CoP: Co-expressed Biological Processes

Gene omics information

Query gene ID At3g59060

Gene name PIL6 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 6)

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 At3g59060 825075 PIL6 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 6) Encodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family. Involved in shade avoidance. Functions as negative regulator of PhyB. Protein levels are modulated by phytochrome B. S.X. H.G.
0.55 70.6 At5g44190 834442 GLK2 (GOLDEN2-LIKE 2) Encodes GLK2, Golden2-like 2, one of a pair of partially redundant nuclear transcription factors that regulate chloroplast development in a cell-autonomous manner. GLK1, Golden2-like 1, is encoded by At2g20570. GLK1 and GLK2 regulate the expression of the photosynthetic apparatus. S.X. H.G.
0.52 67.4 At2g22990 816830 SNG1 (SINAPOYLGLUCOSE 1) sinapoylglucose:malate sinapoyltransferase. Catalyzes the formation of sinapoylmalate from sinapoylglucose. Mutants accumulate excess sinapoylglucose. S.X. H.G.
0.50 65.3 At3g16520 820900 UDP-glucoronosyl/UDP-glucosyl transferase family protein F:in 6 functions;P:metabolic process;C:cellular_component unknown;PMVBOF S.X. H.G.
0.49 63.5 At2g25080 817046 ATGPX1 (GLUTATHIONE PEROXIDASE 1) Encodes glutathione peroxidase. S.X. H.G.
0.48 62.5 At2g43010 818903 PIF4 (phytochrome interacting factor 4) Isolated as a semidominant mutation defective in red -light responses. Encodes a nuclear localized bHLH protein that interacts with active PhyB protein. Negatively regulates phyB mediated red light responses. Involved in shade avoidance response. Protein abundance is negatively regulated by PhyB. S.X. H.G.
0.46 59.8 At1g03130 838400 PSAD-2 (photosystem I subunit D-2) Encodes a protein predicted by sequence similarity with spinach PsaD to be photosystem I reaction center subunit II (PsaD2) S.X. H.G.
0.46 59.8 At2g42750 818875 DNAJ heat shock N-terminal domain-containing protein F:unfolded protein binding, heat shock protein binding;P:protein folding;C:chloroplast;BOMFPAV S.X. H.G.
0.46 59.8 At3g50750 824239 brassinosteroid signalling positive regulator-related F:transcription regulator activity;P:biological_process unknown;C:vacuole;OPFMB S.X. H.G.
0.44 57.2 At3g08940 820043 LHCB4.2 (light harvesting complex PSII) Lhcb4.2 protein (Lhcb4.2, protein involved in the light harvesting complex of photosystem II S.X. H.G.
Click here to hide the above table.

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
28.8 99.7 GSM244443 Arabidopsis wild-type_T0 (not inoculated)_biological rep2_exp2 GSE9674 Expression data from Arabidopsis plants misexpressing AtMYB30 after Xanthomonas inoculation at early timepoints
28.2 99.7 GSM253159 4h into an extended nightB GSE10016 Expression data of Arabidopsis thaliana rosettes in an extended night
27.6 99.7 GSM253158 4h into an extended nightA GSE10016 Expression data of Arabidopsis thaliana rosettes in an extended night
25.4 99.6 GSM77180 04h low CO2 + dark replicate B GSE3423 Carbon fixation (endogenous sugar) and light-dependent gene expression
23.9 99.6 GSM253160 6h into an extended night GSE10016 Expression data of Arabidopsis thaliana rosettes in an extended night
22.9 99.6 GSM77177 04h low CO2 + dark replicate A GSE3423 Carbon fixation (endogenous sugar) and light-dependent gene expression
21.8 99.6 E-ATMX-30-raw-cel-1513696675
19.8 99.6 GSM268247 WT-drought-1, biological rep 1 GSE10643 Transcription profiling of Arabidopsis dor mutant and wild-type plants in response to drought stress.
18.0 99.5 GSM253161 8h into an extended nightA GSE10016 Expression data of Arabidopsis thaliana rosettes in an extended night
17.1 99.5 GSM253162 8h into an extended nightB GSE10016 Expression data of Arabidopsis thaliana rosettes in an extended night
Click here to hide the above table.

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
0.33 3e-58 226 At2g43010 818903 PIF4 (phytochrome interacting factor 4) Isolated as a semidominant mutation defective in red -light responses. Encodes a nuclear localized bHLH protein that interacts with active PhyB protein. Negatively regulates phyB mediated red light responses. Involved in shade avoidance response. Protein abundance is negatively regulated by PhyB. C.G. S.X.
0.10 1e-23 111 At2g20180 816538 PIL5 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 5) Encodes a novel Myc-related bHLH transcription factor that has transcriptional activation activity in the dark. It is a key negative regulator of phytochrome-mediated seed germination and acts by inhibiting chlorophyll biosynthesis, light-mediated suppression of hypocotyl elongation and far-red light-mediated suppression of seed germination, and promoting negative gravitropism in hypocotyls. Light reduces this activity in a phy-dependent manner. The protein preferentially interacts with the Pfr forms of Phytochrome A (PhyA) and Phytochrome B (PhyB), is physically associated with APRR1/TOC1 and is degraded in red (R) and far-red (FR) light through the ubiquitin (ub)-26S proteasome pathway to optimize photomorphogenic development in Arabidopsis. It also negatively regulates GA3 oxidase expression. C.G. S.X.
0.04 3e-6 54 At4g36930 829847 SPT (SPATULA) Encodes a transcription factor of the bHLH protein family. Mutants have abnormal, unfused carpels and reduced seed dormancy. C.G. S.X.
0.02 3e-6 54 At2g24260 816961 basic helix-loop-helix (bHLH) family protein F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;PMFO C.G. S.X.
Click here to hide the above table.

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
0.05 3e-10 67 Glycine max GmaAffx.79730.1.S1_at BF325482 - - 2e-21 At1g09530 PIF3 (PHYTOCHROME INTERACTING FACTOR 3) C.G. S.X.
0.03 5e-3 42 Hordeum vulgare EBpi01_SQ003_I06_at EBpi01_SQ003_I06 - - 8e-1 At5g63740 zinc finger protein-related C.G. S.X.
0.05 2e-8 61 Oryza sativa Os12g0610200 AK066763.1 - Phytochrome-interacting factor 3(Phytochrome-associated protein 3) (Basichelix-loop-helix protein 8) (bHLH8) (AtbHLH008) 5e-12 At2g43010 PIF4 (phytochrome interacting factor 4) C.G. S.X.
0.13 8e-23 109 Populus trichocarpa PtpAffx.1627.1.S1_a_at AJ767188 hypothetical protein - 3e-18 At2g43010 PIF4 (phytochrome interacting factor 4) C.G. S.X.
0.03 3e-3 44 Triticum aestivum Ta.18193.1.S1_at CA631013 - - 2e-1 At3g04370 PDLP4 (PLASMODESMATA-LOCATED PROTEIN 4) C.G. S.X.
0.03 8e-4 44 Vitis vinifera 1615168_at CF602900 hypothetical protein LOC100250140 - 4e+0 At4g31580 SRZ-22 C.G. S.X.
0.02 5e-3 42 Zea mays Zm.9892.1.A1_at BM351413 - - 6e-3 At3g59060 PIL6 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 6) C.G. S.X.
Click here to hide the above table.

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:0009585 The sequence of reactions within a cell required to convert absorbed photons from red or far-red light into a molecular signal; the red, far-red light range is defined as having a wavelength within the range 660-730 nm.
X GO:0009693 The chemical reactions and pathways resulting in the formation of ethylene (C2-H4, ethene), a simple hydrocarbon gas that can function in plants as a growth regulator.
Click here to hide the above table.

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
Click here to hide the above table.

Back to the CoP portal site

Back to the KAGIANA project homepage