CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Os04g0644600

Gene name
Homology with Arabidopsis Similar to At1g52510: hydrolase, alpha/beta fold family protein (HF=4e-21)

Module size 6 genes

NF 0.57

%ile 78.1

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. Ev AGI code Arabidopsis gene name O.I. H.G. S.X. Other DB
0.91 98.9 0.96 Os04g0644600 AK099966.1 - Epoxide hydrolase family protein 4e-21 At1g52510 hydrolase, alpha/beta fold family protein O.I. H.G. S.X.
0.71 89.6 0.96 Os08g0114100 AK099560.1 - Conserved hypothetical protein 4e-27 At1g64680 unknown protein O.I. H.G. S.X.
0.50 68.0 0.98 Os07g0171100 AK066475.1 - TPR-like domain containing protein 2e-16 At1g55480 binding / protein binding O.I. H.G. S.X.
0.47 62.3 0.96 Os04g0448600 AK068709.1 - ChaC-like protein family protein 2e-3 At1g44790 ChaC-like family protein O.I. H.G. S.X.
0.47 62.3 0.96 Os03g0704100 AK070474.1 - PAP fibrillin family protein 2e+0 At1g35410 - O.I. H.G. S.X.
0.39 48.3 0.96 Os01g0912700 AK068528.1 - Conserved hypothetical protein 1e-1 At2g01340 unknown protein O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	Ev	AGI code	Arabidopsis gene name	O.I.	H.G.	S.X.
0.91	98.9	0.96	Os04g0644600	AK099966.1	-	Epoxide hydrolase family protein	4e-21	At1g52510	hydrolase, alpha/beta fold family protein	O.I.	H.G.	S.X.
0.71	89.6	0.96	Os08g0114100	AK099560.1	-	Conserved hypothetical protein	4e-27	At1g64680	unknown protein	O.I.	H.G.	S.X.
0.50	68.0	0.98	Os07g0171100	AK066475.1	-	TPR-like domain containing protein	2e-16	At1g55480	binding / protein binding	O.I.	H.G.	S.X.
0.47	62.3	0.96	Os04g0448600	AK068709.1	-	ChaC-like protein family protein	2e-3	At1g44790	ChaC-like family protein	O.I.	H.G.	S.X.
0.47	62.3	0.96	Os03g0704100	AK070474.1	-	PAP fibrillin family protein	2e+0	At1g35410	-	O.I.	H.G.	S.X.
0.39	48.3	0.96	Os01g0912700	AK068528.1	-	Conserved hypothetical protein	1e-1	At2g01340	unknown protein	O.I.	H.G.	S.X.

Click More genes

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
76.8 99.9 GSM422676 Control GSE16865 Heterologous microarrays for the study of drought stress in Musa
33.9 99.8 GSM422672 Drought GSE16865 Heterologous microarrays for the study of drought stress in Musa
9.6 97.9 GSM377075 Genomic DNA - 45 day old leaf sample - mutant g650 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.8 97.8 GSM377084 Genomic DNA - 45 day old leaf sample - mutant f1856 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.1 97.7 GSM377071 Genomic DNA - 45 day old leaf sample - mutant d256 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.0 97.6 GSM377073 Genomic DNA - 45 day old leaf sample - mutant d2943 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.2 97.4 GSM377074 Genomic DNA - 45 day old leaf sample - mutant g282 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.1 97.4 GSM377080 Genomic DNA - 45 day old leaf sample - mutant g6728 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.1 97.4 GSM377086 Genomic DNA - 45 day old leaf sample - IR64 wtcheck GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.1 97.4 GSM377078 Genomic DNA - 45 day old leaf sample - mutant g6603 GSE15071 Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
76.8	99.9	GSM422676	Control	GSE16865	Heterologous microarrays for the study of drought stress in Musa
33.9	99.8	GSM422672	Drought	GSE16865	Heterologous microarrays for the study of drought stress in Musa
9.6	97.9	GSM377075	Genomic DNA - 45 day old leaf sample - mutant g650	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.8	97.8	GSM377084	Genomic DNA - 45 day old leaf sample - mutant f1856	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.1	97.7	GSM377071	Genomic DNA - 45 day old leaf sample - mutant d256	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
8.0	97.6	GSM377073	Genomic DNA - 45 day old leaf sample - mutant d2943	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.2	97.4	GSM377074	Genomic DNA - 45 day old leaf sample - mutant g282	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.1	97.4	GSM377080	Genomic DNA - 45 day old leaf sample - mutant g6728	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.1	97.4	GSM377086	Genomic DNA - 45 day old leaf sample - IR64 wtcheck	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
7.1	97.4	GSM377078	Genomic DNA - 45 day old leaf sample - mutant g6603	GSE15071	Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.063 1 GO:0006725 The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
0.063 1 GO:0007242 A series of reactions within the cell that occur as a result of a single trigger reaction or compound.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.063	1	GO:0006725	The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
0.063	1	GO:0007242	A series of reactions within the cell that occur as a result of a single trigger reaction or compound.

Inter-species module comparison

A co-expression module including the Arabidopsis gene, At1g52510, orthologous to the query gene, Os04g0644600

VF %ile Gene ID Repr. ID Gene Name Func. O.I. H.G. S.X. Other DB
1.00 100.0 At1g52510 841682 hydrolase, alpha/beta fold family protein F:hydrolase activity, catalytic activity;P:unknown;C:chloroplast, chloroplast envelope;BOPMFA O.I. H.G. S.X.
0.78 88.6 At3g54050 824572 fructose-1,6-bisphosphatase, putative / D-fructose-1,6-bisphosphate 1-phosphohydrolase, putative / FBPase, putative F:fructose 1,6-bisphosphate 1-phosphatase activity, phosphoric ester hydrolase activity;P:response to cold, fructose metabolic process;C:apoplast, stromule, chloroplast stroma, chloroplast;BOMPFA O.I. H.G. S.X.
0.75 86.9 At5g19220 832042 APL1 (ADP GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 1) Encodes the large subunit of ADP-glucose pyrophosphorylase which catalyzes the first, rate limiting step in starch biosynthesis. The large subunit plays a regulatory role whereas the small subunit (ApS) is the catalytic isoform. Four isoforms (ApL1-4) have been identified. ApL1 is the major large subunit isoform present in leaves. Mutational analysis of APS1 suggests that APL1 and APL2 can compensate for loss of APS1 catalytic activity,suggesting both have catalytic as well as regulatory functions. O.I. H.G. S.X.
0.73 85.5 At1g15980 838168 NDF1 (NDH-DEPENDENT CYCLIC ELECTRON FLOW 1) encodes a novel subunit of the chloroplast NAD(P)H dehydrogenase complex, involved in cyclic electron flow around photosystem I to produce ATP. O.I. H.G. S.X.
0.73 85.5 At1g51110 841534 plastid-lipid associated protein PAP / fibrillin family protein F:structural molecule activity;P:tryptophan biosynthetic process;C:chloroplast thylakoid membrane, chloroplast, membrane;PBO O.I. H.G. S.X.
0.71 84.2 At3g63140 825489 CSP41A (CHLOROPLAST STEM-LOOP BINDING PROTEIN OF 41 KDA) Encodes a protein with ribonuclease activity that is involved in plastid rRNA maturation. O.I. H.G. S.X.
0.71 84.2 At1g65230 842830 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PB O.I. H.G. S.X.
0.71 84.2 At5g43750 834396 unknown protein F:molecular_function unknown;P:response to oxidative stress;C:chloroplast thylakoid membrane, chloroplast;P O.I. H.G. S.X.
0.66 80.1 At1g18060 838386 unknown protein F:unknown;P:biological_process unknown;C:chloroplast;PBO O.I. H.G. S.X.
0.66 80.1 At3g48420 824000 haloacid dehalogenase-like hydrolase family protein F:hydrolase activity, catalytic activity;P:metabolic process;C:chloroplast, chloroplast stroma, chloroplast envelope;BOPMFAV O.I. H.G. S.X.
0.66 80.1 At3g10060 820167 immunophilin, putative / FKBP-type peptidyl-prolyl cis-trans isomerase, putative F:FK506 binding, peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:thylakoid, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;BMOPFA O.I. H.G. S.X.
0.66 80.1 At1g56500 842103 haloacid dehalogenase-like hydrolase family protein F:hydrolase activity, oxidoreductase activity, catalytic activity;P:metabolic process, cell redox homeostasis;C:chloroplast, chloroplast stroma;BOMPAFV O.I. H.G. S.X.
0.65 79.6 At1g19150 838498 LHCA6 PSI type II chlorophyll a/b-binding protein (Lhca21) mRNA, O.I. H.G. S.X.
0.65 79.6 At5g23120 832376 HCF136 encodes a stability and/or assembly factor of photosystem II O.I. H.G. S.X.
0.64 78.9 At1g09340 837455 CRB (CHLOROPLAST RNA BINDING) Encodes CHLOROPLAST RNA BINDING (CRB), a putative RNA-binding protein. CRB is important for the proper functioning of the chloroplast. Mutations in CRB also affects the circadian system, altering the expression of both oscillator and output genes. O.I. H.G. S.X.
0.62 77.3 At1g76450 843978 oxygen-evolving complex-related F:unknown;P:unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;PO O.I. H.G. S.X.
0.61 76.7 At1g45474 841099 LHCA5 Encodes a component of the light harvesting complex of photosystem I. O.I. H.G. S.X.
0.61 76.7 At5g27290 832787 unknown protein F:unknown;P:unknown;C:chloroplast;PBO O.I. H.G. S.X.
0.60 75.7 At5g36700 833635 PGLP1 (2-PHOSPHOGLYCOLATE PHOSPHATASE 1) F:phosphoglycolate phosphatase activity;P:metabolic process;C:chloroplast stroma, chloroplast;BOMFAP O.I. H.G. S.X.
0.60 75.7 At5g58260 835938 - Encodes subunit NDH-N of NAD(P)H:plastoquinone dehydrogenase complex (Ndh complex) present in the thylakoid membrane of chloroplasts. This subunit is thought to be required for Ndh complex assembly. O.I. H.G. S.X.
0.60 75.7 At5g09660 830825 PMDH2 (peroxisomal NAD-malate dehydrogenase 2) encodes a microbody NAD-dependent malate dehydrogenase encodes an peroxisomal NAD-malate dehydrogenase that is involved in fatty acid beta-oxidation through providing NAD to the process of converting fatty acyl CoA to acetyl CoA. O.I. H.G. S.X.
0.59 74.7 At1g32060 840098 PRK (PHOSPHORIBULOKINASE) F:protein binding, phosphoribulokinase activity, ATP binding;P:response to cold, defense response to bacterium, peptidyl-cysteine S-nitrosylation, biosynthetic process;C:in 8 components;BPOMFAV O.I. H.G. S.X.
0.59 74.7 At4g35250 829678 vestitone reductase-related F:transcription repressor activity, binding, catalytic activity;P:regulation of nitrogen utilization, metabolic process;C:chloroplast;BOPFMA O.I. H.G. S.X.
0.58 73.8 At4g22890 828388 PGR5-LIKE A Encodes PGRL1A, a transmembrane protein present in thylakoids. PGRL1A has a highly homologous isoform PGRL1B encoded by At4g11960. Plants lacking PGRL1 show perturbation of cyclic electron flow, similar to PGR5-deficient plants. PGRL1 and PGR5 interact physically and associate with PSI (photosystem I). O.I. H.G. S.X.
0.58 73.8 At3g61080 825280 fructosamine kinase family protein F:kinase activity;P:biological_process unknown;C:mitochondrion, chloroplast;BOMFPA O.I. H.G. S.X.
0.57 73.8 At1g42970 840895 GAPB (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE B SUBUNIT) Encodes chloroplast localized glyceraldehyde-3-phosphate dehydrogenase. O.I. H.G. S.X.
0.57 73.8 At3g55800 824746 SBPASE (sedoheptulose-bisphosphatase) Encodes the chloroplast enzyme sedoheptulose-1,7-bisphosphatase (SBPase), involved in the carbon reduction of the Calvin cycle. Increase in SBPase activity in transgenic lines accumulate up to 50% more sucrose and starch than wild-type. O.I. H.G. S.X.
0.57 73.8 At1g20020 838591 FNR2 (FERREDOXIN-NADP(+)-OXIDOREDUCTASE 2) Encodes a leaf-type ferredoxin:NADP(H) oxidoreductase. It is present in both chloroplast stroma and thylakoid membranes but is more abundant in the stroma O.I. H.G. S.X.
0.57 73.8 At1g32080 840100 membrane protein, putative F:unknown;P:unknown;C:chloroplast, chloroplast inner membrane, membrane, chloroplast envelope;BOFPA O.I. H.G. S.X.
0.57 73.8 At5g42270 834232 VAR1 (VARIEGATED 1) VAR1 contains a conserved motif for ATPase and a metalloprotease characteristic to FtsH proteins, and is targeted into chloroplasts. A VAR1-fusion protein synthesized in vitro exhibited ATPase activity and partial metalloprotease activity. This protein is located to the thylakoid membrane and forms a complex with VAR2. FtsH1 (VAR1) and FtsH5 are interchangeable in thylakoid membranes. O.I. H.G. S.X.
0.57 73.8 At5g66190 836751 FNR1 (FERREDOXIN-NADP(+)-OXIDOREDUCTASE 1) Encodes a leaf-type ferredoxin:NADP(H) oxidoreductase. It is present in both chloroplast stroma and thylakoid membranes but is more abundant in the thylakoid. The affinity of this enzyme for ferredoxin is slightly, but significantly, higher than AtLFNR2, an isoform of the same enzyme. AtLFNR1 forms a heterodimer with AtFNR2 and is also a prerequisite to attach AtFNR2 to the thylakoid membrane. O.I. H.G. S.X.
0.56 73.0 At4g27700 828884 rhodanese-like domain-containing protein F:molecular_function unknown;P:aging;C:chloroplast thylakoid membrane, chloroplast;BPOA O.I. H.G. S.X.
0.55 70.6 At1g50320 841454 ATHX encodes a prokaryotic thioredoxin O.I. H.G. S.X.
0.54 69.5 At1g67700 843095 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast, chloroplast envelope;PO O.I. H.G. S.X.
0.53 68.6 At3g61870 825360 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast, chloroplast inner membrane, chloroplast envelope;BOP O.I. H.G. S.X.
0.53 68.6 At5g38660 833856 APE1 (ACCLIMATION OF PHOTOSYNTHESIS TO ENVIRONMENT) mutant has Altered acclimation responses; O.I. H.G. S.X.
0.53 68.6 At1g77090 844043 thylakoid lumenal 29.8 kDa protein F:calcium ion binding;P:photosynthesis;C:thylakoid, thylakoid lumen, chloroplast thylakoid lumen, chloroplast stroma, chloroplast;POB O.I. H.G. S.X.
0.53 68.6 At3g50820 824246 PSBO2 (PHOTOSYSTEM II SUBUNIT O-2) Encodes a protein which is an extrinsic subunit of photosystem II and which has been proposed to play a central role in stabilization of the catalytic manganese cluster. In Arabidopsis thaliana* the PsbO proteins are encoded by two genes: psbO1 and psbO2. PsbO2 is the minor isoform in the wild-type. Mutants defective in this gene have been shown to be affected in the dephosphorylation of the D1 protein of PSII. O.I. H.G. S.X.
0.52 67.4 At3g14415 820664 (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative F:glycolate oxidase activity, electron carrier activity, oxidoreductase activity, FMN binding, catalytic activity;P:metabolic process;C:in 6 components;OBFMPA O.I. H.G. S.X.
0.51 66.3 At5g08650 830766 GTP-binding protein LepA, putative F:GTP binding, translation elongation factor activity, GTPase activity;P:unknown;C:chloroplast;BOMFPA O.I. H.G. S.X.
0.51 66.3 At3g23700 821951 S1 RNA-binding domain-containing protein F:RNA binding;P:response to cold;C:chloroplast stroma, nucleus, chloroplast;BOPMFA O.I. H.G. S.X.
0.50 65.3 At1g54780 841919 thylakoid lumen 18.3 kDa protein F:molecular_function unknown;P:biological_process unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;BPOM O.I. H.G. S.X.
0.50 65.3 At3g01500 821134 CA1 (CARBONIC ANHYDRASE 1) F:carbonate dehydratase activity, zinc ion binding;P:response to cold, defense response to bacterium, carbon utilization;C:in 8 components;BOPFMA O.I. H.G. S.X.
0.49 63.5 At5g35170 833471 adenylate kinase family protein F:nucleobase, nucleoside, nucleotide kinase activity, nucleotide kinase activity, phosphotransferase activity, phosphate group as acceptor, adenylate kinase activity, ATP binding;P:nucleobase, nucleoside, nucleotide and nucleic acid metabolic process, anaerobic respiration, nucleotide metabolic process;C:chloroplast thylakoid membrane, chloroplast, chloroplast envelope;BOMFPA O.I. H.G. S.X.
0.48 62.5 At2g01110 814640 APG2 (ALBINO AND PALE GREEN 2) mutant is Albino and pale green; Chloroplast Protein Translocation (tatC). Core subunit of the chloroplast Tat translocase. Integral chloroplast thylakoid membrane protein. O.I. H.G. S.X.
0.48 62.5 At5g07020 830593 proline-rich family protein F:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast;PMFVO O.I. H.G. S.X.
0.47 61.2 At3g12780 820461 PGK1 (PHOSPHOGLYCERATE KINASE 1) nuclear phosphoglycerate kinase (PGK1) O.I. H.G. S.X.
0.47 61.2 At2g43560 818958 immunophilin / FKBP-type peptidyl-prolyl cis-trans isomerase family protein F:FK506 binding, peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:thylakoid, thylakoid lumen, chloroplast thylakoid lumen, chloroplast;BMOPFA O.I. H.G. S.X.
0.46 59.8 At1g11860 837733 aminomethyltransferase, putative F:aminomethyltransferase activity;P:response to cadmium ion;C:in 6 components;OBMFAP O.I. H.G. S.X.
0.46 59.8 At2g27680 817314 aldo/keto reductase family protein F:oxidoreductase activity, aldo-keto reductase activity;P:oxidation reduction;C:chloroplast stroma, chloroplast, chloroplast envelope, plant-type cell wall;BOFPAM O.I. H.G. S.X.
0.45 58.3 At5g03880 831679 electron carrier F:electron carrier activity;P:cell redox homeostasis;C:chloroplast thylakoid membrane, chloroplast;BOPAFM O.I. H.G. S.X.
0.45 58.3 At1g44575 841033 NPQ4 (NONPHOTOCHEMICAL QUENCHING) Encoding PSII-S (CP22), a ubiquitous pigment-binding protein associated with photosystem II (PSII) of higher plants. Involved in nonphotochemical quenching rather than in photosynthesis. Mutant has a normal violaxanthin cycle but has a limited capacity of quenching singlet excited chlorophylls and is tolerant to lipid peroxidation. O.I. H.G. S.X.
0.45 58.3 At3g01480 821137 CYP38 (cyclophilin 38) Encodes a chloroplast cyclophilin functioning in the assembly and maintenance of photosystem II (PSII) supercomplexes. O.I. H.G. S.X.
0.44 57.2 At4g32590 829394 ferredoxin-related F:electron carrier activity, iron-sulfur cluster binding;P:unknown;C:chloroplast;OBPF O.I. H.G. S.X.
0.44 57.2 At3g02730 821260 TRXF1 (THIOREDOXIN F-TYPE 1) F:enzyme activator activity;P:positive regulation of catalytic activity;C:chloroplast, chloroplast stroma;BOMPFAV O.I. H.G. S.X.
0.43 55.3 At2g21960 816732 unknown protein F:unknown;P:unknown;C:chloroplast;PBO O.I. H.G. S.X.
0.43 55.3 At1g20810 838672 immunophilin / FKBP-type peptidyl-prolyl cis-trans isomerase family protein F:FK506 binding, peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:thylakoid lumen, chloroplast thylakoid lumen, chloroplast;BOPMF O.I. H.G. S.X.
0.42 53.9 At2g30950 817646 VAR2 (VARIEGATED 2) Metalloprotease that functions in thylakoid membrane biogenesis. Involved in the repair of PSII following damaged incurred during photoinhibition. Forms a complex with VAR1. Mutants show a variegated phenotype, which decreases during development. Transcript and protein levels increase with light intensity. O.I. H.G. S.X.
0.42 53.9 At4g04640 825797 ATPC1 One of two genes (with ATPC2) encoding the gamma subunit of Arabidopsis chloroplast ATP synthase. O.I. H.G. S.X.
0.41 52.4 At1g65260 842833 PTAC4 (PLASTID TRANSCRIPTIONALLY ACTIVE4) F:unknown;P:biological_process unknown;C:in 8 components;BOMVFPA O.I. H.G. S.X.
0.39 48.4 At1g67740 843099 PSBY PsbY precursor (psbY) mRNA. This single nuclear gene is imported into the chloroplasts where it is processed into two integral membrane proteins with identical topology (PsbY-1 and PsbY-2). The protein appears to bind manganese but its role is not well understood. O.I. H.G. S.X.
0.39 48.4 At4g03280 827996 PETC (PHOTOSYNTHETIC ELECTRON TRANSFER C) Encodes the Rieske FeS center of cytochrome b6f complex. Gene is expressed in shoot but not in root. Mutant has reduced electron transport at saturating light intensities and Q-cycle activity is hypersensitive to acidification of the thylakoid lumen. O.I. H.G. S.X.
0.39 48.4 At4g09650 826551 ATPD (ATP SYNTHASE DELTA-SUBUNIT GENE) Encodes the chloroplast ATPase delta-subunit. O.I. H.G. S.X.
0.37 45.0 At5g51110 835185 4-alpha-hydroxytetrahydrobiopterin dehydratase F:4-alpha-hydroxytetrahydrobiopterin dehydratase activity;P:tetrahydrobiopterin biosynthetic process;C:chloroplast;OBPAF O.I. H.G. S.X.
0.37 45.0 At2g34860 818051 EDA3 (embryo sac development arrest 3) F:unfolded protein binding, heat shock protein binding;P:megagametogenesis;C:chloroplast thylakoid membrane, chloroplast;BOPAMF O.I. H.G. S.X.
0.37 45.0 At3g56650 824832 thylakoid lumenal 20 kDa protein F:unknown;P:unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid lumen, chloroplast stroma, chloroplast;PBO O.I. H.G. S.X.

VF	%ile	Gene ID	Repr. ID	Gene Name	Func.	O.I.	H.G.	S.X.
1.00	100.0	At1g52510	841682	hydrolase, alpha/beta fold family protein	F:hydrolase activity, catalytic activity;P:unknown;C:chloroplast, chloroplast envelope;BOPMFA	O.I.	H.G.	S.X.
0.78	88.6	At3g54050	824572	fructose-1,6-bisphosphatase, putative / D-fructose-1,6-bisphosphate 1-phosphohydrolase, putative / FBPase, putative	F:fructose 1,6-bisphosphate 1-phosphatase activity, phosphoric ester hydrolase activity;P:response to cold, fructose metabolic process;C:apoplast, stromule, chloroplast stroma, chloroplast;BOMPFA	O.I.	H.G.	S.X.
0.75	86.9	At5g19220	832042	APL1 (ADP GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 1)	Encodes the large subunit of ADP-glucose pyrophosphorylase which catalyzes the first, rate limiting step in starch biosynthesis. The large subunit plays a regulatory role whereas the small subunit (ApS) is the catalytic isoform. Four isoforms (ApL1-4) have been identified. ApL1 is the major large subunit isoform present in leaves. Mutational analysis of APS1 suggests that APL1 and APL2 can compensate for loss of APS1 catalytic activity,suggesting both have catalytic as well as regulatory functions.	O.I.	H.G.	S.X.
0.73	85.5	At1g15980	838168	NDF1 (NDH-DEPENDENT CYCLIC ELECTRON FLOW 1)	encodes a novel subunit of the chloroplast NAD(P)H dehydrogenase complex, involved in cyclic electron flow around photosystem I to produce ATP.	O.I.	H.G.	S.X.
0.73	85.5	At1g51110	841534	plastid-lipid associated protein PAP / fibrillin family protein	F:structural molecule activity;P:tryptophan biosynthetic process;C:chloroplast thylakoid membrane, chloroplast, membrane;PBO	O.I.	H.G.	S.X.
0.71	84.2	At3g63140	825489	CSP41A (CHLOROPLAST STEM-LOOP BINDING PROTEIN OF 41 KDA)	Encodes a protein with ribonuclease activity that is involved in plastid rRNA maturation.	O.I.	H.G.	S.X.
0.71	84.2	At1g65230	842830	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PB	O.I.	H.G.	S.X.
0.71	84.2	At5g43750	834396	unknown protein	F:molecular_function unknown;P:response to oxidative stress;C:chloroplast thylakoid membrane, chloroplast;P	O.I.	H.G.	S.X.
0.66	80.1	At1g18060	838386	unknown protein	F:unknown;P:biological_process unknown;C:chloroplast;PBO	O.I.	H.G.	S.X.
0.66	80.1	At3g48420	824000	haloacid dehalogenase-like hydrolase family protein	F:hydrolase activity, catalytic activity;P:metabolic process;C:chloroplast, chloroplast stroma, chloroplast envelope;BOPMFAV	O.I.	H.G.	S.X.
0.66	80.1	At3g10060	820167	immunophilin, putative / FKBP-type peptidyl-prolyl cis-trans isomerase, putative	F:FK506 binding, peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:thylakoid, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;BMOPFA	O.I.	H.G.	S.X.
0.66	80.1	At1g56500	842103	haloacid dehalogenase-like hydrolase family protein	F:hydrolase activity, oxidoreductase activity, catalytic activity;P:metabolic process, cell redox homeostasis;C:chloroplast, chloroplast stroma;BOMPAFV	O.I.	H.G.	S.X.
0.65	79.6	At1g19150	838498	LHCA6	PSI type II chlorophyll a/b-binding protein (Lhca2*1) mRNA,	O.I.	H.G.	S.X.
0.65	79.6	At5g23120	832376	HCF136	encodes a stability and/or assembly factor of photosystem II	O.I.	H.G.	S.X.
0.64	78.9	At1g09340	837455	CRB (CHLOROPLAST RNA BINDING)	Encodes CHLOROPLAST RNA BINDING (CRB), a putative RNA-binding protein. CRB is important for the proper functioning of the chloroplast. Mutations in CRB also affects the circadian system, altering the expression of both oscillator and output genes.	O.I.	H.G.	S.X.
0.62	77.3	At1g76450	843978	oxygen-evolving complex-related	F:unknown;P:unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;PO	O.I.	H.G.	S.X.
0.61	76.7	At1g45474	841099	LHCA5	Encodes a component of the light harvesting complex of photosystem I.	O.I.	H.G.	S.X.
0.61	76.7	At5g27290	832787	unknown protein	F:unknown;P:unknown;C:chloroplast;PBO	O.I.	H.G.	S.X.
0.60	75.7	At5g36700	833635	PGLP1 (2-PHOSPHOGLYCOLATE PHOSPHATASE 1)	F:phosphoglycolate phosphatase activity;P:metabolic process;C:chloroplast stroma, chloroplast;BOMFAP	O.I.	H.G.	S.X.
0.60	75.7	At5g58260	835938	-	Encodes subunit NDH-N of NAD(P)H:plastoquinone dehydrogenase complex (Ndh complex) present in the thylakoid membrane of chloroplasts. This subunit is thought to be required for Ndh complex assembly.	O.I.	H.G.	S.X.
0.60	75.7	At5g09660	830825	PMDH2 (peroxisomal NAD-malate dehydrogenase 2)	encodes a microbody NAD-dependent malate dehydrogenase encodes an peroxisomal NAD-malate dehydrogenase that is involved in fatty acid beta-oxidation through providing NAD to the process of converting fatty acyl CoA to acetyl CoA.	O.I.	H.G.	S.X.
0.59	74.7	At1g32060	840098	PRK (PHOSPHORIBULOKINASE)	F:protein binding, phosphoribulokinase activity, ATP binding;P:response to cold, defense response to bacterium, peptidyl-cysteine S-nitrosylation, biosynthetic process;C:in 8 components;BPOMFAV	O.I.	H.G.	S.X.
0.59	74.7	At4g35250	829678	vestitone reductase-related	F:transcription repressor activity, binding, catalytic activity;P:regulation of nitrogen utilization, metabolic process;C:chloroplast;BOPFMA	O.I.	H.G.	S.X.
0.58	73.8	At4g22890	828388	PGR5-LIKE A	Encodes PGRL1A, a transmembrane protein present in thylakoids. PGRL1A has a highly homologous isoform PGRL1B encoded by At4g11960. Plants lacking PGRL1 show perturbation of cyclic electron flow, similar to PGR5-deficient plants. PGRL1 and PGR5 interact physically and associate with PSI (photosystem I).	O.I.	H.G.	S.X.
0.58	73.8	At3g61080	825280	fructosamine kinase family protein	F:kinase activity;P:biological_process unknown;C:mitochondrion, chloroplast;BOMFPA	O.I.	H.G.	S.X.
0.57	73.8	At1g42970	840895	GAPB (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE B SUBUNIT)	Encodes chloroplast localized glyceraldehyde-3-phosphate dehydrogenase.	O.I.	H.G.	S.X.
0.57	73.8	At3g55800	824746	SBPASE (sedoheptulose-bisphosphatase)	Encodes the chloroplast enzyme sedoheptulose-1,7-bisphosphatase (SBPase), involved in the carbon reduction of the Calvin cycle. Increase in SBPase activity in transgenic lines accumulate up to 50% more sucrose and starch than wild-type.	O.I.	H.G.	S.X.
0.57	73.8	At1g20020	838591	FNR2 (FERREDOXIN-NADP(+)-OXIDOREDUCTASE 2)	Encodes a leaf-type ferredoxin:NADP(H) oxidoreductase. It is present in both chloroplast stroma and thylakoid membranes but is more abundant in the stroma	O.I.	H.G.	S.X.
0.57	73.8	At1g32080	840100	membrane protein, putative	F:unknown;P:unknown;C:chloroplast, chloroplast inner membrane, membrane, chloroplast envelope;BOFPA	O.I.	H.G.	S.X.
0.57	73.8	At5g42270	834232	VAR1 (VARIEGATED 1)	VAR1 contains a conserved motif for ATPase and a metalloprotease characteristic to FtsH proteins, and is targeted into chloroplasts. A VAR1-fusion protein synthesized in vitro exhibited ATPase activity and partial metalloprotease activity. This protein is located to the thylakoid membrane and forms a complex with VAR2. FtsH1 (VAR1) and FtsH5 are interchangeable in thylakoid membranes.	O.I.	H.G.	S.X.
0.57	73.8	At5g66190	836751	FNR1 (FERREDOXIN-NADP(+)-OXIDOREDUCTASE 1)	Encodes a leaf-type ferredoxin:NADP(H) oxidoreductase. It is present in both chloroplast stroma and thylakoid membranes but is more abundant in the thylakoid. The affinity of this enzyme for ferredoxin is slightly, but significantly, higher than AtLFNR2, an isoform of the same enzyme. AtLFNR1 forms a heterodimer with AtFNR2 and is also a prerequisite to attach AtFNR2 to the thylakoid membrane.	O.I.	H.G.	S.X.
0.56	73.0	At4g27700	828884	rhodanese-like domain-containing protein	F:molecular_function unknown;P:aging;C:chloroplast thylakoid membrane, chloroplast;BPOA	O.I.	H.G.	S.X.
0.55	70.6	At1g50320	841454	ATHX	encodes a prokaryotic thioredoxin	O.I.	H.G.	S.X.
0.54	69.5	At1g67700	843095	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast, chloroplast envelope;PO	O.I.	H.G.	S.X.
0.53	68.6	At3g61870	825360	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast, chloroplast inner membrane, chloroplast envelope;BOP	O.I.	H.G.	S.X.
0.53	68.6	At5g38660	833856	APE1 (ACCLIMATION OF PHOTOSYNTHESIS TO ENVIRONMENT)	mutant has Altered acclimation responses;	O.I.	H.G.	S.X.
0.53	68.6	At1g77090	844043	thylakoid lumenal 29.8 kDa protein	F:calcium ion binding;P:photosynthesis;C:thylakoid, thylakoid lumen, chloroplast thylakoid lumen, chloroplast stroma, chloroplast;POB	O.I.	H.G.	S.X.
0.53	68.6	At3g50820	824246	PSBO2 (PHOTOSYSTEM II SUBUNIT O-2)	Encodes a protein which is an extrinsic subunit of photosystem II and which has been proposed to play a central role in stabilization of the catalytic manganese cluster. In Arabidopsis thaliana the PsbO proteins are encoded by two genes: psbO1 and psbO2. PsbO2 is the minor isoform in the wild-type. Mutants defective in this gene have been shown to be affected in the dephosphorylation of the D1 protein of PSII.	O.I.	H.G.	S.X.
0.52	67.4	At3g14415	820664	(S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative	F:glycolate oxidase activity, electron carrier activity, oxidoreductase activity, FMN binding, catalytic activity;P:metabolic process;C:in 6 components;OBFMPA	O.I.	H.G.	S.X.
0.51	66.3	At5g08650	830766	GTP-binding protein LepA, putative	F:GTP binding, translation elongation factor activity, GTPase activity;P:unknown;C:chloroplast;BOMFPA	O.I.	H.G.	S.X.
0.51	66.3	At3g23700	821951	S1 RNA-binding domain-containing protein	F:RNA binding;P:response to cold;C:chloroplast stroma, nucleus, chloroplast;BOPMFA	O.I.	H.G.	S.X.
0.50	65.3	At1g54780	841919	thylakoid lumen 18.3 kDa protein	F:molecular_function unknown;P:biological_process unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;BPOM	O.I.	H.G.	S.X.
0.50	65.3	At3g01500	821134	CA1 (CARBONIC ANHYDRASE 1)	F:carbonate dehydratase activity, zinc ion binding;P:response to cold, defense response to bacterium, carbon utilization;C:in 8 components;BOPFMA	O.I.	H.G.	S.X.
0.49	63.5	At5g35170	833471	adenylate kinase family protein	F:nucleobase, nucleoside, nucleotide kinase activity, nucleotide kinase activity, phosphotransferase activity, phosphate group as acceptor, adenylate kinase activity, ATP binding;P:nucleobase, nucleoside, nucleotide and nucleic acid metabolic process, anaerobic respiration, nucleotide metabolic process;C:chloroplast thylakoid membrane, chloroplast, chloroplast envelope;BOMFPA	O.I.	H.G.	S.X.
0.48	62.5	At2g01110	814640	APG2 (ALBINO AND PALE GREEN 2)	mutant is Albino and pale green; Chloroplast Protein Translocation (tatC). Core subunit of the chloroplast Tat translocase. Integral chloroplast thylakoid membrane protein.	O.I.	H.G.	S.X.
0.48	62.5	At5g07020	830593	proline-rich family protein	F:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast;PMFVO	O.I.	H.G.	S.X.
0.47	61.2	At3g12780	820461	PGK1 (PHOSPHOGLYCERATE KINASE 1)	nuclear phosphoglycerate kinase (PGK1)	O.I.	H.G.	S.X.
0.47	61.2	At2g43560	818958	immunophilin / FKBP-type peptidyl-prolyl cis-trans isomerase family protein	F:FK506 binding, peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:thylakoid, thylakoid lumen, chloroplast thylakoid lumen, chloroplast;BMOPFA	O.I.	H.G.	S.X.
0.46	59.8	At1g11860	837733	aminomethyltransferase, putative	F:aminomethyltransferase activity;P:response to cadmium ion;C:in 6 components;OBMFAP	O.I.	H.G.	S.X.
0.46	59.8	At2g27680	817314	aldo/keto reductase family protein	F:oxidoreductase activity, aldo-keto reductase activity;P:oxidation reduction;C:chloroplast stroma, chloroplast, chloroplast envelope, plant-type cell wall;BOFPAM	O.I.	H.G.	S.X.
0.45	58.3	At5g03880	831679	electron carrier	F:electron carrier activity;P:cell redox homeostasis;C:chloroplast thylakoid membrane, chloroplast;BOPAFM	O.I.	H.G.	S.X.
0.45	58.3	At1g44575	841033	NPQ4 (NONPHOTOCHEMICAL QUENCHING)	Encoding PSII-S (CP22), a ubiquitous pigment-binding protein associated with photosystem II (PSII) of higher plants. Involved in nonphotochemical quenching rather than in photosynthesis. Mutant has a normal violaxanthin cycle but has a limited capacity of quenching singlet excited chlorophylls and is tolerant to lipid peroxidation.	O.I.	H.G.	S.X.
0.45	58.3	At3g01480	821137	CYP38 (cyclophilin 38)	Encodes a chloroplast cyclophilin functioning in the assembly and maintenance of photosystem II (PSII) supercomplexes.	O.I.	H.G.	S.X.
0.44	57.2	At4g32590	829394	ferredoxin-related	F:electron carrier activity, iron-sulfur cluster binding;P:unknown;C:chloroplast;OBPF	O.I.	H.G.	S.X.
0.44	57.2	At3g02730	821260	TRXF1 (THIOREDOXIN F-TYPE 1)	F:enzyme activator activity;P:positive regulation of catalytic activity;C:chloroplast, chloroplast stroma;BOMPFAV	O.I.	H.G.	S.X.
0.43	55.3	At2g21960	816732	unknown protein	F:unknown;P:unknown;C:chloroplast;PBO	O.I.	H.G.	S.X.
0.43	55.3	At1g20810	838672	immunophilin / FKBP-type peptidyl-prolyl cis-trans isomerase family protein	F:FK506 binding, peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:thylakoid lumen, chloroplast thylakoid lumen, chloroplast;BOPMF	O.I.	H.G.	S.X.
0.42	53.9	At2g30950	817646	VAR2 (VARIEGATED 2)	Metalloprotease that functions in thylakoid membrane biogenesis. Involved in the repair of PSII following damaged incurred during photoinhibition. Forms a complex with VAR1. Mutants show a variegated phenotype, which decreases during development. Transcript and protein levels increase with light intensity.	O.I.	H.G.	S.X.
0.42	53.9	At4g04640	825797	ATPC1	One of two genes (with ATPC2) encoding the gamma subunit of Arabidopsis chloroplast ATP synthase.	O.I.	H.G.	S.X.
0.41	52.4	At1g65260	842833	PTAC4 (PLASTID TRANSCRIPTIONALLY ACTIVE4)	F:unknown;P:biological_process unknown;C:in 8 components;BOMVFPA	O.I.	H.G.	S.X.
0.39	48.4	At1g67740	843099	PSBY	PsbY precursor (psbY) mRNA. This single nuclear gene is imported into the chloroplasts where it is processed into two integral membrane proteins with identical topology (PsbY-1 and PsbY-2). The protein appears to bind manganese but its role is not well understood.	O.I.	H.G.	S.X.
0.39	48.4	At4g03280	827996	PETC (PHOTOSYNTHETIC ELECTRON TRANSFER C)	Encodes the Rieske FeS center of cytochrome b6f complex. Gene is expressed in shoot but not in root. Mutant has reduced electron transport at saturating light intensities and Q-cycle activity is hypersensitive to acidification of the thylakoid lumen.	O.I.	H.G.	S.X.
0.39	48.4	At4g09650	826551	ATPD (ATP SYNTHASE DELTA-SUBUNIT GENE)	Encodes the chloroplast ATPase delta-subunit.	O.I.	H.G.	S.X.
0.37	45.0	At5g51110	835185	4-alpha-hydroxytetrahydrobiopterin dehydratase	F:4-alpha-hydroxytetrahydrobiopterin dehydratase activity;P:tetrahydrobiopterin biosynthetic process;C:chloroplast;OBPAF	O.I.	H.G.	S.X.
0.37	45.0	At2g34860	818051	EDA3 (embryo sac development arrest 3)	F:unfolded protein binding, heat shock protein binding;P:megagametogenesis;C:chloroplast thylakoid membrane, chloroplast;BOPAMF	O.I.	H.G.	S.X.
0.37	45.0	At3g56650	824832	thylakoid lumenal 20 kDa protein	F:unknown;P:unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid lumen, chloroplast stroma, chloroplast;PBO	O.I.	H.G.	S.X.

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Gene ID	Os04g0644600
Gene name
Homology with Arabidopsis	Similar to At1g52510: hydrolase, alpha/beta fold family protein (HF=4e-21)
Module size	6 genes
NF	0.57
%ile	78.1

Co-expression analysis

Gene ID Os04g0644600 Gene name Homology with ArabidopsisSimilar to At1g52510: hydrolase, alpha/beta fold family protein (HF=4e-21) Module size 6 genes NF 0.57 %ile 78.1

Co-expressed genes

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Specific experiments for the module

Biological processes inferred to relate to the module

Inter-species module comparison

Select a plant to compare co-expressed genes between species.Glycine_maxHordeum_vulgarePopulus_trichocarpaTriticum_aestivumVitis_viniferaZea_mays

Gene ID Os04g0644600

Gene name
Homology with Arabidopsis Similar to At1g52510: hydrolase, alpha/beta fold family protein (HF=4e-21)

Module size 6 genes

NF 0.57

%ile 78.1

Select a plant to compare co-expressed genes between species.
Glycine_max
Hordeum_vulgare
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays