probe ID.

VF %ile Gene/Probe ID Repr.ID Gene Name Functional Description S.X. H.G. Other DB
1.00 100.0 At4g28520 828970 CRU3 (CRUCIFERIN 3) Encodes a 12S seed storage protein that is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds. S.X. H.G.
0.97 97.6 At5g44120 834435 CRA1 (CRUCIFERINA) Encodes a 12S seed storage protein. The Landsberg erecta genome contains another copy of 12S globulin gene, CRA2, which is located tandemly with CRA1. Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds. S.X. H.G.
0.90 95.1 At3g27660 822388 OLEO4 (OLEOSIN 4) Encodes oleosin4 (Plant Cell, 2006, 18:1961), a protein found in oil bodies, involved in seed lipid accumulation. Functions in freezing tolerance of seeds. Note: also referred to as OLE3 in Plant Journal 2008, 55:798. S.X. H.G.
0.88 94.0 At4g25140 828617 OLEO1 (OLEOSIN 1) Encodes oleosin1, a protein found in oil bodies, involved in seed lipid accumulation. Suppression of OLEO1 (and OLEO2) resulted in an aberrant phenotype of embryo cells that contain unusually large oilbodies that are not normally observed in seeds. Changes in the size of oilbodies caused disruption of storage organelles, altering accumulation of lipids and proteins and causing delay in germination. Functions in freezing tolerance of seeds. S.X. H.G.
0.88 94.0 At5g54740 835563 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein F:lipid binding, nutrient reservoir activity;P:lipid transport, pollen development;C:endomembrane system;PO S.X. H.G.
0.86 93.1 At3g22640 821835 PAP85 F:nutrient reservoir activity;P:biological_process unknown;C:plant-type cell wall;POM S.X. H.G.
0.85 92.4 At2g28490 817397 cupin family protein F:nutrient reservoir activity;P:biological_process unknown;C:endomembrane system;BMPOFVA S.X. H.G.
0.84 91.9 At5g40420 834040 OLEO2 (OLEOSIN 2) Encodes oleosin2, a protein found in oil bodies, involved in seed lipid accumulation. Suppression of OLEO1 (and OLEO2) resulted in an aberrant phenotype of embryo cells that contain unusually large oilbodies that are not normally observed in seeds. Changes in the size of oilbodies caused disruption of storage organelles, altering accumulation of lipids and proteins and causing delay in germination. Functions in freezing tolerance of seeds. S.X. H.G.
0.83 91.4 At1g48130 841231 ATPER1 encodes a protein similar to the 1-cysteine (1-Cys) peroxiredoxin family of antioxidants. Expression is limited to seed (aleurone and embryo) and is not induced by ABA or drought. S.X. H.G.
0.79 89.1 At4g27160 828824 AT2S3 F:lipid binding, nutrient reservoir activity;P:lipid transport;C:endomembrane system;PO S.X. H.G.
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Specifically expressed experiments

As this page just shows up to 10 assays to the query, if you wish to have the complete list of assays that the query gene/probe was specifically expressed, click here.
Std2 GX %ile GSM ID Assay Name GSE ID Experiment Title
194.5 100.0 GSM133817 Yang_1-2_old-pod_Rep1_ATH1 GSE5736 To identify changes in gene expression during silique senescence in Arabidopsis thaliana
167.7 100.0 GSM10483 lec1-1 Post-Mature Green Seed 1 GSE1051 Seed development in LEAFY COTYLEDON1 mutants
164.2 99.9 GSM10451 WT Mature Green Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
162.3 99.9 GSM10481 lec1-1 Mature Green Seed 1 GSE1051 Seed development in LEAFY COTYLEDON1 mutants
160.3 99.9 GSM10456 WT Post-Mature Green Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
157.4 99.9 GSM10454 WT Post-Mature Green Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
156.5 99.9 GSM305284 estradiol induced, biological replicate 2 GSE12137 LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis thaliana
138.9 99.9 GSM10453 WT Mature Green Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
132.2 99.9 GSM131704 ATGE_83_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
130.8 99.9 E-ATMX-1-raw-cel-1112746209
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Homologous genes

Paralogous genes

Click Gene ID to show a list of homologous genes.

HF Ev BS Gene ID Repr. ID Gene Name Functional description C.G. S.X. Other DB
0.07 9e-10 65 At5g44120 834435 CRA1 (CRUCIFERINA) Encodes a 12S seed storage protein. The Landsberg erecta genome contains another copy of 12S globulin gene, CRA2, which is located tandemly with CRA1. Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds. C.G. S.X.
0.06 1e-5 52 At1g03880 839383 CRU2 (CRUCIFERIN 2) Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds. C.G. S.X.
0.01 8e-1 36 At5g15950 831452 adenosylmethionine decarboxylase family protein F:adenosylmethionine decarboxylase activity;P:spermidine biosynthetic process, spermine biosynthetic process, polyamine biosynthetic process;C:cellular_component unknown;PMFOB C.G. S.X.
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Orthologous genes

Click Gene ID to show a list of orthologous genes.

HF Ev BS Species Gene ID Repr. ID Gene Name Functional description Ev AGI code Arabidopsis gene name C.G. S.X. Other DB
0.02 4e+0 34 Glycine max PsAffx.psMY010iA10r_s_at PsAffx.psMY010iA10r - - 1e-1 At1g12390 cornichon family protein C.G. S.X.
0.02 2e+0 34 Hordeum vulgare Contig3855_at Contig3855 - - 6e-2 At2g21100 disease resistance-responsive protein-related / dirigent protein-related C.G. S.X.
0.02 6e+0 34 Oryza sativa Os01g0380850 NM_193907.1 - - 3e-1 At1g20320 NLI interacting factor (NIF) family protein C.G. S.X.
0.02 3e-1 38 Populus trichocarpa PtpAffx.135079.1.S1_s_at DN496393 hypothetical protein - 1e-19 At5g38660 APE1 (ACCLIMATION OF PHOTOSYNTHESIS TO ENVIRONMENT) C.G. S.X.
0.02 8e-1 36 Triticum aestivum TaAffx.5479.1.S1_at CA709524 - - 2e-1 At4g28520 CRU3 (CRUCIFERIN 3) C.G. S.X.
0.02 6e-2 38 Vitis vinifera 1620111_at CF568854 - - 1e-9 At1g05850 POM1 (POM-POM1) C.G. S.X.
0.02 3e-1 36 Zea mays Zm.5963.1.S1_at BG842522 hypothetical protein LOC100193568 - 5e-13 At2g47640 small nuclear ribonucleoprotein D2, putative / snRNP core protein D2, putative / Sm protein D2, putative C.G. S.X.
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Biological processes

Click GO ID to show a list of genes that are associated with the GO ID.

ECC GO ID Process Name
X GO:0009737 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 an abscisic acid stimulus.
S GO:0009793 The process whose specific outcome is the progression of the embryo over time, from zygote formation to the end of seed dormancy. An example of this process is found in Arabidopsis thaliana.
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Metabolic pathways

Click KaPPA-View ID to show a list of genes that are assigned to the KaPPA-View ID.

KaPPA-View ID Link to Kappa-View Pathway Name

Click KEGG PATHWAY ID to show a list of genes that are assigned to the KEGG PATHWAY ID.

KEGG PATHWAY ID Link to KEGG PATHWAY Pathway Name
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