Skip to Main Content
Table 2.

Fold changes in gene expression in early prism larvae (40 h post-fertilization) that developed under Moderate CO2 conditions compared with early prism larvae raised under Control CO2conditions

GeneGene IDFold change (FCUL → FCLL)Protein information
Acid–base and ion regulation    
   Atp13a3 SPU_011933 –2.08 → –1.03 H+/K+-ATPase 
   Aqp SPU_021388 –1.68 → –1.18 Aquaporin, water and potentially CO2 transport 
   Aqp4 SPU_012222 –1.64 → +1.06 Aquaporin, water transport 
   Atp7a SPU_028504 –1.68 → –1.09 Cu2+-ATPase 
   Atp1a3 SPU_025815 –1.84 → +1.14 Na+/K+-ATPase 
   Atp6ap1 SPU_012695 –1.60 → +1.05 Vacuolar H+-ATPase (V-ATPase) 
   Slc22a13 SPU_027502 –1.58 → –1.01 Organic cation transporter 
Apoptosis    
   Bruce/BIRC6 SPU_001262 –1.60 → –1.01 Baculoviral IAP repeat-containing 6, inhibitor of apoptosis 
   Survivin/BIRC5 SPU_008878 –1.63 → +1.07 Baculoviral IAP repeat-containing 5, inhibitor of apoptosis 
   RAIDD SPU_023153 –1.56 → +1.01 RIP-associated ICH1/CED3 homologous protein with death domain, Cell Extrinsic apoptosis 
   Caspase-8-like SPU_016039 –1.54 → +1.01 Cysteine protease, cell extrinsic apoptosis 
Biomineralization    
   cyclophilin 2 SPU_007484 –1.53 → –1.07 Peptidylpropyl cis-trans isomerases 
   Other cyclophilins SPU_008305 –1.61 → +1.02 Peptidylpropyl cis-trans isomerases 
   MSP130 SPU_013821 –1.58 → –1.01 Primary mesenchyme cell (PMC)-specific protein 
   MSP130-related 3 SPU_013823 –1.65 → –1.01 PMC-specific protein 
   COLP3α SPU_003768 –1.53 → –1.02 Most abundant collagen in PMCs, non-fibrillar collagen 
   COLP4α SPU_015708 –1.69 → +1.07 Next most abundant collagen, non-fibrillar collagen 
   Other collagens SPU_009076 –1.56 → +1.00 Mostly fibrillar collagens 
   Other collagens SPU_022116 –1.63 → +1.05 Mostly fibrillar collagens 
   P19 SPU_004136 –1.65 → +1.05 PMC-specific protein 
   P16 SPU_018408 –1.55 → –1.06 PMC-specific protein essential for skeletal rod elongation 
   P16-like SPU_018405 –1.60 → +1.03 PMC-specific protein essential for skeletal rod elongation 
   osteonectin SPU_028275 –1.61 → 1.00 Glycoprotein that binds calcium 
   Runt-1 SPU_025612 –1.66 → +1.01 Transcription factor, triggers differentiation of skeletogenic cells 
Cell cycle    
   Cdc27/Apc3 SPU_022322 –1.59 → +1.04 Anaphase promoting complex 3, ubiquitin-proteolysis pathway 
   MCM4 SPU_024515 –1.59 → +1.04 Mini chromosome maintenance 4 
   Psf2 SPU_021616 –1.52 → +1.01 DNA replication complex GINS protein 
   Chk2 SPU_004975 –1.60 → –1.06 Checkpoint kinase 2 
   Cyclin T SPU_021812 –1.58 → –1.01 CDK regulatory subunit involved in transcription 
   SMC4 SPU_013617 –1.74 → +1.11 Structural maintenance of chromosome 4 
   CDK8 SPU_001690 –1.56 → +1.02 Cyclin-dependent kinase, initiates transcription 
   CDK1 SPU_002210 –1.53 → 1.00 Cyclin-dependent kinase, regulates mitosis 
Cellular stress response    
   Protein homeostasis    
      NSFL1C SPU_015012 –1.66 → –1.04 p97 ATPase cofactor p47, protein degradation 
      PSMC3 SPU_003847 –1.63 → +1.01 26S proteasome subunit, protein degradation 
      Hsp40A SPU_016562 –1.52 → 1.00 40kDa Heat shock protein, co-chaperone of Hsp70 
   Antioxidant defense    
      MGST-3 SPU_016492 –1.84 → –1.01 Glutathione S-transferase, microsomal 
      GST pi SPU_017373 –1.66 → +1.08 Glutathione S-transferase, cytosolic 
   Toxicant, metal and xenobiotic defense    
      Cyp3-like 16 SPU_014092 –1.74 → –1.03 Cytochrome P450 monooxygenase 
      Cyp2-like9 SPU_003606 –1.77 → +1.03 Cytochrome P450 monooxygenase 
      Tf SPU_026949 –1.65 → +1.03 Homolog of transferrin, metal detoxification 
      Ugt1-like SPU_012199 –1.68 → +1.06 UDP glucuronosyltransferase 
      Shr2 SPU_008117 –1.58 → +1.04 Nuclear receptor that binds estradiol 
Development    
   Wnt8 SPU_020371 –1.52 → –1.02 Component of gene regulatory network (GRN) that controls differentiation of Skeletogenic micromeres 
   Blimp1 SPU_027235 –1.68 → –1.05 Stabilizes the GRN thru its interaction with Wnt8 
   Smad1/5/8 SPU_020722 –1.77 → +1.09 Regulation of transcription, DNA dependent 
   GataE SPU_010635 –1.58 → +1.01 GATA-binding transcription factor E, stabilizes GRN 
   Smad5 SPU_000739 –1.55 → –1.01 Regulation of transcription, DNA dependent 
   PKS-like SPU_002895 –1.55 → –1.05 Polyketide synthase, involved in pigmentation 
   Ap4 SPU_003179 –1.56 → +1.01 Regulation of transcription 
   Dac SPU_028061 –1.55 → +1.01 Regulation of transcription, anatomical stru 
Kinome    
   MLCKa SPU_023876 –1.55 → –1.02 Myosin light chain kinase 
   MLCKc SPU_019751 –1.54 → –1.01 Myosin light chain kinase 
   MAPKAPK5b SPU_028463 –1.73 → +1.10 Mitogen-activated protein kinase signaling 
   NLK SPU_010846 –1.60 → +1.03 Nemo-like kinase 
Metabolism – energy metabolism    
   Tricarboxylic acid cycle    
      Suclg1 SPU_025397 –1.90 → –1.01 Succinyl-CoA synthetase, LG uses GTP 
      Idh3a SPU_027710 –1.66 → +1.01 Isocitrate dehydrogenase 3a 
      Idh3g SPU_002807 –1.65 → +1.03 Isocitrate dehydrogenase 3g 
      Sdhb SPU_026295 –1.70 → +1.09 Succinate dehydrogenase b 
      Aco2a SPU_005839 –1.40 → –1.10 Aconitase 2a, mitochondrial 
   Electron transport chain    
      Atp5d SPU_028873 –1.61 → –1.09 ATP synthase, H+ transporting, F1 complex 
      Atp5f1 SPU_000022 –1.62 → +1.02 ATP synthase, H+ transporting, F0 complex 
      Atp5i SPU_001183 –1.57 → –1.01 ATP synthase, H+ transporting, F0 complex 
      Ndufs6 SPU_019206 –1.60 → –1.04 NADH dehydrogenase (ubiquinone) Fe-S protein 6 
      Ndufv2 SPU_026881 –1.66 → +1.08 NADH dehydrogenase (ubiquinone) flavoprotein 2 
      Ndufa12 SPU_002128 –1.70 → +1.09 NADH dehydrogenase 
      Uqcrh SPU_013225 –1.58 → –1.05 Cytochrome c reductase, hinge protein 
      Cox4i1 SPU_014478 –1.62 → +1.06 Cytochrome c oxidase 
   Mitochondrial membrane transporters    
      Slc25a5 SPU_004813 –1.86 → –1.18 ADP, ATP carrier protein 2, energy transfer 
      Slc25a3 SPU_009872 –1.70 → –1.01 Phosphate carrier, energy transfer 
   Other metabolism genes    
      HMGcs1 SPU_007114 –1.53 → –1.03 Hydroxymethylglutaryl-CoA synthase 1, lipid biosynthesis 
      Acs-like 1 SPU_012875 –1.51 → –1.03 Acyl-CoA synthetase, lipid biosynthesis 
      Slc23a2 SPU_009217 –1.44 → –1.06 Na+/l-ascorbic acid transporter, vitamin C transport 
   Protein synthesis – translational control    
      elF2Bβ SPU_004173 –1.70 → –1.04 Translation factor – initiation 
      elF2γ SPU_020412 –1.51 → –1.01 Translation factor – initiation 
      elF3e SPU_007226 –1.60 → +1.05 Translation factor – initiation 
      elF3j SPU_013398 –1.80 → –1.08 Translation factor – initiation 
      elF3k SPU_010303 –1.67 → +1.06 Translation factor – initiation 
      elF4G SPU_024859 –1.65 → +1.07 Translation factor – initiation 
      VARS-B SPU_002908 –1.55 → –1.02 Translation factor – elongation 
      VARS-A SPU_008058 –1.62 → +1.03 Translation factor – elongation 
      PABPN1 SPU_028828 –1.44 → –1.07 Translation factor – termination 
      hnRNP K SPU_008011 –1.64 → +1.02 IRES-dependent translation 
      PTB SPU_000961 –1.65 → +1.05 IRES-dependent translation 
GeneGene IDFold change (FCUL → FCLL)Protein information
Acid–base and ion regulation    
   Atp13a3 SPU_011933 –2.08 → –1.03 H+/K+-ATPase 
   Aqp SPU_021388 –1.68 → –1.18 Aquaporin, water and potentially CO2 transport 
   Aqp4 SPU_012222 –1.64 → +1.06 Aquaporin, water transport 
   Atp7a SPU_028504 –1.68 → –1.09 Cu2+-ATPase 
   Atp1a3 SPU_025815 –1.84 → +1.14 Na+/K+-ATPase 
   Atp6ap1 SPU_012695 –1.60 → +1.05 Vacuolar H+-ATPase (V-ATPase) 
   Slc22a13 SPU_027502 –1.58 → –1.01 Organic cation transporter 
Apoptosis    
   Bruce/BIRC6 SPU_001262 –1.60 → –1.01 Baculoviral IAP repeat-containing 6, inhibitor of apoptosis 
   Survivin/BIRC5 SPU_008878 –1.63 → +1.07 Baculoviral IAP repeat-containing 5, inhibitor of apoptosis 
   RAIDD SPU_023153 –1.56 → +1.01 RIP-associated ICH1/CED3 homologous protein with death domain, Cell Extrinsic apoptosis 
   Caspase-8-like SPU_016039 –1.54 → +1.01 Cysteine protease, cell extrinsic apoptosis 
Biomineralization    
   cyclophilin 2 SPU_007484 –1.53 → –1.07 Peptidylpropyl cis-trans isomerases 
   Other cyclophilins SPU_008305 –1.61 → +1.02 Peptidylpropyl cis-trans isomerases 
   MSP130 SPU_013821 –1.58 → –1.01 Primary mesenchyme cell (PMC)-specific protein 
   MSP130-related 3 SPU_013823 –1.65 → –1.01 PMC-specific protein 
   COLP3α SPU_003768 –1.53 → –1.02 Most abundant collagen in PMCs, non-fibrillar collagen 
   COLP4α SPU_015708 –1.69 → +1.07 Next most abundant collagen, non-fibrillar collagen 
   Other collagens SPU_009076 –1.56 → +1.00 Mostly fibrillar collagens 
   Other collagens SPU_022116 –1.63 → +1.05 Mostly fibrillar collagens 
   P19 SPU_004136 –1.65 → +1.05 PMC-specific protein 
   P16 SPU_018408 –1.55 → –1.06 PMC-specific protein essential for skeletal rod elongation 
   P16-like SPU_018405 –1.60 → +1.03 PMC-specific protein essential for skeletal rod elongation 
   osteonectin SPU_028275 –1.61 → 1.00 Glycoprotein that binds calcium 
   Runt-1 SPU_025612 –1.66 → +1.01 Transcription factor, triggers differentiation of skeletogenic cells 
Cell cycle    
   Cdc27/Apc3 SPU_022322 –1.59 → +1.04 Anaphase promoting complex 3, ubiquitin-proteolysis pathway 
   MCM4 SPU_024515 –1.59 → +1.04 Mini chromosome maintenance 4 
   Psf2 SPU_021616 –1.52 → +1.01 DNA replication complex GINS protein 
   Chk2 SPU_004975 –1.60 → –1.06 Checkpoint kinase 2 
   Cyclin T SPU_021812 –1.58 → –1.01 CDK regulatory subunit involved in transcription 
   SMC4 SPU_013617 –1.74 → +1.11 Structural maintenance of chromosome 4 
   CDK8 SPU_001690 –1.56 → +1.02 Cyclin-dependent kinase, initiates transcription 
   CDK1 SPU_002210 –1.53 → 1.00 Cyclin-dependent kinase, regulates mitosis 
Cellular stress response    
   Protein homeostasis    
      NSFL1C SPU_015012 –1.66 → –1.04 p97 ATPase cofactor p47, protein degradation 
      PSMC3 SPU_003847 –1.63 → +1.01 26S proteasome subunit, protein degradation 
      Hsp40A SPU_016562 –1.52 → 1.00 40kDa Heat shock protein, co-chaperone of Hsp70 
   Antioxidant defense    
      MGST-3 SPU_016492 –1.84 → –1.01 Glutathione S-transferase, microsomal 
      GST pi SPU_017373 –1.66 → +1.08 Glutathione S-transferase, cytosolic 
   Toxicant, metal and xenobiotic defense    
      Cyp3-like 16 SPU_014092 –1.74 → –1.03 Cytochrome P450 monooxygenase 
      Cyp2-like9 SPU_003606 –1.77 → +1.03 Cytochrome P450 monooxygenase 
      Tf SPU_026949 –1.65 → +1.03 Homolog of transferrin, metal detoxification 
      Ugt1-like SPU_012199 –1.68 → +1.06 UDP glucuronosyltransferase 
      Shr2 SPU_008117 –1.58 → +1.04 Nuclear receptor that binds estradiol 
Development    
   Wnt8 SPU_020371 –1.52 → –1.02 Component of gene regulatory network (GRN) that controls differentiation of Skeletogenic micromeres 
   Blimp1 SPU_027235 –1.68 → –1.05 Stabilizes the GRN thru its interaction with Wnt8 
   Smad1/5/8 SPU_020722 –1.77 → +1.09 Regulation of transcription, DNA dependent 
   GataE SPU_010635 –1.58 → +1.01 GATA-binding transcription factor E, stabilizes GRN 
   Smad5 SPU_000739 –1.55 → –1.01 Regulation of transcription, DNA dependent 
   PKS-like SPU_002895 –1.55 → –1.05 Polyketide synthase, involved in pigmentation 
   Ap4 SPU_003179 –1.56 → +1.01 Regulation of transcription 
   Dac SPU_028061 –1.55 → +1.01 Regulation of transcription, anatomical stru 
Kinome    
   MLCKa SPU_023876 –1.55 → –1.02 Myosin light chain kinase 
   MLCKc SPU_019751 –1.54 → –1.01 Myosin light chain kinase 
   MAPKAPK5b SPU_028463 –1.73 → +1.10 Mitogen-activated protein kinase signaling 
   NLK SPU_010846 –1.60 → +1.03 Nemo-like kinase 
Metabolism – energy metabolism    
   Tricarboxylic acid cycle    
      Suclg1 SPU_025397 –1.90 → –1.01 Succinyl-CoA synthetase, LG uses GTP 
      Idh3a SPU_027710 –1.66 → +1.01 Isocitrate dehydrogenase 3a 
      Idh3g SPU_002807 –1.65 → +1.03 Isocitrate dehydrogenase 3g 
      Sdhb SPU_026295 –1.70 → +1.09 Succinate dehydrogenase b 
      Aco2a SPU_005839 –1.40 → –1.10 Aconitase 2a, mitochondrial 
   Electron transport chain    
      Atp5d SPU_028873 –1.61 → –1.09 ATP synthase, H+ transporting, F1 complex 
      Atp5f1 SPU_000022 –1.62 → +1.02 ATP synthase, H+ transporting, F0 complex 
      Atp5i SPU_001183 –1.57 → –1.01 ATP synthase, H+ transporting, F0 complex 
      Ndufs6 SPU_019206 –1.60 → –1.04 NADH dehydrogenase (ubiquinone) Fe-S protein 6 
      Ndufv2 SPU_026881 –1.66 → +1.08 NADH dehydrogenase (ubiquinone) flavoprotein 2 
      Ndufa12 SPU_002128 –1.70 → +1.09 NADH dehydrogenase 
      Uqcrh SPU_013225 –1.58 → –1.05 Cytochrome c reductase, hinge protein 
      Cox4i1 SPU_014478 –1.62 → +1.06 Cytochrome c oxidase 
   Mitochondrial membrane transporters    
      Slc25a5 SPU_004813 –1.86 → –1.18 ADP, ATP carrier protein 2, energy transfer 
      Slc25a3 SPU_009872 –1.70 → –1.01 Phosphate carrier, energy transfer 
   Other metabolism genes    
      HMGcs1 SPU_007114 –1.53 → –1.03 Hydroxymethylglutaryl-CoA synthase 1, lipid biosynthesis 
      Acs-like 1 SPU_012875 –1.51 → –1.03 Acyl-CoA synthetase, lipid biosynthesis 
      Slc23a2 SPU_009217 –1.44 → –1.06 Na+/l-ascorbic acid transporter, vitamin C transport 
   Protein synthesis – translational control    
      elF2Bβ SPU_004173 –1.70 → –1.04 Translation factor – initiation 
      elF2γ SPU_020412 –1.51 → –1.01 Translation factor – initiation 
      elF3e SPU_007226 –1.60 → +1.05 Translation factor – initiation 
      elF3j SPU_013398 –1.80 → –1.08 Translation factor – initiation 
      elF3k SPU_010303 –1.67 → +1.06 Translation factor – initiation 
      elF4G SPU_024859 –1.65 → +1.07 Translation factor – initiation 
      VARS-B SPU_002908 –1.55 → –1.02 Translation factor – elongation 
      VARS-A SPU_008058 –1.62 → +1.03 Translation factor – elongation 
      PABPN1 SPU_028828 –1.44 → –1.07 Translation factor – termination 
      hnRNP K SPU_008011 –1.64 → +1.02 IRES-dependent translation 
      PTB SPU_000961 –1.65 → +1.05 IRES-dependent translation 

Data are presented as the upper (FCUL) and lower (FCLL) limits of fold change

Close Modal

or Create an Account

Close Modal
Close Modal