Co-expression analysis

Gene ID At4g24120
Gene name YSL1 (YELLOW STRIPE LIKE 1)
Module size 25 genes
NF 0.09
%ile 6.1



Co-expression network

pink confeito: Transcription factor, green bicone: Binding protein, red cone: Enzyme protein, blue sphere: Other protein
large node: VF over 0.50, middle node: over 0.25, small node: 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
1.00100.01.00At4g24120828512YSL1 (YELLOW STRIPE LIKE 1)Member of a small family of oligopeptide transporters similar to the yellow stripe locus of maize (ZmYS1).O.I.H.G.S.X.
0.2420.70.75At2g35940818167BLH1 (BEL1-LIKE HOMEODOMAIN 1)Encodes a member of the BEL-like homeodomain protein family. Ecotopic expression in the embryo sac leads to defects in nuclear migration and cellularization and embryo sacs with multiple egg cells. Loss of function alleles have no female gametophyte defects. The ecotopic expression phenotype requires KNAT3 because it can be suppressed by loss of KNAT3 function alleles. Localized to the nucleus but interaction with OFP1 relocates it to the cytoplasm.O.I.H.G.S.X.
0.2319.30.71At4g12300826839CYP706A4member of CYP706AO.I.H.G.S.X.
0.1811.40.76At5g20280832150ATSPS1F (sucrose phosphate synthase 1F)Encodes a protein with putative sucrose-phosphate synthase activity. When the gene was expressed in transgenic tobacco plants, a clear trend for increased SPS activity was noted.O.I.H.G.S.X.
0.1710.20.73At5g62680836389proton-dependent oligopeptide transport (POT) family proteinF:transporter activity;P:oligopeptide transport;C:plasma membrane, membrane;PMBFOO.I.H.G.S.X.
0.157.80.73At5g02620831855ankyrin repeat family proteinF:protein binding;P:unknown;C:plasma membrane;MOFBPVAO.I.H.G.S.X.
0.157.80.72At2g26740817215ATSEH (Arabidopsis thaliana soluble epoxide hydrolase)Encodes a soluble epoxide hydrolase whose expression is induced by auxin and water stress.O.I.H.G.S.X.
0.146.80.72At5g61520836273hexose transporter, putativeF:carbohydrate transmembrane transporter activity, sugar:hydrogen symporter activity;P:transport, transmembrane transport;C:integral to membrane, membrane;BFMPOAO.I.H.G.S.X.
0.114.10.74At3g28050822429nodulin MtN21 family proteinF:unknown;P:biological_process unknown;C:endomembrane system, membrane;PBOAFMO.I.H.G.S.X.
0.103.40.73At2g31820817739ankyrin repeat family proteinF:protein binding;P:unknown;C:plasma membrane;MOFBPVAO.I.H.G.S.X.
0.103.40.73At3g56620824829integral membrane family protein / nodulin MtN21-relatedF:unknown;P:unknown;C:membrane;BPOAMO.I.H.G.S.X.
0.103.40.71At5g57940835905ATCNGC5 (CYCLIC NUCLEOTIDE GATED CHANNEL 5)member of Cyclic nucleotide gated channel familyO.I.H.G.S.X.
0.092.80.71At2g47070819321SPL1 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 1)member of SPL gene family, encodes DNA binding proteins and putative transcription factors. All have the SBP-box, which encodes the SBP-domain, required for and sufficient for interaction with DNA.O.I.H.G.S.X.
0.092.80.72At1g20980838692SPL14 (squamosa promoter binding protein-like 14)Encodes a nuclear plant-specific protein with features characteristic of a transcriptional regulator, including a nuclear localization signal sequence, a plant-specific DNA binding domain (the SBP box), and a protein interaction motif (ankyrin repeats). It unctions as a transcriptional regulator that plays a role not only in sensitivity to FB1, but also in the development of normal plant architecture.O.I.H.G.S.X.
0.082.30.73At2g47710819384universal stress protein (USP) family proteinF:molecular_function unknown;P:response to stress;C:vacuole;BPOAMFO.I.H.G.S.X.
0.082.30.73At5g50160835081FRO8 (FERRIC REDUCTION OXIDASE 8)Encodes a ferric chelate reductase that is expressed in shoots and flowers.O.I.H.G.S.X.
0.071.90.71At2g03140814843CAAX amino terminal protease family proteinF:unknown;P:proteolysis;C:nucleus;MBOFPVAO.I.H.G.S.X.
0.061.40.72At4g22260828321IM (IMMUTANS)Similar to mitochondrial alternative oxidase. im mutants have a variegated phenotype and fail to differentiate chloroplasts in the majority of their cells under high light intensity continuous illumination. The white tissues of immutans accumulate phytoene, a non-colored C40 carotenoid intermediate. This suggests that immutans controls, either directly or indirectly, the activity of phytoene desaturase (PDS), the enzyme that converts phytoene to zeta-carotene in higher plants. However, im is not the structural gene for PDS. It is located in the lumenar face of the thylakoid membrane. IM is expressed ubiquitously in plant tissues.O.I.H.G.S.X.
0.061.40.71At4g04320825752malonyl-CoA decarboxylase family proteinF:malonyl-CoA decarboxylase activity;P:fatty acid biosynthetic process;C:unknown;OBMPO.I.H.G.S.X.
0.061.40.71At1g03040839446basic helix-loop-helix (bHLH) family proteinF:transcription factor activity, DNA binding;P:regulation of transcription, acetyl-CoA biosynthetic process from pyruvate;C:nucleus;PMO.I.H.G.S.X.
0.051.10.71At5g59400836059unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PO.I.H.G.S.X.
0.040.90.71At4g39450830100unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOO.I.H.G.S.X.
0.040.90.71At4g29010829022AIM1 (ABNORMAL INFLORESCENCE MERISTEM)Functions in beta-oxidation of fatty acids, similar to CuMFP with L-3-hydroxyacyl-CoA hydrolyase , L-3-hydroxyacyl-dehydrogenase, D-3-hydroxyacyl-CoA epimerase, and 3, 2-enoyl-CoA isomerase activitiesO.I.H.G.S.X.
0.030.60.71At4g38360829993unknown proteinF:unknown;P:biological_process unknown;C:endomembrane system;MPFOO.I.H.G.S.X.
0.020.40.71At4g04770825814ATABC1 (ATP BINDING CASSETTE PROTEIN 1)Encodes an iron-stimulated ATPase. A member of the NAP subfamily of ABC transporters. Involved in Fe-S cluster assembly. Similar to SufB. Involved in the regulation of iron homeostasis. Able to form homodimers. Interacts with AtNAP7 inside the chloroplast.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
42.299.8GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
42.099.8GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
39.799.8GSM311279Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
34.899.7GSM266668Arabidopsis, root cells, columella root cap, -Fe, replicate 3GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
34.499.7GSM311292Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
31.899.7GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
30.999.7GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
30.199.7GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
29.499.7GSM311280Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
28.599.7GSM266667Arabidopsis, root cells, columella root cap, -Fe, replicate 2GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
28.399.7GSM266666Arabidopsis, root cells, columella root cap, -Fe, replicate 1GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
26.299.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.799.6GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.499.6GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.199.6GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.999.6GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.799.6GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.599.6GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.399.6GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
21.899.6GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
21.899.6GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
21.799.6GSM142737DH001_ATH1_A4-UNM2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
21.199.6GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
20.499.6GSM311291Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
19.999.6GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
19.999.6GSM128733Hennig_1-5_flowers-CK_021114_2_B_Rep2_ATH1GSE5526Transcriptional Programs of Early Reproductive Stages in ArabidopsisLink to GEO
19.699.6GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.899.5GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.299.5GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
17.499.5GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
16.799.5GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
16.699.5GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
16.099.5GSM67087Arabidopsis_Stigma03GSE3056Arabidopsis Pollination StudyLink to GEO
16.099.5GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.599.5GSM142734DH001_ATH1_A1-UNM1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
15.299.4GSM13780CycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
15.299.4GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
15.299.4GSM184892Arabidopsis, root cells, columella root cap, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
15.099.4GSM184912Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
14.999.4GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.299.4GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
14.299.4GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
13.799.4GSM67086Arabidopsis_Stigma02GSE3056Arabidopsis Pollination StudyLink to GEO
13.799.4GSM13779Dexamethasone plus cycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
13.599.4GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.399.4GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
13.299.4GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
12.299.3GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
11.799.3GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.599.3GSM142735DH001_ATH1_A2-BCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
11.299.2GSM13784Cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
10.599.2GSM13783Dexamethasone plus cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
10.499.2E-MEXP-807-raw-cel-1173273060
10.499.2GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.799.1E-MEXP-807-raw-cel-1173273223
9.499.1GSM184894Arabidopsis, root cells, columella root cap, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.299.1E-MEXP-807-raw-cel-1173273088
8.799.0GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0741GO:0010201A 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 the detection of a continuous far red light stimulus by the high-irradiance response system. Far red light is electromagnetic radiation of wavelength 700-800nm. The activity of the high-irradiance response system is characterized by stronger effects of continuous than pulsed light at equal total fluence.Link to AmiGO
0.0611GO:0005985The chemical reactions and pathways involving sucrose, the disaccharide fructofuranosyl-glucopyranoside.Link to AmiGO
0.0591GO:0009610A 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 stimulus from a symbiotic fungus, a fungus living in close physical association with another organism.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.037100592alpha-Linolenic acid metabolismLink to KEGG PATHWAY
0.018100500Starch and sucrose metabolismLink to KEGG PATHWAY
0.006101070Biosynthesis of plant hormonesLink to KEGG PATHWAY

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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