Co-expression analysis

Gene ID At2g24120
Gene name SCA3 (SCABRA 3)
Module size 20 genes
NF 0.31
%ile 39.8



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
1.00100.01.00At2g24120816946SCA3 (SCABRA 3)F:DNA-directed RNA polymerase activity, DNA binding;P:transcription;C:mitochondrion;OFPMVBO.I.H.G.S.X.
0.5570.60.91At4g27340828842Met-10+ like family proteinF:unknown;P:biological_process unknown;C:unknown;BAOMFPO.I.H.G.S.X.
0.5065.30.90At3g10270820189ATP binding / DNA binding / DNA topoisomerase (ATP-hydrolyzing)Protein targeting to mitochondria is influenced by UTR sequences.O.I.H.G.S.X.
0.4152.40.90At1g09900837522pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:membrane;POMFBAO.I.H.G.S.X.
0.4050.80.92At4g31210829248DNA topoisomerase family proteinF:DNA topoisomerase activity, DNA topoisomerase type I activity, DNA binding, nucleic acid binding;P:DNA topological change, DNA unwinding during replication, DNA metabolic process;C:chromosome;OBMFAPVO.I.H.G.S.X.
0.3643.60.91At4g02990828116mitochondrial transcription termination factor family protein / mTERF family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFBO.I.H.G.S.X.
0.3541.60.89At4g09730826559DEAD/DEAH box helicase, putativeF:helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding;P:unknown;C:chloroplast;BOMFPAVO.I.H.G.S.X.
0.3541.60.89At1g69200843251kinaseF:kinase activity;P:acetate fermentation, sucrose biosynthetic process, sucrose catabolic process, using beta-fructofuranosidase;C:nucleoid;BOPAMFO.I.H.G.S.X.
0.3439.80.90At3g02060821294DEAD/DEAH box helicase, putativeF:transcription factor activity, helicase activity, nucleic acid binding, ATP-dependent helicase activity, ATP binding;P:regulation of transcription, DNA-dependent;C:chloroplast;BOMFPAVO.I.H.G.S.X.
0.3235.70.91At5g11270830997OCP3 (OVEREXPRESSOR OF CATIONIC PEROXIDASE 3)Encodes a homeodomain transcription factor involved in mediating resistance to infection by necrotrophic pathogens dependent on perception of jasmonic acid through COI1. Expressed in the nucleus. Downregulated upon fungal infection. Also involved in drought tolerance.O.I.H.G.S.X.
0.3235.70.92At3g47450823899NOA1 (NO ASSOCIATED 1)Encodes a protein with similarity to the bacterial YqeH GTPase required for proper ribosome assembly. In Arabidopsis, mutant analyses show that this protein regulates growth and hormonal signaling in plants. It also attenuates oxidative stress and reactive oxygen species (ROS). It also seems to be involved in regulating leaf senescence and cell death. This gene product is also involved in nitric oxide biosynthesis in response to ABA but not exogenous H2O2. This protein also appears to be required for proper plastid biogenesis. Levels of several plastid-localized proteins, including RBCL, ClpP1, and the MEP biosynthesis enzymes DXS and DXR are altered in rif1-1 mutants. This protein was originally characterized as a mitrochondrial-localized nitric oxide synthase, but, the synthase activity was later disproven. In addition, new studies with GFP fusion proteins and chloroplast import assays suggest that this protein is found in chloroplasts.O.I.H.G.S.X.
0.3032.10.89At1g48460841267unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast envelope;PO.I.H.G.S.X.
0.2726.20.89At3g27180822337unknown proteinF:unknown;P:unknown;C:chloroplast;BOMPAFO.I.H.G.S.X.
0.2726.20.89At3g46740823827TOC75-III (TRANSLOCON AT THE OUTER ENVELOPE MEMBRANE OF CHLOROPLASTS 75-III)Component of the translocon outer membrane (TOC) complex. Forms the outer envelope translocation channel (beta-barrel). Plays a role in preprotein conductance. Imported into chloroplast. Expressed in young dividing photosynthetic tissues. Knockout mutants are embryo lethal with arrested development at the two-cell stage. Knockout mutants have abnormal etioplasts.O.I.H.G.S.X.
0.2726.20.91At2g31890817747RAPProtein contains putative RNA binding domain. Expressed in response to Pseudomonas syringae infection. Resistance requires silencing of AtRAP suggesting it functions as a negative regulator of plant disease resistance.O.I.H.G.S.X.
0.2624.40.90At1g74850843824PTAC2 (PLASTID TRANSCRIPTIONALLY ACTIVE2)Present in transcriptionally active plastid chromosomes. Involved in plastid gene expression.O.I.H.G.S.X.
0.1811.40.89At3g02450821139cell division protein ftsH, putativeF:in 6 functions;P:unknown;C:integral to membrane, chloroplast;BOMFPAVO.I.H.G.S.X.
0.146.80.90At5g16620831524TIC40chloroplast protein import (Tic40)O.I.H.G.S.X.
0.146.80.89At4g20960827843cytidine/deoxycytidylate deaminase family proteinencodes diaminohydroxyphosphoribosylaminopyrimidine deaminase catalyzing the second step in the riboflavin biosynthesisO.I.H.G.S.X.
0.124.90.91At3g17970819660atToc64-III (Arabidopsis thaliana translocon at the outer membrane of chloroplasts 64-III)F:binding, carbon-nitrogen ligase activity, with glutamine as amido-N-donor;P:unknown;C:chloroplast;BOMFPAO.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
89.199.9E-MEXP-1443-raw-cel-1581869515
76.599.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
68.099.9E-MEXP-1443-raw-cel-1581869573
65.599.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
59.399.8GSM133775Lindsey_1-27_torpedo-meristem_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
57.699.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
54.599.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
51.899.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
50.899.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
49.999.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
49.299.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
49.099.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.699.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.099.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
46.999.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
46.699.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
46.399.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.699.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.499.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
45.299.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.599.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.599.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.699.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.599.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.799.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.499.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.099.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
37.699.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
28.599.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
20.799.6GSM133774Lindsey_1-26_torpedo-meristem_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
18.899.5E-ATMX-35-raw-cel-1574334832
14.899.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.699.3GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
12.099.3E-ATMX-35-raw-cel-1574334816
11.899.3E-ATMX-35-raw-cel-1574334800
11.099.2GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
10.999.2GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.199.1GSM142734DH001_ATH1_A1-UNM1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1082GO:0006265The process by which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.Link to AmiGO
0.0951GO:0010322Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of isopentenyl diphosphate produced via the methylerythritol (MEP) pathway (mevalonate-independent).Link to AmiGO
0.0932GO:0006259The chemical reactions and pathways involving DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.087100150Androgen and estrogen metabolismLink to KEGG PATHWAY
0.083100440Phosphonate and phosphinate metabolismLink to KEGG PATHWAY
0.071100740Riboflavin metabolismLink 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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