Co-expression analysis

Gene ID At3g02180
Gene name SP1L3 (SPIRAL 1-LIKE3)
Module size 14 genes
NF 0.20
%ile 18.0



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
1.00100.01.00At3g02180821277SP1L3 (SPIRAL 1-LIKE3)SPIRAL1-LIKE3 belongs to a six-member gene family in Arabidopsis; all members share high sequence similarity in amino- and carboxy-terminal regions. Regulates cortical microtubule organization. Mutant plants exhibit altered patterns of root, leaf and petal growth as a result of defective anisotropic cell expansion.O.I.H.G.S.X.
0.3133.80.91At2g03680814896SPR1 (SPIRAL1)The SPR1 gene encodes a plant-specific 12-kD protein which has a repeated motif at both ends, separated by a predicted rod-like domain, suggesting that it may act as an intermolecular linker. Ubiquitously expressed and belongs to a six-member gene family in Arabidopsis; expressed in transgenic seedlings localized to microtubules within the cortical array, preprophase band, phragmoplast, and mitotic spindle.O.I.H.G.S.X.
0.2930.30.91At1g78040844139pollen Ole e 1 allergen and extensin family proteinF:molecular_function unknown;P:in 10 processes;C:endomembrane system;PO.I.H.G.S.X.
0.2930.30.90At5g10560830921glycosyl hydrolase family 3 proteinF:xylan 1,4-beta-xylosidase activity, hydrolase activity, hydrolyzing O-glycosyl compounds;P:carbohydrate metabolic process;C:plasma membrane, vacuole;BOFPAMO.I.H.G.S.X.
0.2930.30.91At5g48810834939CB5-D (CYTOCHROME B5 ISOFORM D)Encodes a cytochrome b5 isoform that localizes to the ER. The C-terminal portion of the protein appears to be capable of inserting into a plant microsomal membrane in vitro and the protein appears to be subject to glycosylation.O.I.H.G.S.X.
0.2319.30.91At3g12290820409tetrahydrofolate dehydrogenase/cyclohydrolase, putativeF:binding, catalytic activity;P:folic acid and derivative biosynthetic process, metabolic process;C:chloroplast;OBMFPAO.I.H.G.S.X.
0.2115.80.90At1g14140837973mitochondrial substrate carrier family proteinF:transporter activity, binding;P:transport, mitochondrial transport;C:mitochondrial inner membrane, membrane;MFPOVO.I.H.G.S.X.
0.1912.70.91At4g18060827531clathrin bindingF:clathrin binding;P:unknown;C:unknown;MOFPBO.I.H.G.S.X.
0.1710.20.91At4g38040829960exostosin family proteinF:catalytic activity;P:biological_process unknown;C:chloroplast, membrane;PMOBFVO.I.H.G.S.X.
0.168.80.91At1g42960840894-expressed protein localized to the inner membrane of the chloroplast.O.I.H.G.S.X.
0.168.80.90At2g47170819330ARF1A1CGene encoding ADP-ribosylation factor and similar to other ARFs and ARF-like proteins. Members of this family are known to be essential for vesicle coating and uncoating and functions in GTP-binding. The gene is shown to play a role in cell division, cell expansion and cellulose production using antisense construct.O.I.H.G.S.X.
0.124.90.91At4g40030830164histone H3.2F:DNA binding;P:nucleosome assembly;C:nucleus, nucleosome;MFPOO.I.H.G.S.X.
0.114.10.90At1g49140841337NADH-ubiquinone oxidoreductase-relatedF:unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;FPMO.I.H.G.S.X.
0.114.10.90At2g19790816498clathrin adaptor complex small chain family proteinF:protein transporter activity, protein binding;P:intracellular protein transport, transport, vesicle-mediated transport, protein transport;C:membrane coat, clathrin vesicle coat;MOFPO.I.H.G.S.X.

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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
54.599.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
54.499.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
40.799.8GSM133303RIKEN-NAKABAYASHI1AGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
37.399.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.399.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.299.7GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
37.199.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.699.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.499.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
36.399.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.299.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.199.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.999.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.999.7E-MEXP-1451-raw-cel-1585200202
34.499.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.699.7E-MEXP-1451-raw-cel-1585200266
33.699.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.399.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.699.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.599.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.399.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.999.7GSM131706ATGE_84_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
30.199.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.099.7E-MEXP-1451-raw-cel-1585200234
29.199.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.499.7E-MEXP-1451-raw-cel-1585200170
28.099.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.799.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.199.7GSM131708ATGE_84_DGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
27.199.7GSM131655ATGE_27_AGSE5633AtGenExpress: Developmental series (shoots and stems)Link to GEO
26.499.7GSM10480lec1-1 Cotyledon Stage Seed 2GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
25.299.6GSM147965lec1-1 Globular Stage Seed 1GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
24.999.6E-MEXP-1451-raw-cel-1585200362
24.999.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
24.599.6GSM131707ATGE_84_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
22.299.6GSM311295Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
22.099.6GSM131703ATGE_83_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
21.799.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.699.6GSM131656ATGE_27_BGSE5633AtGenExpress: Developmental series (shoots and stems)Link to GEO
21.299.6GSM131657ATGE_27_CGSE5633AtGenExpress: Developmental series (shoots and stems)Link to GEO
21.099.6GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.099.6GSM131705ATGE_83_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
20.799.6E-MEXP-285-raw-cel-440783213
20.799.6GSM147963WT Globular Stage Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
20.799.6GSM10479lec1-1 Cotyledon Stage Seed 1GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
20.499.6GSM131701ATGE_82_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
20.399.6E-MEXP-285-raw-cel-440783152
19.699.6GSM131702ATGE_82_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
19.599.6GSM131700ATGE_82_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
19.599.6GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
19.599.6GSM131704ATGE_83_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
19.399.6GSM133304RIKEN-NAKABAYASHI1BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
18.799.5GSM147966lec1-1 Globular Stage Seed 2GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
18.599.5GSM10449WT Cotyledon Stage Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
17.199.5GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
16.999.5GSM147964WT Globular Stage Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
14.699.4GSM10448WT Cotyledon Stage Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
13.099.4GSM133117RIKEN-YAMAUCHI1AGSE5687AtGenExpress: Different temperature treatment of seedsLink to GEO
12.999.3GSM133962Fukuda_1-7_6A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
12.699.3GSM311293Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
12.099.3GSM133820Yang_1-5_young-pod_Rep3_ATH1GSE5736To identify changes in gene expression during silique senescence in Arabidopsis thalianaLink to GEO
11.999.3GSM10454WT Post-Mature Green Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
11.899.3E-MEXP-265-raw-cel-414618394
11.699.3GSM133309RIKEN-NAKABAYASHI4BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
11.099.2E-MEXP-265-raw-cel-414618291
10.999.2E-MEXP-1451-raw-cel-1585200330
10.899.2GSM10456WT Post-Mature Green Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
10.899.2GSM133963Fukuda_1-8_6B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
10.699.2GSM133753Turner_A-7-Turne-WT-Base1_SLDGSE5729Role of COV in vascular patterningLink to GEO
10.299.2GSM131600ATGE_40_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.899.1GSM10442WT Ovule 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
9.499.1GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.299.1E-MEXP-265-raw-cel-414618491
9.199.1GSM131687ATGE_76_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
8.899.0GSM131601ATGE_40_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
8.699.0GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1181GO:0051211The process by which a cell irreversibly increases in size in one or more axes, where the growth rate varies according to the direction of growth. Growth may be limited to a particular axis, axes, or to particular locations on the surface of the cell.Link to AmiGO
0.0831GO:0009396The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.Link to AmiGO
0.0431GO:0009853A light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved. The substrate is glycolate formed in large quantities in chloroplasts from 2-phosphoglycolate generated from ribulose 1,5-bisphosphate by the action of ribulose-bisphosphate carboxylase; the glycolate enters the peroxisomes where it is converted by glycolate oxidase to glyoxylate which undergoes transamination to glycine. This then passes into the mitochondria where it is decarboxylated forming one molecule of serine for every two molecules of glycine. This pathway also exists in photosynthetic bacteria.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.065100670One carbon pool by folateLink to KEGG PATHWAY
0.043100630Glyoxylate and dicarboxylate metabolismLink to KEGG PATHWAY
0.013100190Oxidative phosphorylationLink 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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