Co-expression analysis

Gene ID At4g18610
Gene name LSH9 (LIGHT SENSITIVE HYPOCOTYLS 9)
Module size 11 genes
NF 0.31
%ile 39.1



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
0.6176.71.00At4g18610827595LSH9 (LIGHT SENSITIVE HYPOCOTYLS 9)F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMO.I.H.G.S.X.
0.4659.80.75At1g18880838469proton-dependent oligopeptide transport (POT) family proteinF:transporter activity;P:oligopeptide transport;C:membrane;PMBFOO.I.H.G.S.X.
0.4659.80.78At3g19370821471-F:unknown;P:unknown;C:plasma membrane;MOBFPAVO.I.H.G.S.X.
0.4355.30.77At5g25890832658IAA28 (INDOLE-3-ACETIC ACID INDUCIBLE 28)encodes a protein that may be a negative regulator of lateral root formation in response to auxin. It is a member of IAA/ARF gene family and is plant-specific. Gain of function mutations in this gene suppresses lateral root formation and is resistant to inhibition of root elongation by auxin, cytokinin, and ethylene.O.I.H.G.S.X.
0.3541.60.78At3g16340820881PDR1F:ATPase activity, coupled to transmembrane movement of substances;P:multidrug transport;C:plasma membrane;BOMFAPVO.I.H.G.S.X.
0.3541.60.79At2g37280818305PDR5 (PLEIOTROPIC DRUG RESISTANCE 5)F:ATPase activity, coupled to transmembrane movement of substances;P:multidrug transport;C:plasma membrane;BOMAFPVO.I.H.G.S.X.
0.3338.10.76At1g55610842010BRL1 (BRI 1 LIKE)mutant has Altered vascular cell differentiation; LRR Receptor KinaseO.I.H.G.S.X.
0.3133.80.82At5g65970836727MLO10 (MILDEW RESISTANCE LOCUS O 10)A member of a large family of seven-transmembrane domain proteins specific to plants, homologs of the barley mildew resistance locus o (MLO) protein. The Arabidopsis genome contains 15 genes encoding MLO proteins, with localization in plasma membrane. Phylogenetic analysis revealed four clades of closely-related AtMLO genes. ATMLO10 belongs to the clade III, with AtMLO5, AtMLO7, AtMLO8, and AtMLO9. The gene is expressed in root and cotyledon vascular system, in root-shoot junction and lateral root primordia and in developing siliques, as shown by GUS activity patterns. The expression of several phylogenetically closely-related AtMLO genes showed similar or overlapping tissue specificity and analogous responsiveness to external stimuli, suggesting functional redundancy, co-function, or antagonistic function(sO.I.H.G.S.X.
0.2217.50.78At3g61850825358DAG1 (dof affecting germination 1)Zinc finger transcription factor of the Dof family involved in the control of seed germination.O.I.H.G.S.X.
0.146.80.78At3g17420821006GPK1serine/threonine protein kinase-like proteinO.I.H.G.S.X.
0.146.80.80At2g26650817206AKT1 (ARABIDOPSIS K TRANSPORTER 1)Shaker-like inward rectifying potassium channel predominantly expressed in predominantly in root hairs and root endodermis.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
101.899.9GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
88.699.9GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
80.499.9GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
77.599.9GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
68.199.9GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
65.199.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
64.799.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
62.599.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
54.999.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
50.299.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
48.399.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
48.399.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
46.899.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.199.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.899.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.899.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.899.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.199.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.399.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.899.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
28.499.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.399.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
22.199.6GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
21.999.6E-MEXP-807-raw-cel-1173273144
21.699.6E-MEXP-807-raw-cel-1173273252
18.599.5E-MEXP-807-raw-cel-1173273116
17.999.5GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
17.399.5E-MEXP-807-raw-cel-1173273088
17.299.5E-MEXP-807-raw-cel-1173273060
17.099.5E-MEXP-807-raw-cel-1173273170
16.899.5GSM131453AtGen_6-9321_Heatstress-Roots-3.0h_Rep1GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
16.099.5GSM131454AtGen_6-9322_Heatstress-Roots-3.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
15.999.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
15.299.4E-MEXP-807-raw-cel-1173273196
14.799.4GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.399.4GSM131449AtGen_6-9221_Heatstress-Roots-1.0h_Rep1GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
13.699.4GSM131452AtGen_6-9312_Heatstress-Shoots-3.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
13.399.4GSM131451AtGen_6-9311_Heatstress-Shoots-3.0h_Rep1GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
13.199.4GSM131447AtGen_6-9211_Heatstress-Shoots-1.0h_Rep1GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
12.799.3GSM13783Dexamethasone plus cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
12.699.3GSM131450AtGen_6-9222_Heatstress-Roots-1.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
11.999.3GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.599.3GSM131448AtGen_6-9212_Heatstress-Shoots-1.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
11.299.2E-MEXP-807-raw-cel-1173273223
10.499.2GSM13784Cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
10.399.2GSM184482Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.399.1GSM13779Dexamethasone plus cycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
8.999.0GSM13780CycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1051GO:0006417Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.Link to AmiGO
0.0831GO:0010102The process by which the anatomical structures of lateral root are generated and organized. Morphogenesis pertains to the creation of form. A lateral root is one formed from pericycle cells located on the xylem radius of the root, as opposed to the initiation of the main root from the embryo proper.Link to AmiGO
0.0771GO:0048767The process by which the root hair grows longer.Link to AmiGO

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_max
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays



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