Co-expression analysis

Gene ID At4g27440
Gene name PORB (PROTOCHLOROPHYLLIDE OXIDOREDUCTASE B)
Module size 52 genes
NF 0.33
%ile 44.1



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
1.00100.01.00At4g27440828853PORB (PROTOCHLOROPHYLLIDE OXIDOREDUCTASE B)light-dependent NADPH:protochlorophyllide oxidoreductase BO.I.H.G.S.X.
0.5469.50.88At3g18050821330unknown proteinF:molecular_function unknown;P:biological_process unknown;C:anchored to membrane;PO.I.H.G.S.X.
0.4862.50.88At2g40490818644HEME2F:uroporphyrinogen decarboxylase activity;P:porphyrin biosynthetic process;C:chloroplast, chloroplast stroma, chloroplast envelope;OBMAFPO.I.H.G.S.X.
0.4457.20.88At2g3722081829929 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein cp29, putativeEncodes a chloroplast RNA binding protein. A substrate of the type III effector HopU1 (mono-ADP-ribosyltransferase). Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds.O.I.H.G.S.X.
0.4457.20.89At5g08280830724HEMC (HYDROXYMETHYLBILANE SYNTHASE)Encodes a protein with porphobilinogen deaminase activity. This protein is targeted to the chloroplast.O.I.H.G.S.X.
0.4355.30.89At3g14930820722HEME1F:uroporphyrinogen decarboxylase activity;P:porphyrin biosynthetic process;C:chloroplast stroma, chloroplast;OBMFAPO.I.H.G.S.X.
0.4355.30.87At5g45930834633CHLI2 (MAGNESIUM CHELATASE I2)encodes a second Chl I gene (CHLI2), a subunit of magnesium chelatase which is required for chlorophyll biosynthesis. Has ATPase activity, regulated by TRX-f. Involved in the assembly of the Mg chelatase complex.O.I.H.G.S.X.
0.4355.30.88At3g08920820041rhodanese-like domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PBOMO.I.H.G.S.X.
0.4253.90.87At1g03475839489LIN2 (LESION INITIATION 2)Encodes coproporphyrinogen III oxidase, a key enzyme in the biosynthetic pathway of chlorophyll and heme, a tetrapyrrole pathway. Mutants express cytological and molecular markers associated with the defense responses, usually activated by pathogen infection.O.I.H.G.S.X.
0.4050.80.89At2g43030818905ribosomal protein L3 family proteinF:structural constituent of ribosome;P:translation;C:ribosome, chloroplast stroma, chloroplast, membrane;BOAMFPO.I.H.G.S.X.
0.3948.40.88At1g50900841512-F:molecular_function unknown;P:biological_process unknown;C:chloroplast, chloroplast stroma;POO.I.H.G.S.X.
0.3948.40.87At1g22700838876tetratricopeptide repeat (TPR)-containing proteinEncodes a TPR protein with homology to Ycf37 from Synechocystis that is localized to the thylakoid membrane and is involved in photosystem I biogenesis.O.I.H.G.S.X.
0.3948.40.87At3g52150824379RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast stroma, chloroplast, chloroplast envelope;MPOFBAO.I.H.G.S.X.
0.3948.40.86At1g07320837243RPL4encodes a plastid ribosomal protein L4O.I.H.G.S.X.
0.3846.70.88At3g1312082050030S ribosomal protein S10, chloroplast, putativeF:structural constituent of ribosome, RNA binding;P:translation;C:small ribosomal subunit, chloroplast;BOMAPFO.I.H.G.S.X.
0.3846.70.87At3g15190820750chloroplast 30S ribosomal protein S20, putativeF:structural constituent of ribosome, RNA binding;P:translation, ribosome biogenesis;C:ribosome, chloroplast stroma, chloroplast, membrane;BOPMO.I.H.G.S.X.
0.3745.00.87At1g12090837761ELP (EXTENSIN-LIKE PROTEIN)extensin-like protein (ELP)O.I.H.G.S.X.
0.3745.00.87At3g116308203352-cys peroxiredoxin, chloroplast (BAS1)Encodes a 2-Cys peroxiredoxin (2-Cys PrxA) that contains two catalytic Cys residues.O.I.H.G.S.X.
0.3745.00.86At1g05190839273emb2394 (embryo defective 2394)F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation;C:chloroplast stroma, chloroplast, large ribosomal subunit, membrane, chloroplast envelope;BOAFPMO.I.H.G.S.X.
0.3643.60.87At1g78630844199emb1473 (embryo defective 1473)F:structural constituent of ribosome;P:embryonic development ending in seed dormancy, translation;C:thylakoid, ribosome, chloroplast, chloroplast stroma;BOMFAPO.I.H.G.S.X.
0.3541.60.86At5g13510831195ribosomal protein L10 family proteinF:structural constituent of ribosome;P:translation, ribosome biogenesis;C:cytosolic ribosome, ribosome, chloroplast, chloroplast stroma;BOAPMFO.I.H.G.S.X.
0.3541.60.87At5g14910831343heavy-metal-associated domain-containing proteinF:metal ion binding;P:metal ion transport;C:thylakoid, chloroplast thylakoid membrane, chloroplast stroma, chloroplast;PO.I.H.G.S.X.
0.3541.60.86At2g3345081791050S ribosomal protein L28, chloroplast (CL28)F:structural constituent of ribosome;P:translation;C:ribosome, chloroplast, membrane;BOPFO.I.H.G.S.X.
0.3439.80.88At4g26370828743antitermination NusB domain-containing proteinF:RNA binding;P:regulation of transcription, DNA-dependent;C:chloroplast;BOPO.I.H.G.S.X.
0.3439.80.87At5g53490835431thylakoid lumenal 17.4 kDa protein, chloroplastthylakoid lumenal 17.4 kDa protein, chloroplast, identical to SP:P81760 Thylakoid lumenal 17.4 kDa protein, chloroplast precursor (P17.4) {Arabidopsis thaliana}. Putative pentapeptide protein.O.I.H.G.S.X.
0.3439.80.87At2g37660818343binding / catalytic/ coenzyme bindingF:coenzyme binding, binding, catalytic activity;P:defense response to bacterium;C:thylakoid, apoplast, chloroplast stroma, chloroplast;BOPFAMO.I.H.G.S.X.
0.3439.80.87At4g01690827991PPOXEncodes protoporphyrinogen oxidase (PPOX).O.I.H.G.S.X.
0.3439.80.86At1g3568084047250S ribosomal protein L21, chloroplast / CL21 (RPL21)F:structural constituent of ribosome, RNA binding;P:response to cold, translation;C:ribosome, chloroplast stroma, nucleus, chloroplast, chloroplast envelope;BOPMFO.I.H.G.S.X.
0.3338.10.87At3g54210824588ribosomal protein L17 family proteinF:structural constituent of ribosome;P:translation;C:ribosome, chloroplast;BOMFPO.I.H.G.S.X.
0.3235.70.87At2g26900817231bile acid:sodium symporter family proteinF:transporter activity, bile acid:sodium symporter activity;P:sodium ion transport, organic anion transport;C:membrane, chloroplast envelope;OBMPAFO.I.H.G.S.X.
0.3133.80.87At1g74470843788geranylgeranyl reductaseEncodes for a multifunctional protein with geranylgeranyl reductase activity shown to catalyze the reduction of prenylated geranylgeranyl-chlorophyll a to phytyl-chlorophyll a (chlorophyll a) and free geranylgeranyl pyrophosphate to phytyl pyrophosphate.O.I.H.G.S.X.
0.3032.10.87At2g48070819419RPH1 (RESISTANCE TO PHYTOPHTHORA 1)Encodes a chloroplast protein RPH1 (resistance to Phytophthora 1). Involved in immune response to Phytophthora brassicae. rph1 mutant plants (in Ws background) are susceptible to P. brassicae.O.I.H.G.S.X.
0.3032.10.87At3g16140820859PSAH-1 (photosystem I subunit H-1)Encodes subunit H of photosystem I reaction center subunit VI.O.I.H.G.S.X.
0.2930.30.87At1g31330840021PSAF (photosystem I subunit F)Encodes subunit F of photosystem I.O.I.H.G.S.X.
0.2930.30.86At2g20260816545PSAE-2 (photosystem I subunit E-2)Encodes subunit E of photosystem I.O.I.H.G.S.X.
0.2930.30.87At1g15820838151LHCB6 (LIGHT HARVESTING COMPLEX PSII SUBUNIT 6)Lhcb6 protein (Lhcb6), light harvesting complex of photosystem II.O.I.H.G.S.X.
0.2930.30.86At1g55670842016PSAG (PHOTOSYSTEM I SUBUNIT G)Encodes subunit G of photosystem I, an 11-kDa membrane protein that plays an important role in electron transport between plastocyanin and PSI and is involved in the stability of the PSI complex. PSI-G subunit is bound to PSI-B and is in contact with Lhca1. The protein inserts into thylakoids by a direct or "spontaneous" pathway that does not involve the activities of any known chloroplast protein-targeting machinery. PSI-G appears to be directly or indirectly involved in the interaction between Photosystem I and plastocyanin.O.I.H.G.S.X.
0.2930.30.87At4g05180825866PSBQ-2Encodes the PsbQ subunit of the oxygen evolving complex of photosystem II.O.I.H.G.S.X.
0.2830.30.86At5g66570836789PSBO1 (PS II OXYGEN-EVOLVING COMPLEX 1)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. PsbO1 is the major isoform in the wild-type.O.I.H.G.S.X.
0.2726.20.87At5g46110834652APE2 (ACCLIMATION OF PHOTOSYNTHESIS TO ENVIRONMENT 2)mutant has Altered acclimation responses; Chloroplast Triose Phosphate TranslocatorO.I.H.G.S.X.
0.2726.20.86At1g54780841919thylakoid lumen 18.3 kDa proteinF:molecular_function unknown;P:biological_process unknown;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;BPOMO.I.H.G.S.X.
0.2624.40.86At1g06680837178PSBP-1 (PHOTOSYSTEM II SUBUNIT P-1)Encodes a 23 kD extrinsic protein that is part of photosystem II and participates in the regulation of oxygen evolution.O.I.H.G.S.X.
0.2624.40.87At5g01530830325chlorophyll A-B binding protein CP29 (LHCB4)F:chlorophyll binding;P:response to blue light, response to red light, response to far red light, photosynthesis;C:in 6 components;POMO.I.H.G.S.X.
0.2522.60.87At1g03680839436ATHM1encodes a chloroplast thioredoxin similar to prokaryotic thioredoxins.O.I.H.G.S.X.
0.2522.60.86At5g14260831276SET domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMFOO.I.H.G.S.X.
0.2522.60.88At1g20020838591FNR2 (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 stromaO.I.H.G.S.X.
0.2522.60.86At3g15360820775TRX-M4 (ARABIDOPSIS THIOREDOXIN M-TYPE 4)encodes a prokaryotic thioredoxinO.I.H.G.S.X.
0.2522.60.86At4g04640825797ATPC1One of two genes (with ATPC2) encoding the gamma subunit of Arabidopsis chloroplast ATP synthase.O.I.H.G.S.X.
0.2420.70.86At5g55710835665-F:molecular_function unknown;P:biological_process unknown;C:chloroplast thylakoid membrane, chloroplast;OBPO.I.H.G.S.X.
0.2420.70.86At3g32930823057unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast envelope;PO.I.H.G.S.X.
0.2217.50.86At1g21600838761PTAC6 (PLASTID TRANSCRIPTIONALLY ACTIVE6)Present in transcriptionally active plastid chromosomes. Involved in plastid gene expression.O.I.H.G.S.X.
0.1710.20.88At4g04340825754early-responsive to dehydration protein-related / ERD protein-relatedF:unknown;P:unknown;C:plasma membrane;FPMOBO.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
68.199.9GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
62.999.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
58.599.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
56.799.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
56.699.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
55.999.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
52.799.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
52.399.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
51.799.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.799.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.499.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.099.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.799.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.099.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.599.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
40.199.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.099.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.899.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.699.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.599.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
28.299.7GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.899.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.299.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
25.499.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.299.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.399.5GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
16.099.5GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.999.5GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
15.699.5GSM311291Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
14.799.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.999.4GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
12.499.3GSM311292Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
11.899.3GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
11.099.2GSM284390Arabidopsis GPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
10.199.2GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.199.2GSM284391Arabidopsis GPE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.499.1GSM284387Arabidopsis GSUS4bGSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1184GO:0006779The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.Link to AmiGO
0.1034GO:0015995The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, from less complex precursors.Link to AmiGO
0.0986GO:0015979The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.144900195PhotosynthesisLink to KEGG PATHWAY
0.077300860Porphyrin and chlorophyll metabolismLink to KEGG PATHWAY
0.056200196Photosynthesis - antenna proteinsLink 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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