Reddy et al.
SupplementaryTable S1
Identified spot / Affymetrix ID(s) / Sample set(s) / Name / Function / Phos state / Protein peak CT / mRNA cycle / Category / mRNA peak CT0610038K03Rik / - / 6 / RIKEN cDNA 0610038K03 / Unknown / Y / CT08 / - / -
Acaa2 (1) / 95064_at / 3 + 6 / Acetyl-Coenzyme A acyltransferase 2 / Fatty acid metabolism / Y / CT20 / Possibly Rhythmic / C
Acaa2 (2) / 95064_at / 6 / Acetyl-Coenzyme A acyltransferase 2 / Fatty acid metabolism / Y / CT20 / Possibly Rhythmic / C
Aco2 / 96870_at / 6 / Aconitase 2, mitochondrial / Citric acid cycle / Y / CT20 / Definitely Rhythmic / A / CT14
Akr1a4 / 96888_at / 3 / Aldo-keto reductase family 1, member A4 (aldehyde reductase) / Unknown / ? / Night / Probably Rhythmic / B
Akr7a5 (Afar) / 96069_at / 6 / Aldo-keto reductase family 7, member A5 (aflatoxin aldehyde reductase) / Aldehyde and carbohydrate metabolism / N / CT04 / Possibly Rhythmic / C
Alb / - / 3 + 6 / Albumin (serum albumin) / Metabolite transport. Maintenance of oncotic pressure in blood. / Y / CT00 / - / -
Aldh1a1 / 100068_at / 6 / Aldehyde dehydrogenase family 1, subfamily A1 / Retinoic acid metabolism / Y / CT04 / Not Rhythmic / D
Aldh2 (1) / 96058_s_at / 6 / Aldehyde dehydrogenase 2, mitochondrial / Alcohol metabolism / N / CT00 / Possibly Rhythmic / C
Aldh2 (2) / 96058_s_at / 6 / Aldehyde dehydrogenase 2, mitochondrial / Alcohol metabolism / N / CT20 / Possibly Rhythmic / C
Aldh2 (3) / 96058_s_at / 6 / Aldehyde dehydrogenase 2, mitochondrial / Alcohol metabolism / Y / CT20 / Possibly Rhythmic / C
Aldh-M1 / 96058_s_at / 6 / Aldehyde dehydrogenase AHD-M1 / Alcohol metabolism / Y / CT20 / Possibly Rhythmic / C
Aldo2 / 101531_at / 6 / Aldolase 2, B isoform / Glycolysis / Y / CT16 / Definitely Rhythmic / A / CT18
Apoa4 / 100078_at / 3 / Apolipoprotein A-IV precursor / Lipid transport, regulation of cholesterol absorption (lipoprotein metabolism) / ? / Night / Probably Rhythmic / B
Arg1 / 93097_at / 6 / Arginase 1, liver / Urea cycle / ? / CT04 / Possibly Rhythmic / C
Ass1 / 97521_at / 6 / Argininosuccinate synthetase 1 / Urea cycle / Y / CT20 / Possibly Rhythmic / C
Atp5a1 / 100753_at / 3 / ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1 / ATP synthesis / ? / Night / Not Rhythmic / D
Atp5b / - / 6 / ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit / ATP synthesis / N / CT12 / - / -
Bhmt / 94049_at / 6 / Betaine-homocysteine methyltransferase / Methionine biosynthesis / Y / CT00 / Definitely Rhythmic / A / CT22
Calr / 93523_at / 3 / Calreticulin / Cytoskeletal organisation / ? / Night / Not Rhythmic / D
Cat (1) / 161877_f_at / 3 + 6 / Catalase / Response to oxidative stress and electron transport / Y / CT00 / Not Rhythmic / D
Cat (2) / 161877_f_at / 3 + 6 / Catalase / Response to oxidative stress and electron transport / Y / CT20 / Not Rhythmic / D
Cps1 (1) / 93824_at / 3 + 6 / Carbamoyl-phosphate synthetase 1 / Urea cycle (rate-limiting step) / N / CT00 / Possibly Rhythmic / C
Cps1 (2) / 93824_at / 3 + 6 / Carbamoyl-phosphate synthetase 1 / Urea cycle (rate-limiting step) / N / CT00 / Possibly Rhythmic / C
Cps1 (3) / 93824_at / 3 + 6 / Carbamoyl-phosphate synthetase 1 / Urea cycle (rate-limiting step) / N / CT16 / Possibly Rhythmic / C
Cps1 (4) / 93824_at / 3 + 6 / Carbamoyl-phosphate synthetase 1 / Urea cycle (rate-limiting step) / Y / CT16 / Possibly Rhythmic / C
Cps1 (5) / 93824_at / 3 + 6 / Carbamoyl-phosphate synthetase 1 / Urea cycle (rate-limiting step) / ? / CT00 / Possibly Rhythmic / C
Cps1 (6) / 93824_at / 3 + 6 / Carbamoyl-phosphate synthetase 1 / Urea cycle (rate-limiting step) / ? / CT04 / Possibly Rhythmic / C
Eef1d / 160129_at / 6 / Eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein) / Protein biosynthesis (elongation in translation) / Y / CT12 / Not Rhythmic / D
Eif3s4d / - / 6 / Eukaryotic translation initiation factor 3, subunit 4 (delta) / Protein biosynthesis (translation initiation) / N / CT20 / - / -
Eno1 / 160568_at / 3 + 6 / Enolase 1, alpha non-neuron / Glycolysis / N / CT16 / Possibly Rhythmic / C
Gnpat / 94562_at / 3 / Glyceronephosphate O-acyltransferase / Membrane biosynthesis (ether lipid biogenesis) / ? / Night / Possibly Rhythmic / C
Grp58 / 101060_at / 6 / Glucose regulated protein, 58 kDa / Electron transport and acts as a molecular chaperone / N / CT20 / Not Rhythmic / D
Gstm1 / 93543_f_at / 3 / Glutathione S-transferase, mu 1 / Xenobiotic metabolism / ? / Night / Possibly Rhythmic / C
Hao1 / 114928_at, 115340_at / 6 / Hydroxyacid oxidase 1, liver / Response to oxidative stress and electron transport / Y / CT04 / - / -
Hnrpa2b1 / 93118_at / 6 / Heterogenous nuclear ribonucleoprotein A2/B1 / RNA processing / N / CT16 / Not Rhythmic / D
Hspa9a / 97914_at / 3 + 6 / Heat shock protein, A / Protein folding / N / CT08 / Probably Rhythmic / B
Hspd1 / 93277_at / 3 / Heat shock protein 1 (chaperonin) / Protein folding / ? / Day / Definitely Rhythmic / A / CT10
Khk / 104323_at / 6 / Ketohexokinase / Fructose metabolism / ? / CT00 / Not Rhythmic / D
LOC236937 / - / 6 / Similar to interferon-inducible protein 10 (IP-10) receptor / Unknown / Y / CT16 / - / -
Mup1 / 101566_f_at, 102096_f_at, 137167_at / 3 / Major urinary protein 1 / Pheromone stabilisation / Type I (allergic) hypersensitivity responses / ? / Day / Not Rhythmic / D
Prdx6 (1) / 100622_at,168447_r_at / 6 / Peroxoredoxin 6 / Response to oxidative stress / Y / CT00 / Definitely Rhythmic / A / CT14
Prdx6 (2) / 100622_at,168447_r_at / 6 / Peroxoredoxin 6 / Response to oxidative stress / Y / CT12 / Definitely Rhythmic / A / CT14
Rgn / 93766_at / 6 / Regucalcin / Calcium homeostasis / Y / CT12 / Not Rhythmic / D
Scp2 / 93278_at95787_s_at / 6 / Sterol carirer proetin / Cholesterol transport and bile acid metabolism / Y / CT20 / Not Rhythmic / D
Sdh1 / 162078_at, 164338_f_at, 170584_at, 171355_at / 6 / Sorbitol dehydrogenase 1 / Fructose metabolism / Y / CT20 / Not Rhythmic / D
Selenbp1 / 100596_at, 162030_r_at, 170910_r_at / 3 / Selenium binding protein / Unknown / ? / Day / Probably Rhythmic / B
Serpina1a / 101565_f_at, 100329_at, 101572_f_at / 3 / Alpha-1 -antitrytypsin 1-3 precursor / Acute phase response (innate immune response) / ? / Night / Not Rhythmic / D
Serpina1d / 101565_f_at, 100329_at, 101572_f_at / 6 / Serine (or cysteine) proteinase inhibitor, clade A, member 1d / Acute phase response (innate immune response) / Y / CT00 / Not Rhythmic / D
Table S1. Circadian proteins and their relationship to mRNA expression as reported by Genechip assays. All rhythmic proteins as determined by 2D-DIGE analysis are shown. For some proteins, there are a number of different spots on the 2D-gels, representing different forms of the same protein, illustrated with parentheses. Proteins that were found by the 6-point analysis alone (“6”), the 3-point analysis alone (“3”), or by both analyses (“3+6”) are indicated as such. Phosphorylation state of each is shown (as determined by phospho-staining of the 2D-gels). If phosphorylation state could not be determined unequivocally, this is indicated by “?” (i.e. it was indeterminate). The timing of peak expression of each protein is shown, as is the peak for its cognate mRNA, if this mRNA was significantly rhythmic. If rhythmicity was only found in the 3-point analysis (see main text), then the proteins are simply segregated into Day (peak expression at CT11/35) or Night (peak expression at CT23) clusters as shown. The category into which each mRNA “cycle” falls in terms of its rhythmicity is also illustrated (see Figure S1 for details of the categories). Relevant Affymetrix IDs for transcripts are given where available; more than one ID is given if the transcript is represented more than once on the Genechips.