Co-expression analysis

Gene ID At1g75010
Gene name ARC3 (ACCUMULATION AND REPLICATION OF CHLOROPLASTS 3)
Module size 28 genes
NF 0.29
%ile 34.8



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
0.8391.41.00At1g75010843839ARC3 (ACCUMULATION AND REPLICATION OF CHLOROPLASTS 3)Encodes ARC3 (Accumulation and Replication of Chloroplast 3), a chloroplast division factor functioning in the initiation of chloroplast division. ARC3 is a chimera of the prokaryotic FtsZ and part of the eukaryotic phosphatidylinositol-4-phosphate 5-kinase (PIP5K). Located on the outer surface of the chloroplast in a ring-like structure at the early stage of chloroplast division. The arc3 mutant has a small number of abnormally large chloroplasts in the cell.O.I.H.G.S.X.
0.4659.80.91At1g752108438585' nucleotidase family proteinF:5'-nucleotidase activity;P:biological_process unknown;C:chloroplast;MPBOO.I.H.G.S.X.
0.4659.80.92At5g03420831846-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BMOFPAVO.I.H.G.S.X.
0.4457.20.92At1g06820837193CRTISO (CAROTENOID ISOMERASE)Encodes carotenoid isomerase. Catalyzes the isomerization of poly-cis-carotenoids to all-trans-carotenoids. Together with PDS and ZDS, CRTiso is required to complete the synthesis of lycopene from phytoene.O.I.H.G.S.X.
0.4253.90.91At5g04710830349aspartyl aminopeptidase, putativeF:aminopeptidase activity, zinc ion binding;P:proteolysis;C:chloroplast, vacuole;BOFMPAO.I.H.G.S.X.
0.4050.80.92At1g65410842852ATNAP11 (ARABIDOPSIS THALIANA NON-INTRINSIC ABC PROTEIN 11)member of NAP subfamilyO.I.H.G.S.X.
0.3643.60.91At1g19800838568TGD1 (TRIGALACTOSYLDIACYLGLYCEROL 1)Encodes a permease-Like protein involved in lipid transfer from the ER to the chloroplast, more specifically, transfer of phosphatidate across the chloroplast inner membrane. Mutant leaves accumulate trigalactosyldiacylglycerol, triacylglycerol and phosphatidate. Chloroplast lipids are altered in their fatty acid composition and as a consequence the development of chloroplasts in the mutants are impacted. The mutant seeds has a higher abortion rate.O.I.H.G.S.X.
0.3338.10.92At3g20320821576TGD2 (TRIGALACTOSYLDIACYLGLYCEROL2)Encodes a permease-like component of an ABC transporter involved in lipid transfer from ER to chloroplast. A phosphatidic acid-binding protein with a predicted mycobacterial cell entry domain. It is tethered to the inner chloroplast envelope membrane facing the outer envelope membrane. Presumed bacterial orthologs of TGD1 and TGD2 in Gram-negative bacteria are typically organized in transcriptional units, suggesting their involvement in a common biological process.O.I.H.G.S.X.
0.3338.10.91At3g60620825233phosphatidate cytidylyltransferase family proteinF:phosphatidate cytidylyltransferase activity, transferase activity, transferring phosphorus-containing groups;P:phospholipid biosynthetic process;C:chloroplast, membrane, chloroplast envelope;BOMFPO.I.H.G.S.X.
0.3235.70.91At1g31500840040endonuclease/exonuclease/phosphatase family proteinF:hydrolase activity;P:biological_process unknown;C:cellular_component unknown;MFOPBO.I.H.G.S.X.
0.3235.70.91At5g44785834508OSB3 (ORGANELLAR SINGLE-STRANDED DNA BINDING PROTEIN 3)F:single-stranded DNA binding;P:biological_process unknown;C:mitochondrion, chloroplast;PBOMO.I.H.G.S.X.
0.3235.70.91At5g50280835093EMB1006 (embryo defective 1006)F:unknown;P:embryonic development ending in seed dormancy;C:chloroplast;POMFBAO.I.H.G.S.X.
0.3133.80.91At3g46100823753ATHRS1 (HISTIDYL-TRNA SYNTHETASE 1)histidyl-tRNA synthetaseO.I.H.G.S.X.
0.3032.10.91At3g13490820551OVA5 (OVULE ABORTION 5)Encodes a dual targeted lysyl-tRNA ligase that is found both in the mitochondrion and the chloroplast. Plants mutated in this gene exhibit an ovule abortion phenotype.O.I.H.G.S.X.
0.3032.10.91At1g50575841479lysine decarboxylase family proteinF:carboxy-lyase activity;P:metabolic process;C:chloroplast;BOPFMAO.I.H.G.S.X.
0.2830.30.91At1g80600844399WIN1 (HOPW1-1-INTERACTING 1)Encodes HopW1-1-Interacting protein 1 (WIN1). Interacts with the P. syringae effector HopW1-1. WIN1 is a putative acetylornithine transaminase. Modulates plant defenses against bacteria. Three WIN proteins are identified so far (WIN1: AT1G80600; WIN2: AT4G31750; WIN3: AT5G13320).O.I.H.G.S.X.
0.2830.30.91At5g62650836386unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.2830.30.91At5g50860835158protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:plasma membrane;MPOFBVAO.I.H.G.S.X.
0.2624.40.91At5g48830834941unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;BPOO.I.H.G.S.X.
0.2624.40.92At3g02660821282emb2768 (EMBRYO DEFECTIVE 2768)F:RNA binding, tyrosine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:embryonic development ending in seed dormancy, tRNA aminoacylation for protein translation;C:mitochondrion, chloroplast;OBFMPAO.I.H.G.S.X.
0.2522.60.91At4g14190827059-F:molecular_function unknown;P:biological_process unknown;C:chloroplast;POMFAO.I.H.G.S.X.
0.2319.30.91At5g03430831843phosphoadenosine phosphosulfate (PAPS) reductase family proteinF:transferase activity;P:Mo-molybdopterin cofactor biosynthetic process, metabolic process;C:cellular_component unknown;BOMFAPO.I.H.G.S.X.
0.1912.70.91At2g32040817764integral membrane transporter family proteinThe At2g32040 gene product has been demonstrated to mediate folate monoglutamate transport involved in tetrahydrofolate biosynthesis. It also mediates transport of antifolates, such as methotrexate and aminopterin. The gene is expressed in both chloroplast and non-green plastids.O.I.H.G.S.X.
0.1912.70.91At5g53860835467emb2737 (embryo defective 2737)F:unknown;P:embryonic development ending in seed dormancy;C:chloroplast;PO.I.H.G.S.X.
0.1710.20.91At5g19370832057rhodanese-like domain-containing protein / PPIC-type PPIASE domain-containing proteinF:isomerase activity;P:biological_process unknown;C:chloroplast;BOMFPAO.I.H.G.S.X.
0.1710.20.91At2g36250818197FTSZ2-1Encodes one of two FtsZ proteins, tubulin-like proteins, in Arabidopsis. It is involved in chloroplast division.O.I.H.G.S.X.
0.1710.20.91At3g10670820236ATNAP7Plastidic SufC-like ATP-binding cassette/ATPase essential for Arabidopsis embryogenesis. Involved in the biogenesis and/or repair of oxidatively damaged FeS clusters. Expressed in embryos and meristems.O.I.H.G.S.X.
0.157.80.91At2g31170817673SYCO ARATHF:cysteine-tRNA ligase activity, nucleotide binding, aminoacyl-tRNA ligase activity, ATP binding;P:cysteinyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:mitochondrion, chloroplast;OBMAFPVO.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
42.599.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
42.099.8GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
36.899.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.699.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.899.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.699.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.499.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.399.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.799.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.599.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.699.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.999.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.499.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.799.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.499.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.499.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.999.6GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.299.6GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
20.799.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
20.599.6GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.699.4GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.399.3GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.599.3GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
11.499.3E-MEXP-509-raw-cel-829148420
11.499.3GSM311294Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
10.799.2E-MEXP-509-raw-cel-829148525
10.199.2GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.199.2E-MEXP-509-raw-cel-829148276
9.799.1GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.799.1E-MEXP-509-raw-cel-829148240
9.099.1GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
8.799.0E-MEXP-509-raw-cel-829148348

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1032GO:0010020The division of a chloroplast within a cell to form two or more separate chloroplast compartments. This division occurs independently of mitosis.Link to AmiGO
0.0863GO:0006418The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.Link to AmiGO
0.0671GO:0009662A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an etioplast. An etioplast is a plastid arrested in the development of chloroplasts from proplastids due to absence of light or low light conditions.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.107400970Aminoacyl-tRNA biosynthesisLink to KEGG PATHWAY
0.040100906Carotenoid biosynthesisLink to KEGG PATHWAY
0.026100330Arginine and proline 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



Back to the CoP portal site

Back to the KAGIANA project homepage