CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g09650

Gene name HCF152 (HIGH CHLOROPHYLL FLUORESCENCE 152)

Module size 81 genes

NF 0.25

%ile 26.4

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : 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
1.00 100.0 1.00 At3g09650 820122 HCF152 (HIGH CHLOROPHYLL FLUORESCENCE 152) RNA binding protein involved in the processing of chloroplast psbB-psbT-psbH-petB-petD transcript unit. O.I. H.G. S.X.
0.46 59.8 0.83 At1g73170 843649 ATP binding / ATP-dependent peptidase/ nucleoside-triphosphatase/ nucleotide binding / serine-type endopeptidase F:nucleoside-triphosphatase activity, ATP-dependent peptidase activity, nucleotide binding, serine-type endopeptidase activity, ATP binding;P:proteolysis;C:chloroplast;BOPMAF O.I. H.G. S.X.
0.45 58.3 0.82 At3g01180 820294 AtSS2 (starch synthase 2) F:transferase activity, transferring glycosyl groups;P:cellulose biosynthetic process, glucan biosynthetic process, biosynthetic process, glycogen biosynthetic process;C:chloroplast;OPBMFAV O.I. H.G. S.X.
0.43 55.3 0.82 At3g06510 819829 SFR2 (SENSITIVE TO FREEZING 2) Encodes a protein with beta-glucosidase activity, mutants show increased sensitivity to freezing O.I. H.G. S.X.
0.42 53.9 0.85 At3g19170 821451 ATPREP1 (PRESEQUENCE PROTEASE 1) Zinc metalloprotease pitrilysin subfamily A. Signal peptide degrading enzyme targeted to mitochondria and chloroplasts. Expressed only in siliques and flowers O.I. H.G. S.X.
0.42 53.9 0.82 At5g58870 836004 ftsh9 (FtsH protease 9) encodes an FtsH protease that is localized to the chloroplast O.I. H.G. S.X.
0.38 46.7 0.84 At4g02260 828096 RSH1 (RELA-SPOT HOMOLOG 1) F:catalytic activity;P:response to wounding;C:chloroplast;BOPMAFV O.I. H.G. S.X.
0.36 43.6 0.81 At5g46390 834682 peptidase S41 family protein F:serine-type peptidase activity, protein binding;P:proteolysis, intracellular signaling cascade;C:thylakoid lumen, chloroplast thylakoid lumen;BOMP O.I. H.G. S.X.
0.36 43.6 0.83 At5g10470 830911 kinesin motor protein-related F:microtubule motor activity, ATP binding;P:microtubule-based movement;C:plasma membrane, membrane, chloroplast envelope;MOFPBAV O.I. H.G. S.X.
0.36 43.6 0.82 At3g29290 822586 emb2076 (embryo defective 2076) F:unknown;P:embryonic development ending in seed dormancy;C:unknown;POFMBA O.I. H.G. S.X.
0.36 43.6 0.83 At4g04770 825814 ATABC1 (ATP BINDING CASSETTE PROTEIN 1) Encodes an iron-stimulated ATPase. A member of the NAP subfamily of ABC transporters. Involved in Fe-S cluster assembly. Similar to SufB. Involved in the regulation of iron homeostasis. Able to form homodimers. Interacts with AtNAP7 inside the chloroplast. O.I. H.G. S.X.
0.35 41.6 0.83 At2g23390 816871 - F:molecular_function unknown;P:biological_process unknown;C:unknown;OBP O.I. H.G. S.X.
0.35 41.6 0.83 At3g04870 819647 ZDS (ZETA-CAROTENE DESATURASE) Involved in the biosynthesis of carotenes and xanthophylls, reduces zeta-carotene to lycopene. O.I. H.G. S.X.
0.35 41.6 0.83 At4g29750 829097 RNA binding F:RNA binding;P:unknown;C:chloroplast;PMOFA O.I. H.G. S.X.
0.35 41.6 0.83 At4g33630 829504 EX1 (EXECUTER1) F:unknown;P:response to singlet oxygen;C:thylakoid membrane;MOPFBV O.I. H.G. S.X.
0.35 41.6 0.81 At2g46340 819242 SPA1 (SUPPRESSOR OF PHYA-105 1) Encodes a member of the SPA (suppressor of phyA-105) protein family (SPA1-SPA4). SPA proteins contain an N-terminal serine/threonine kinase-like motif followed by a coiled-coil structure and a C-terminal WD-repeat domain. SPA1 is a PHYA signaling intermediate, putative regulator of PHYA signaling pathway. Light responsive repressor of photomorphogenesis. Involved in regulating circadian rhythms and flowering time in plants. Under constant light, the abundance of SPA1 protein exhibited circadian regulation, whereas under constant darkness, SPA1 protein levels remained unchanged. In addition, the spa1-3 mutation slightly shortened circadian period of CCA1, TOC1/PRR1 and SPA1 transcript accumulation under constant light. O.I. H.G. S.X.
0.34 39.8 0.83 At5g03430 831843 phosphoadenosine phosphosulfate (PAPS) reductase family protein F:transferase activity;P:Mo-molybdopterin cofactor biosynthetic process, metabolic process;C:cellular_component unknown;BOMFAP O.I. H.G. S.X.
0.34 39.8 0.82 At3g24190 822005 ABC1 family protein F:protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:chloroplast;OBMPFAV O.I. H.G. S.X.
0.34 39.8 0.82 At5g50920 835165 CLPC1 Encodes a protein that is similar to ATP-dependent Clp protease ATP-binding subunit / ClpC. Involved in protein import into the chloroplast. May provide ATP source that drives the TIC (Translocon at the Inner envelope membrane of Chloroplasts) translocation machinery. O.I. H.G. S.X.
0.34 39.8 0.83 At1g54350 841876 ABC transporter family protein F:ATPase activity, coupled to transmembrane movement of substances;P:transport;C:chloroplast;BOMFAPV O.I. H.G. S.X.
0.33 38.1 0.82 At3g63520 825527 CCD1 (CAROTENOID CLEAVAGE DIOXYGENASE 1) Encodes a protein with 9-cis-epoxycarotenoid dioxygenase activity. The enzyme was shown to act on a variety of carotenoid including β-carotene, lutein, zeaxanthin, and all-trans-violaxanthin. When those compounds are used as substrates, the major reaction product detected is a C14 dialdehyde: 4,9-dimethyldodeca-2,4,6,8,10-pentaene-1,12-dial. The enzyme did not cleave as efficiently carotenoids containing 9-cis-double or allenic bonds. O.I. H.G. S.X.
0.33 38.1 0.82 At5g44000 834423 glutathione S-transferase C-terminal domain-containing protein F:glutathione transferase activity;P:unknown;C:chloroplast;BOFPMA O.I. H.G. S.X.
0.33 38.1 0.81 At5g49970 835061 ATPPOX (A. THALIANA PYRIDOXIN (PYRODOXAMINE) 5'-PHOSPHATE OXIDASE) encodes the bifunctional pyridoxine (pyridoxamine) 5�-phosphate oxidase (PPOX)(EC 1.4.3.5) that is involved in the formation of pyridoxal 5'-phosphate (member of the vitamin B6 group) O.I. H.G. S.X.
0.32 35.7 0.83 At1g18660 838447 zinc finger (C3HC4-type RING finger) family protein F:protein binding, ATP-dependent peptidase activity, binding, zinc ion binding;P:ATP-dependent proteolysis;C:unknown;MOPFBVA O.I. H.G. S.X.
0.32 35.7 0.82 At5g52030 835278 TraB protein-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BMOAP O.I. H.G. S.X.
0.32 35.7 0.82 At1g71810 843511 ABC1 family protein F:protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:chloroplast, plastoglobule;OBMPFAV O.I. H.G. S.X.
0.31 33.8 0.82 At3g53920 824559 SIGC (RNA POLYMERASE SIGMA-SUBUNIT C) Encodes a sigma-like transcription factor, Sigma 3 (SIG3 or SIGC). As a subunit of chloroplast RNA polymerase, SIG3 confers the ability to recognize promoter sequences on the core enzyme. SIG3 transcribes specifically the psbN gene in plastids. O.I. H.G. S.X.
0.31 33.8 0.82 At2g15820 816078 OTP51 (ORGANELLE TRANSCRIPT PROCESSING 51) Encodes a protein that promotes splicing of type II introns. otp51 mutants fail to splice intron 2 of plastid ycf3 transcripts, a factor required for the assembly of Photosystem I. Therefore, homozygous otp51 mutants have profound photosynthetic defects and can only survive in sucrose-supplemented in vitro cultures under low light conditions. OTP51 may also be involved in splicing several other transcripts and precursor forms of the trnL, trnG, trnI, and trnA transcripts also accumulate in otp51 mutants. Although OTP51 shares some homology with DNA endonucleases, it lacks key catalytic residues suggesting that it does not participate in DNA cleavage. O.I. H.G. S.X.
0.31 33.8 0.83 At5g42310 834236 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:unknown;C:chloroplast;POMFBA O.I. H.G. S.X.
0.30 32.1 0.81 At2g03390 814868 uvrB/uvrC motif-containing protein F:DNA binding, nuclease activity;P:nucleotide-excision repair;C:chloroplast;OBMFP O.I. H.G. S.X.
0.29 30.3 0.82 At3g19720 821509 ARC5 (ACCUMULATION AND REPLICATION OF CHLOROPLAST 5) Encodes a novel chloroplast division protein. Mutants of exhibit defects in chloroplast constriction, have enlarged, dumbbell-shaped chloroplasts. The ARC5 gene product shares similarity with the dynamin family of GTPases, which mediate endocytosis, mitochondrial division, and other organellar fission and fusion events in eukaryotes. Phylogenetic analysis showed that ARC5 is related to a group of dynamin-like proteins unique to plants. A GFP�ARC5 fusion protein localizes to a ring at the chloroplast division site. Chloroplast import and protease protection assays indicate that the ARC5 ring is positioned on the outer surface of the chloroplast. Facilitates separation of the two daughter chloroplasts. O.I. H.G. S.X.
0.29 30.3 0.82 At5g48730 834931 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:biological_process unknown;C:chloroplast;POMFBA O.I. H.G. S.X.
0.29 30.3 0.83 At3g57190 824886 peptide chain release factor, putative F:translation release factor activity, codon specific, translation release factor activity;P:translational termination;C:cytoplasm;BOMPF O.I. H.G. S.X.
0.29 30.3 0.83 At1g06690 837179 aldo/keto reductase family protein F:oxidoreductase activity, aldo-keto reductase activity, ATPase activity, ATP binding;P:oxidation reduction;C:chloroplast thylakoid membrane, chloroplast, plastoglobule, chloroplast envelope;BOMFPA O.I. H.G. S.X.
0.29 30.3 0.82 At3g10230 820185 LYC (LYCOPENE CYCLASE) Encodes a protein with lycopene β-cyclase activity. This enzyme uses the linear, symmetrical lycopene as substrate. However, unlike the ε-cyclase which adds only one ring, the β-cyclase introduces a ring at both ends of lycopene to form the bicyclic β-carotene. O.I. H.G. S.X.
0.27 26.2 0.82 At1g70070 843343 EMB25 (EMBRYO DEFECTIVE 25) Allelic to ISE2(increased size exclusion limit of plasmodesmata 2). Mutants maintain dilated plasmodesmata at the embryonic torpedo stage. O.I. H.G. S.X.
0.27 26.2 0.82 At1g75210 843858 5' nucleotidase family protein F:5'-nucleotidase activity;P:biological_process unknown;C:chloroplast;MPBO O.I. H.G. S.X.
0.27 26.2 0.82 At2g01290 814657 ribose-5-phosphate isomerase F:ribose-5-phosphate isomerase activity;P:glucose catabolic process to lactate and acetate, 5-phosphoribose 1-diphosphate biosynthetic process, reductive pentose-phosphate cycle, D-ribose catabolic process, pentose-phosphate shunt, non-oxidative branch;C:cytoplasm;BOAFMP O.I. H.G. S.X.
0.26 24.4 0.83 At3g10970 820268 haloacid dehalogenase-like hydrolase family protein F:hydrolase activity, catalytic activity;P:metabolic process;C:chloroplast;BOPAMF O.I. H.G. S.X.
0.26 24.4 0.81 At3g27820 822402 MDAR4 (MONODEHYDROASCORBATE REDUCTASE 4) Encodes a peroxisome membrane-bound monodehydroascorbate reductase, involved in the ascorbate-glutathione cycle which removes toxic H2O2 O.I. H.G. S.X.
0.26 24.4 0.82 At4g31850 829314 PGR3 (PROTON GRADIENT REGULATION 3) encodes a protein containing 27 pentatrico-peptide repeat (PPR) motifs O.I. H.G. S.X.
0.26 24.4 0.83 At1g17220 838293 FUG1 (fu-gaeri1) Encodes a chloroplast localized protein with similarity to translation initiation factor 2. Can complement loss of INFB in E.coli suggesting FUG1 does function as a translation initiation factor in vivo. Identified as a suppressor of the leaf variegation mutant var2-6. Suppression is only seen in hypomorphs as complete loss of function alleles are embryo lethal. O.I. H.G. S.X.
0.26 24.4 0.82 At5g03900 831927 - F:molecular_function unknown;P:biological_process unknown;C:chloroplast envelope;BPO O.I. H.G. S.X.
0.25 22.6 0.83 At5g24300 832497 SSI1 (SUPPRESSOR OF SALICYLIC ACID INSENSITIVITY 1) SSI is a plastidial enzyme and crucial for the synthesis of normal amylopectin in the leaves of Arabidopsis. The absence of SSI results in a deficiency in the number of shorter glucans which in turn affect the formation and connection of the amylopectin clusters in starch. O.I. H.G. S.X.
0.25 22.6 0.81 At2g24820 817019 TIC55 (TRANSLOCON AT THE INNER ENVELOPE MEMBRANE OF CHLOROPLASTS 55) F:electron carrier activity, oxidoreductase activity, 2 iron, 2 sulfur cluster binding;P:oxidation reduction;C:chloroplast, chloroplast envelope;BOPMFA O.I. H.G. S.X.
0.25 22.6 0.83 At3g53700 824537 MEE40 (maternal effect embryo arrest 40) F:unknown;P:embryonic development ending in seed dormancy;C:chloroplast;POMFBA O.I. H.G. S.X.
0.25 22.6 0.82 At5g13650 831209 elongation factor family protein F:GTP binding, translation elongation factor activity, GTPase activity;P:unknown;C:chloroplast, chloroplast stroma;BOMFPA O.I. H.G. S.X.
0.24 20.7 0.82 At4g29590 829080 methyltransferase F:methyltransferase activity;P:metabolic process;C:chloroplast;BOPAF O.I. H.G. S.X.
0.23 19.3 0.81 At1g36320 840539 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;PO O.I. H.G. S.X.
0.23 19.3 0.81 At5g03910 830269 ATATH12 member of ATH subfamily O.I. H.G. S.X.
0.22 17.5 0.81 At1g62750 842573 SCO1 (SNOWY COTYLEDON 1) Nuclear encoded protein consists of the five domains conserved in EF-G proteins, with two GTP-binding sites in the first domain, and an additional transit peptide at the N-terminus. Localized in chloroplasts. Point mutation results in a delay in the onset of germination. At early developmental stage embryos still contain undifferentiated proplastids. The greening of cotyledons is severely impaired in light-grown mutant sco1 seedlings, whereas the following true leaves develop normally as in wild-type plants. O.I. H.G. S.X.
0.22 17.5 0.83 At3g02060 821294 DEAD/DEAH box helicase, putative F:transcription factor activity, helicase activity, nucleic acid binding, ATP-dependent helicase activity, ATP binding;P:regulation of transcription, DNA-dependent;C:chloroplast;BOMFPAV O.I. H.G. S.X.
0.21 15.8 0.83 At4g28740 828995 - F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PBO O.I. H.G. S.X.
0.21 15.8 0.82 At3g02050 821063 KUP3 (K+ UPTAKE TRANSPORTER 3) potassium transporter KUP3p (KUP3) O.I. H.G. S.X.
0.21 15.8 0.83 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.
0.21 15.8 0.83 At3g57990 824968 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OPFMB O.I. H.G. S.X.
0.20 14.4 0.82 At4g36530 829805 hydrolase, alpha/beta fold family protein F:hydrolase activity;P:unknown;C:chloroplast;BOMPFAV O.I. H.G. S.X.
0.20 14.4 0.82 At4g14210 827061 PDS3 (PHYTOENE DESATURASE 3) Encodes phytoene desaturase (phytoene dehydrogenase), an enzyme that catalyzes the desaturation of phytoene to zeta-carotene during carotenoid biosynthesis. Processed protein is localized to the plastid. O.I. H.G. S.X.
0.20 14.4 0.86 At1g73990 843737 SPPA Encodes a putative protease SppA (SppA). O.I. H.G. S.X.
0.19 12.7 0.81 At2g41720 818771 EMB2654 (EMBRYO DEFECTIVE 2654) F:unknown;P:embryonic development ending in seed dormancy;C:unknown;POMFBA O.I. H.G. S.X.
0.19 12.7 0.85 At1g48650 841287 helicase domain-containing protein F:in 6 functions;P:unknown;C:intracellular;BMOFPVA O.I. H.G. S.X.
0.19 12.7 0.82 At1g75010 843839 ARC3 (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.
0.18 11.4 0.82 At4g02510 827934 TOC159 (TRANSLOCON AT THE OUTER ENVELOPE MEMBRANE OF CHLOROPLASTS 159) An integral membrane GTPase that functions as a transit-sequence receptor required for the import of proteins necessary for chloroplast biogenesis. Located in the outer chloroplast membrane. O.I. H.G. S.X.
0.18 11.4 0.83 At5g42130 834218 mitochondrial substrate carrier family protein F:binding;P:transport, mitochondrial transport;C:mitochondrial inner membrane, chloroplast;MFPO O.I. H.G. S.X.
0.18 11.4 0.83 At5g57930 835904 APO2 (ACCUMULATION OF PHOTOSYSTEM ONE 2) ACCUMULATION OF PHOTOSYSTEM ONE 2 O.I. H.G. S.X.
0.18 11.4 0.82 At3g29230 822578 pentatricopeptide (PPR) repeat-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFB O.I. H.G. S.X.
0.17 10.2 0.82 At5g08740 830775 NDC1 (NAD(P)H dehydrogenase C1) F:NADH dehydrogenase activity;P:unknown;C:intrinsic to mitochondrial inner membrane, cell wall, chloroplast, plastoglobule;BOFMAP O.I. H.G. S.X.
0.17 10.2 0.82 At3g25410 822125 bile acid:sodium symporter family protein F:transporter activity, bile acid:sodium symporter activity;P:sodium ion transport;C:chloroplast, membrane;OBMPA O.I. H.G. S.X.
0.17 10.2 0.83 At4g00370 827908 ANTR2 Encodes an inorganic phosphate transporter (PHT4;4). O.I. H.G. S.X.
0.16 8.8 0.82 At4g39960 830157 DNAJ heat shock family protein F:unfolded protein binding, heat shock protein binding, ATP binding;P:protein folding, response to heat;C:chloroplast thylakoid membrane, chloroplast;OBMFPAV O.I. H.G. S.X.
0.16 8.8 0.82 At3g07670 819958 SET domain-containing protein F:[ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity;P:biological_process unknown;C:chloroplast;MFPO O.I. H.G. S.X.
0.15 7.8 0.82 At1g01970 839299 pentatricopeptide (PPR) repeat-containing protein F:molecular_function unknown;P:biological_process unknown;C:unknown;POMF O.I. H.G. S.X.
0.15 7.8 0.81 At5g03420 831846 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BMOFPAV O.I. H.G. S.X.
0.15 7.8 0.82 At1g65410 842852 ATNAP11 (ARABIDOPSIS THALIANA NON-INTRINSIC ABC PROTEIN 11) member of NAP subfamily O.I. H.G. S.X.
0.15 7.8 0.85 At3g52750 824441 FTSZ2-2 Nuclear gene that encodes a plastidial division protein (FtsZ2-2). O.I. H.G. S.X.
0.14 6.8 0.82 At1g06820 837193 CRTISO (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.
0.08 2.3 0.82 At4g14190 827059 - F:molecular_function unknown;P:biological_process unknown;C:chloroplast;POMFA O.I. H.G. S.X.
0.08 2.3 0.83 At3g26380 822242 glycosyl hydrolase family protein 27 / alpha-galactosidase family protein / melibiase family protein F:alpha-galactosidase activity, hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:N-terminal protein myristoylation, carbohydrate metabolic process, metabolic process, lactose catabolic process;C:cell wall;MBFPO O.I. H.G. S.X.
0.06 1.4 0.81 At1g05070 839330 unknown protein F:molecular_function unknown;P:biological_process unknown;C:Golgi apparatus;PBO O.I. H.G. S.X.
0.04 0.9 0.83 At3g52640 824430 nicastrin-related F:unknown;P:protein processing;C:plasma membrane, vacuole;MOPB O.I. H.G. S.X.
0.02 0.4 0.83 At5g48340 834887 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMF O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
1.00	100.0	1.00	At3g09650	820122	HCF152 (HIGH CHLOROPHYLL FLUORESCENCE 152)	RNA binding protein involved in the processing of chloroplast psbB-psbT-psbH-petB-petD transcript unit.	O.I.	H.G.	S.X.
0.46	59.8	0.83	At1g73170	843649	ATP binding / ATP-dependent peptidase/ nucleoside-triphosphatase/ nucleotide binding / serine-type endopeptidase	F:nucleoside-triphosphatase activity, ATP-dependent peptidase activity, nucleotide binding, serine-type endopeptidase activity, ATP binding;P:proteolysis;C:chloroplast;BOPMAF	O.I.	H.G.	S.X.
0.45	58.3	0.82	At3g01180	820294	AtSS2 (starch synthase 2)	F:transferase activity, transferring glycosyl groups;P:cellulose biosynthetic process, glucan biosynthetic process, biosynthetic process, glycogen biosynthetic process;C:chloroplast;OPBMFAV	O.I.	H.G.	S.X.
0.43	55.3	0.82	At3g06510	819829	SFR2 (SENSITIVE TO FREEZING 2)	Encodes a protein with beta-glucosidase activity, mutants show increased sensitivity to freezing	O.I.	H.G.	S.X.
0.42	53.9	0.85	At3g19170	821451	ATPREP1 (PRESEQUENCE PROTEASE 1)	Zinc metalloprotease pitrilysin subfamily A. Signal peptide degrading enzyme targeted to mitochondria and chloroplasts. Expressed only in siliques and flowers	O.I.	H.G.	S.X.
0.42	53.9	0.82	At5g58870	836004	ftsh9 (FtsH protease 9)	encodes an FtsH protease that is localized to the chloroplast	O.I.	H.G.	S.X.
0.38	46.7	0.84	At4g02260	828096	RSH1 (RELA-SPOT HOMOLOG 1)	F:catalytic activity;P:response to wounding;C:chloroplast;BOPMAFV	O.I.	H.G.	S.X.
0.36	43.6	0.81	At5g46390	834682	peptidase S41 family protein	F:serine-type peptidase activity, protein binding;P:proteolysis, intracellular signaling cascade;C:thylakoid lumen, chloroplast thylakoid lumen;BOMP	O.I.	H.G.	S.X.
0.36	43.6	0.83	At5g10470	830911	kinesin motor protein-related	F:microtubule motor activity, ATP binding;P:microtubule-based movement;C:plasma membrane, membrane, chloroplast envelope;MOFPBAV	O.I.	H.G.	S.X.
0.36	43.6	0.82	At3g29290	822586	emb2076 (embryo defective 2076)	F:unknown;P:embryonic development ending in seed dormancy;C:unknown;POFMBA	O.I.	H.G.	S.X.
0.36	43.6	0.83	At4g04770	825814	ATABC1 (ATP BINDING CASSETTE PROTEIN 1)	Encodes an iron-stimulated ATPase. A member of the NAP subfamily of ABC transporters. Involved in Fe-S cluster assembly. Similar to SufB. Involved in the regulation of iron homeostasis. Able to form homodimers. Interacts with AtNAP7 inside the chloroplast.	O.I.	H.G.	S.X.
0.35	41.6	0.83	At2g23390	816871	-	F:molecular_function unknown;P:biological_process unknown;C:unknown;OBP	O.I.	H.G.	S.X.
0.35	41.6	0.83	At3g04870	819647	ZDS (ZETA-CAROTENE DESATURASE)	Involved in the biosynthesis of carotenes and xanthophylls, reduces zeta-carotene to lycopene.	O.I.	H.G.	S.X.
0.35	41.6	0.83	At4g29750	829097	RNA binding	F:RNA binding;P:unknown;C:chloroplast;PMOFA	O.I.	H.G.	S.X.
0.35	41.6	0.83	At4g33630	829504	EX1 (EXECUTER1)	F:unknown;P:response to singlet oxygen;C:thylakoid membrane;MOPFBV	O.I.	H.G.	S.X.
0.35	41.6	0.81	At2g46340	819242	SPA1 (SUPPRESSOR OF PHYA-105 1)	Encodes a member of the SPA (suppressor of phyA-105) protein family (SPA1-SPA4). SPA proteins contain an N-terminal serine/threonine kinase-like motif followed by a coiled-coil structure and a C-terminal WD-repeat domain. SPA1 is a PHYA signaling intermediate, putative regulator of PHYA signaling pathway. Light responsive repressor of photomorphogenesis. Involved in regulating circadian rhythms and flowering time in plants. Under constant light, the abundance of SPA1 protein exhibited circadian regulation, whereas under constant darkness, SPA1 protein levels remained unchanged. In addition, the spa1-3 mutation slightly shortened circadian period of CCA1, TOC1/PRR1 and SPA1 transcript accumulation under constant light.	O.I.	H.G.	S.X.
0.34	39.8	0.83	At5g03430	831843	phosphoadenosine phosphosulfate (PAPS) reductase family protein	F:transferase activity;P:Mo-molybdopterin cofactor biosynthetic process, metabolic process;C:cellular_component unknown;BOMFAP	O.I.	H.G.	S.X.
0.34	39.8	0.82	At3g24190	822005	ABC1 family protein	F:protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:chloroplast;OBMPFAV	O.I.	H.G.	S.X.
0.34	39.8	0.82	At5g50920	835165	CLPC1	Encodes a protein that is similar to ATP-dependent Clp protease ATP-binding subunit / ClpC. Involved in protein import into the chloroplast. May provide ATP source that drives the TIC (Translocon at the Inner envelope membrane of Chloroplasts) translocation machinery.	O.I.	H.G.	S.X.
0.34	39.8	0.83	At1g54350	841876	ABC transporter family protein	F:ATPase activity, coupled to transmembrane movement of substances;P:transport;C:chloroplast;BOMFAPV	O.I.	H.G.	S.X.
0.33	38.1	0.82	At3g63520	825527	CCD1 (CAROTENOID CLEAVAGE DIOXYGENASE 1)	Encodes a protein with 9-cis-epoxycarotenoid dioxygenase activity. The enzyme was shown to act on a variety of carotenoid including β-carotene, lutein, zeaxanthin, and all-trans-violaxanthin. When those compounds are used as substrates, the major reaction product detected is a C14 dialdehyde: 4,9-dimethyldodeca-2,4,6,8,10-pentaene-1,12-dial. The enzyme did not cleave as efficiently carotenoids containing 9-cis-double or allenic bonds.	O.I.	H.G.	S.X.
0.33	38.1	0.82	At5g44000	834423	glutathione S-transferase C-terminal domain-containing protein	F:glutathione transferase activity;P:unknown;C:chloroplast;BOFPMA	O.I.	H.G.	S.X.
0.33	38.1	0.81	At5g49970	835061	ATPPOX (A. THALIANA PYRIDOXIN (PYRODOXAMINE) 5'-PHOSPHATE OXIDASE)	encodes the bifunctional pyridoxine (pyridoxamine) 5�-phosphate oxidase (PPOX)(EC 1.4.3.5) that is involved in the formation of pyridoxal 5'-phosphate (member of the vitamin B6 group)	O.I.	H.G.	S.X.
0.32	35.7	0.83	At1g18660	838447	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, ATP-dependent peptidase activity, binding, zinc ion binding;P:ATP-dependent proteolysis;C:unknown;MOPFBVA	O.I.	H.G.	S.X.
0.32	35.7	0.82	At5g52030	835278	TraB protein-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BMOAP	O.I.	H.G.	S.X.
0.32	35.7	0.82	At1g71810	843511	ABC1 family protein	F:protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:chloroplast, plastoglobule;OBMPFAV	O.I.	H.G.	S.X.
0.31	33.8	0.82	At3g53920	824559	SIGC (RNA POLYMERASE SIGMA-SUBUNIT C)	Encodes a sigma-like transcription factor, Sigma 3 (SIG3 or SIGC). As a subunit of chloroplast RNA polymerase, SIG3 confers the ability to recognize promoter sequences on the core enzyme. SIG3 transcribes specifically the psbN gene in plastids.	O.I.	H.G.	S.X.
0.31	33.8	0.82	At2g15820	816078	OTP51 (ORGANELLE TRANSCRIPT PROCESSING 51)	Encodes a protein that promotes splicing of type II introns. otp51 mutants fail to splice intron 2 of plastid ycf3 transcripts, a factor required for the assembly of Photosystem I. Therefore, homozygous otp51 mutants have profound photosynthetic defects and can only survive in sucrose-supplemented in vitro cultures under low light conditions. OTP51 may also be involved in splicing several other transcripts and precursor forms of the trnL, trnG, trnI, and trnA transcripts also accumulate in otp51 mutants. Although OTP51 shares some homology with DNA endonucleases, it lacks key catalytic residues suggesting that it does not participate in DNA cleavage.	O.I.	H.G.	S.X.
0.31	33.8	0.83	At5g42310	834236	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:unknown;C:chloroplast;POMFBA	O.I.	H.G.	S.X.
0.30	32.1	0.81	At2g03390	814868	uvrB/uvrC motif-containing protein	F:DNA binding, nuclease activity;P:nucleotide-excision repair;C:chloroplast;OBMFP	O.I.	H.G.	S.X.
0.29	30.3	0.82	At3g19720	821509	ARC5 (ACCUMULATION AND REPLICATION OF CHLOROPLAST 5)	Encodes a novel chloroplast division protein. Mutants of exhibit defects in chloroplast constriction, have enlarged, dumbbell-shaped chloroplasts. The ARC5 gene product shares similarity with the dynamin family of GTPases, which mediate endocytosis, mitochondrial division, and other organellar fission and fusion events in eukaryotes. Phylogenetic analysis showed that ARC5 is related to a group of dynamin-like proteins unique to plants. A GFP�ARC5 fusion protein localizes to a ring at the chloroplast division site. Chloroplast import and protease protection assays indicate that the ARC5 ring is positioned on the outer surface of the chloroplast. Facilitates separation of the two daughter chloroplasts.	O.I.	H.G.	S.X.
0.29	30.3	0.82	At5g48730	834931	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:biological_process unknown;C:chloroplast;POMFBA	O.I.	H.G.	S.X.
0.29	30.3	0.83	At3g57190	824886	peptide chain release factor, putative	F:translation release factor activity, codon specific, translation release factor activity;P:translational termination;C:cytoplasm;BOMPF	O.I.	H.G.	S.X.
0.29	30.3	0.83	At1g06690	837179	aldo/keto reductase family protein	F:oxidoreductase activity, aldo-keto reductase activity, ATPase activity, ATP binding;P:oxidation reduction;C:chloroplast thylakoid membrane, chloroplast, plastoglobule, chloroplast envelope;BOMFPA	O.I.	H.G.	S.X.
0.29	30.3	0.82	At3g10230	820185	LYC (LYCOPENE CYCLASE)	Encodes a protein with lycopene β-cyclase activity. This enzyme uses the linear, symmetrical lycopene as substrate. However, unlike the ε-cyclase which adds only one ring, the β-cyclase introduces a ring at both ends of lycopene to form the bicyclic β-carotene.	O.I.	H.G.	S.X.
0.27	26.2	0.82	At1g70070	843343	EMB25 (EMBRYO DEFECTIVE 25)	Allelic to ISE2(increased size exclusion limit of plasmodesmata 2). Mutants maintain dilated plasmodesmata at the embryonic torpedo stage.	O.I.	H.G.	S.X.
0.27	26.2	0.82	At1g75210	843858	5' nucleotidase family protein	F:5'-nucleotidase activity;P:biological_process unknown;C:chloroplast;MPBO	O.I.	H.G.	S.X.
0.27	26.2	0.82	At2g01290	814657	ribose-5-phosphate isomerase	F:ribose-5-phosphate isomerase activity;P:glucose catabolic process to lactate and acetate, 5-phosphoribose 1-diphosphate biosynthetic process, reductive pentose-phosphate cycle, D-ribose catabolic process, pentose-phosphate shunt, non-oxidative branch;C:cytoplasm;BOAFMP	O.I.	H.G.	S.X.
0.26	24.4	0.83	At3g10970	820268	haloacid dehalogenase-like hydrolase family protein	F:hydrolase activity, catalytic activity;P:metabolic process;C:chloroplast;BOPAMF	O.I.	H.G.	S.X.
0.26	24.4	0.81	At3g27820	822402	MDAR4 (MONODEHYDROASCORBATE REDUCTASE 4)	Encodes a peroxisome membrane-bound monodehydroascorbate reductase, involved in the ascorbate-glutathione cycle which removes toxic H2O2	O.I.	H.G.	S.X.
0.26	24.4	0.82	At4g31850	829314	PGR3 (PROTON GRADIENT REGULATION 3)	encodes a protein containing 27 pentatrico-peptide repeat (PPR) motifs	O.I.	H.G.	S.X.
0.26	24.4	0.83	At1g17220	838293	FUG1 (fu-gaeri1)	Encodes a chloroplast localized protein with similarity to translation initiation factor 2. Can complement loss of INFB in E.coli suggesting FUG1 does function as a translation initiation factor in vivo. Identified as a suppressor of the leaf variegation mutant var2-6. Suppression is only seen in hypomorphs as complete loss of function alleles are embryo lethal.	O.I.	H.G.	S.X.
0.26	24.4	0.82	At5g03900	831927	-	F:molecular_function unknown;P:biological_process unknown;C:chloroplast envelope;BPO	O.I.	H.G.	S.X.
0.25	22.6	0.83	At5g24300	832497	SSI1 (SUPPRESSOR OF SALICYLIC ACID INSENSITIVITY 1)	SSI is a plastidial enzyme and crucial for the synthesis of normal amylopectin in the leaves of Arabidopsis. The absence of SSI results in a deficiency in the number of shorter glucans which in turn affect the formation and connection of the amylopectin clusters in starch.	O.I.	H.G.	S.X.
0.25	22.6	0.81	At2g24820	817019	TIC55 (TRANSLOCON AT THE INNER ENVELOPE MEMBRANE OF CHLOROPLASTS 55)	F:electron carrier activity, oxidoreductase activity, 2 iron, 2 sulfur cluster binding;P:oxidation reduction;C:chloroplast, chloroplast envelope;BOPMFA	O.I.	H.G.	S.X.
0.25	22.6	0.83	At3g53700	824537	MEE40 (maternal effect embryo arrest 40)	F:unknown;P:embryonic development ending in seed dormancy;C:chloroplast;POMFBA	O.I.	H.G.	S.X.
0.25	22.6	0.82	At5g13650	831209	elongation factor family protein	F:GTP binding, translation elongation factor activity, GTPase activity;P:unknown;C:chloroplast, chloroplast stroma;BOMFPA	O.I.	H.G.	S.X.
0.24	20.7	0.82	At4g29590	829080	methyltransferase	F:methyltransferase activity;P:metabolic process;C:chloroplast;BOPAF	O.I.	H.G.	S.X.
0.23	19.3	0.81	At1g36320	840539	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;PO	O.I.	H.G.	S.X.
0.23	19.3	0.81	At5g03910	830269	ATATH12	member of ATH subfamily	O.I.	H.G.	S.X.
0.22	17.5	0.81	At1g62750	842573	SCO1 (SNOWY COTYLEDON 1)	Nuclear encoded protein consists of the five domains conserved in EF-G proteins, with two GTP-binding sites in the first domain, and an additional transit peptide at the N-terminus. Localized in chloroplasts. Point mutation results in a delay in the onset of germination. At early developmental stage embryos still contain undifferentiated proplastids. The greening of cotyledons is severely impaired in light-grown mutant sco1 seedlings, whereas the following true leaves develop normally as in wild-type plants.	O.I.	H.G.	S.X.
0.22	17.5	0.83	At3g02060	821294	DEAD/DEAH box helicase, putative	F:transcription factor activity, helicase activity, nucleic acid binding, ATP-dependent helicase activity, ATP binding;P:regulation of transcription, DNA-dependent;C:chloroplast;BOMFPAV	O.I.	H.G.	S.X.
0.21	15.8	0.83	At4g28740	828995	-	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PBO	O.I.	H.G.	S.X.
0.21	15.8	0.82	At3g02050	821063	KUP3 (K+ UPTAKE TRANSPORTER 3)	potassium transporter KUP3p (KUP3)	O.I.	H.G.	S.X.
0.21	15.8	0.83	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.
0.21	15.8	0.83	At3g57990	824968	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OPFMB	O.I.	H.G.	S.X.
0.20	14.4	0.82	At4g36530	829805	hydrolase, alpha/beta fold family protein	F:hydrolase activity;P:unknown;C:chloroplast;BOMPFAV	O.I.	H.G.	S.X.
0.20	14.4	0.82	At4g14210	827061	PDS3 (PHYTOENE DESATURASE 3)	Encodes phytoene desaturase (phytoene dehydrogenase), an enzyme that catalyzes the desaturation of phytoene to zeta-carotene during carotenoid biosynthesis. Processed protein is localized to the plastid.	O.I.	H.G.	S.X.
0.20	14.4	0.86	At1g73990	843737	SPPA	Encodes a putative protease SppA (SppA).	O.I.	H.G.	S.X.
0.19	12.7	0.81	At2g41720	818771	EMB2654 (EMBRYO DEFECTIVE 2654)	F:unknown;P:embryonic development ending in seed dormancy;C:unknown;POMFBA	O.I.	H.G.	S.X.
0.19	12.7	0.85	At1g48650	841287	helicase domain-containing protein	F:in 6 functions;P:unknown;C:intracellular;BMOFPVA	O.I.	H.G.	S.X.
0.19	12.7	0.82	At1g75010	843839	ARC3 (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.
0.18	11.4	0.82	At4g02510	827934	TOC159 (TRANSLOCON AT THE OUTER ENVELOPE MEMBRANE OF CHLOROPLASTS 159)	An integral membrane GTPase that functions as a transit-sequence receptor required for the import of proteins necessary for chloroplast biogenesis. Located in the outer chloroplast membrane.	O.I.	H.G.	S.X.
0.18	11.4	0.83	At5g42130	834218	mitochondrial substrate carrier family protein	F:binding;P:transport, mitochondrial transport;C:mitochondrial inner membrane, chloroplast;MFPO	O.I.	H.G.	S.X.
0.18	11.4	0.83	At5g57930	835904	APO2 (ACCUMULATION OF PHOTOSYSTEM ONE 2)	ACCUMULATION OF PHOTOSYSTEM ONE 2	O.I.	H.G.	S.X.
0.18	11.4	0.82	At3g29230	822578	pentatricopeptide (PPR) repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFB	O.I.	H.G.	S.X.
0.17	10.2	0.82	At5g08740	830775	NDC1 (NAD(P)H dehydrogenase C1)	F:NADH dehydrogenase activity;P:unknown;C:intrinsic to mitochondrial inner membrane, cell wall, chloroplast, plastoglobule;BOFMAP	O.I.	H.G.	S.X.
0.17	10.2	0.82	At3g25410	822125	bile acid:sodium symporter family protein	F:transporter activity, bile acid:sodium symporter activity;P:sodium ion transport;C:chloroplast, membrane;OBMPA	O.I.	H.G.	S.X.
0.17	10.2	0.83	At4g00370	827908	ANTR2	Encodes an inorganic phosphate transporter (PHT4;4).	O.I.	H.G.	S.X.
0.16	8.8	0.82	At4g39960	830157	DNAJ heat shock family protein	F:unfolded protein binding, heat shock protein binding, ATP binding;P:protein folding, response to heat;C:chloroplast thylakoid membrane, chloroplast;OBMFPAV	O.I.	H.G.	S.X.
0.16	8.8	0.82	At3g07670	819958	SET domain-containing protein	F:[ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity;P:biological_process unknown;C:chloroplast;MFPO	O.I.	H.G.	S.X.
0.15	7.8	0.82	At1g01970	839299	pentatricopeptide (PPR) repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;POMF	O.I.	H.G.	S.X.
0.15	7.8	0.81	At5g03420	831846	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BMOFPAV	O.I.	H.G.	S.X.
0.15	7.8	0.82	At1g65410	842852	ATNAP11 (ARABIDOPSIS THALIANA NON-INTRINSIC ABC PROTEIN 11)	member of NAP subfamily	O.I.	H.G.	S.X.
0.15	7.8	0.85	At3g52750	824441	FTSZ2-2	Nuclear gene that encodes a plastidial division protein (FtsZ2-2).	O.I.	H.G.	S.X.
0.14	6.8	0.82	At1g06820	837193	CRTISO (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.
0.08	2.3	0.82	At4g14190	827059	-	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;POMFA	O.I.	H.G.	S.X.
0.08	2.3	0.83	At3g26380	822242	glycosyl hydrolase family protein 27 / alpha-galactosidase family protein / melibiase family protein	F:alpha-galactosidase activity, hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:N-terminal protein myristoylation, carbohydrate metabolic process, metabolic process, lactose catabolic process;C:cell wall;MBFPO	O.I.	H.G.	S.X.
0.06	1.4	0.81	At1g05070	839330	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:Golgi apparatus;PBO	O.I.	H.G.	S.X.
0.04	0.9	0.83	At3g52640	824430	nicastrin-related	F:unknown;P:protein processing;C:plasma membrane, vacuole;MOPB	O.I.	H.G.	S.X.
0.02	0.4	0.83	At5g48340	834887	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMF	O.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
43.8 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.2 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.0 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.9 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.6 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.4 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
40.2 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.8 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.7 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.4 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.0 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.8 99.7 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
36.2 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.7 99.7 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
34.2 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.6 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.5 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.3 99.7 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
32.9 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.8 99.7 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
32.6 99.7 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
30.3 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.2 99.7 GSM184556 Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
24.5 99.6 E-ATMX-35-raw-cel-1574334832
24.2 99.6 E-ATMX-35-raw-cel-1574334800
24.1 99.6 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
19.7 99.6 E-ATMX-35-raw-cel-1574334816
15.0 99.4 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
14.2 99.4 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
13.0 99.4 GSM142737 DH001_ATH1_A4-UNM2 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
11.6 99.3 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
11.5 99.3 GSM133774 Lindsey_1-26_torpedo-meristem_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.4 99.3 GSM142738 DH001_ATH1_A5-BCP2 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
11.2 99.2 GSM184551 Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
10.9 99.2 GSM184499 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
8.8 99.0 E-MEXP-509-raw-cel-829148420
8.8 99.0 GSM184494 Endodermis&Pericycle root cells 2hr KCl control treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
8.6 99.0 GSM184500 Endodermis&Pericycle root cells 2hr continuous KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
43.8	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.2	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.0	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.9	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.6	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.4	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
40.2	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.8	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.7	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.4	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.0	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.8	99.7	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
36.2	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.7	99.7	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
34.2	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.6	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.5	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.3	99.7	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
32.9	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.8	99.7	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
32.6	99.7	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
30.3	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.2	99.7	GSM184556	Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
24.5	99.6	E-ATMX-35-raw-cel-1574334832
24.2	99.6	E-ATMX-35-raw-cel-1574334800
24.1	99.6	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
19.7	99.6	E-ATMX-35-raw-cel-1574334816
15.0	99.4	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
14.2	99.4	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
13.0	99.4	GSM142737	DH001_ATH1_A4-UNM2	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
11.6	99.3	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
11.5	99.3	GSM133774	Lindsey_1-26_torpedo-meristem_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.4	99.3	GSM142738	DH001_ATH1_A5-BCP2	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
11.2	99.2	GSM184551	Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.9	99.2	GSM184499	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
8.8	99.0	E-MEXP-509-raw-cel-829148420
8.8	99.0	GSM184494	Endodermis&Pericycle root cells 2hr KCl control treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
8.6	99.0	GSM184500	Endodermis&Pericycle root cells 2hr continuous KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.069 3 GO:0016120 The chemical reactions and pathways resulting in the formation of carotenes, hydrocarbon carotenoids.
0.043 2 GO:0010020 The division of a chloroplast within a cell to form two or more separate chloroplast compartments. This division occurs independently of mitosis.
0.043 2 GO:0016117 The chemical reactions and pathways resulting in the formation of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail.

SF	Genes	GO ID	Process Name
0.069	3	GO:0016120	The chemical reactions and pathways resulting in the formation of carotenes, hydrocarbon carotenoids.
0.043	2	GO:0010020	The division of a chloroplast within a cell to form two or more separate chloroplast compartments. This division occurs independently of mitosis.
0.043	2	GO:0016117	The chemical reactions and pathways resulting in the formation of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.078 4 00906 Carotenoid biosynthesis
0.026 5 01070 Biosynthesis of plant hormones
0.022 3 01062 Biosynthesis of terpenoids and steroids

SF	Genes	KEGG ID	Pathway name
0.078	4	00906	Carotenoid biosynthesis
0.026	5	01070	Biosynthesis of plant hormones
0.022	3	01062	Biosynthesis of terpenoids and steroids

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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Gene ID	At3g09650
Gene name	HCF152 (HIGH CHLOROPHYLL FLUORESCENCE 152)
Module size	81 genes
NF	0.25
%ile	26.4

Co-expression analysis

Gene ID At3g09650 Gene name HCF152 (HIGH CHLOROPHYLL FLUORESCENCE 152) Module size 81 genes NF 0.25 %ile 26.4

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein: VF over 0.50, : over 0.25, : below 0.25

Co-expressed genes

Click More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Biological processes inferred to relate to the module

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG0.078400906Carotenoid biosynthesis0.026501070Biosynthesis of plant hormones0.022301062Biosynthesis of terpenoids and steroids

Inter-species module comparison

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

Gene ID At3g09650

Gene name HCF152 (HIGH CHLOROPHYLL FLUORESCENCE 152)

Module size 81 genes

NF 0.25

%ile 26.4

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

SF Genes KEGG ID Pathway name Link to KEGG
0.078 4 00906 Carotenoid biosynthesis
0.026 5 01070 Biosynthesis of plant hormones
0.022 3 01062 Biosynthesis of terpenoids and steroids

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