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Table 1 DEGs clustered by their functional similarities based on GO annotation of D. melanogaster homologs and protein motifs described in Pfam database.

From: Molecular determinants of caste differentiation in the highly eusocial honeybee Apis mellifera

Functional Group Official_set_ID Scaffold_ID Gene_name Flybase_ID M Pfam description
Growth (1)       
Protein folding (1.1)       
  GB16563 Group6.34 Trap1-PA CG3152 Q(1.00) Hsp90 protein
       Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
  GB10587 Group13.6 Cct5-PA CG8439 Q(0.95) TCP-1/cpn60 chaperonin family
  GB12619 Group7.16 CG14894-PA CG14894 Q(0.57) Tetratricopeptide repeat
  GB12215 Group4.18 CG8863-PD CG8863 Q(0.52) DnaJ central domain (4 repeats)
DNA binding (1.2)       
  GB12948 GroupUn.293 His3.3A-PA CG5825 Q(0.47) Core histone H2A/H2B/H3/H4
  GB18508 Group2.39 skpA-PE CG16983 Q(0.42) Skp1 family, dimerisation domain
       Skp1 family, tetramerisation domain
  GB19338 Group10.29 crc-PB CG8669 W(0.29) bZIP transcription factor
  GB17426 Group3.15 Sirt6-PA CG6284 W(0.48) Sir2 family
Endopeptidase (1.3)       
  GB18440 Group13.4 Rpn6-PA CG10149 Q(0.69) PCI domain
  GB15218 Group5.21 Pros26.4-PA CG5289 Q(0.40) ATPase family associated with various cellular activities (AAA)
  GB11260 GroupUn.696 Rpn5-PA CG1100 Q(0.38) PCI domain
  GB19406 Group2.43 Rpn7-PA CG5378 Q(0.43) PCI domain
Constituents of ribosome (1.4)       
  GB15503 Group15.29 RpL4-PA CG5502 Q(0.46) Ribosomal protein L4/L1 family
  GB14287 Group7.1 mRpL45-PA CG6949 Q(0.37) Tim 44-like domain
  GB13769 Group8.29 mRpS22-PA CG12261 Q(0.35) --
Protein binding(1.5)       
  GB17469 Group4.23 shot-PG CG18076 W(0.42) Spectrin repeat
       Growth-Arrest-Specific Protein 2 Domain
       Plectin repeat
       EF hand
  GB11456 Group12.27 CREG-PA CG5413 W(0.63) --
  GB14059 GroupUn.5456 Nap1-PA CG5330 Q(0.30) Nucleosome assembly protein (NAP)
  GB19591 GroupUn.549 CG5742-PA CG5742 Q(0.24) Ankyrin repeat
Other proteins (1.6)       
  GB12179 Group3.19 Gyc76C-PC CG8742 Q(0.18) Adenylate and Guanylate cyclase catalytic domain
       Receptor family ligand binding region
       Protein kinase domain
       Protein tyrosine kinase
  GB13416 Group1.40 Trip1-PA CG8882 Q(0.49) WD domain, G-beta repeat
  GB16844 Group5.30 Ef1alpha100E-PC CG1873 Q(0.62) Elongation factor Tu GTP binding domain
       Elongation factor Tu C-terminal domain
       Elongation factor Tu domain 2
  GB18599 Group8.14 CG6287-PA CG6287 Q(0.46) D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
       D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
  GB20148 Group8.12 pyd3-PA CG3027 Q(1.60) Carbon-nitrogen hydrolase
  GB13298 Group3.35 Gasp-PA CG10287 Q(1.07) Chitin binding Peritrophin-A domain
  GB18138 Group15.29 tws-PE CG6235 Q(0.37) WD domain, G-beta repeat
  GB11086 Group10.31 tor-PA CG8274 Q(0.34) TPR/MLP1/MLP2-like protein
  GB11665 GroupUn.5677 Idgf4-PB CG1780 W(0.58) Glycosyl hydrolases family 18
Neurogenesis (2)       
  GB17219 Group4.23 dac-PC CG4952 W(0.28) SKI/SNO/DAC family
  GB18802 Group2.40 Atx2-PB CG5166 W(0.37) Ataxin-2 N-terminal region
  GB17469 Group4.23 shot-PG CG18076 W(0.42) Spectrin repeat
       Growth-Arrest-Specific Protein 2 Domain
       Plectin repeat
       EF hand
  GB17380 Group3.22 fax-PC CG4609 W(0.57)  
  GB14127 Group2.32 CRMP-PB CG1411 W(1.25) Amidohydrolase family
  GB12585 Group14.24 Eph-PE CG1511 W(0.24) Protein tyrosine kinase
       Ephrin receptor ligand binding domain
       Protein kinase domain
       Fibronectin type III domain
       SAM domain (Sterile alpha motif)
       GCC2 and GCC3
  GB19338 Group10.29 crc-PB CG8669 W(0.29) bZIP transcription factor
  GB14751 Group2.38 Tsp5D-PA CG4690 W(0.44) Tetraspanin family
Leg development (3)       
  GB18685 GroupUn.154 Gug-PC CG6964 W(0.49) Atrophin-1 family
       Myb-like DNA-binding domain
  GB17219 Group4.23 dac-PC CG4952 W(0.28) SKI/SNO/DAC family
  GB19338 Group10.29 crc-PB CG8669 W(0.29) bZIP transcription factor
  GB18802 Group2.40 Atx2-PB CG5166 W(0.37) Ataxin-2 N-terminal region
Apoptosis and ovary dev. (4)       
Protein binding (4.1)       
  GB16563 Group6.34 Trap1-PA CG 3152 Q(1.0 0) Hsp90 protein
  GB10850 GroupUn.303 l(2)tid-PC CG5504 Q(0.42) DnaJ C terminal region
       DnaJ domain
       DnaJ central domain (4 repeats)
  GB18249 Group4.15 eff-PA CG7425 Q(0.36) Ubiquitin-conjugating enzyme
  GB10667 Group15.32 Gl-PA CG9206 Q(0.41) CAP-Gly domain
Other proteins (4.2)       
  GB16903 Group8.23 cathD-PA CG1548 W(0.99) Eukaryotic aspartyl protease
  GB18912 Group1.14 26-29-p-PA CG8947 W(0.49) Papain family cysteine protease
       Cathepsin propeptide inhibitor domain (I29)
  GB15106 Group13.9 CG11159-PA CG11159 W(0.57) C-type lysozyme/alpha-lactalbum in family
  GB18802 Group2.40 Atx2-PB CG5166 W(0.37) Ataxin-2 N-terminal region
  GB10394 Group3.12 Traf1-PA CG3048 W(0.36) TRAF-type zinc finger
       MATH domain
  GB11086 Group10.31 tor-PA CG8274 Q(0.34) TPR/M LP1/M LP2-like protein
Cytoskeleton and others (5)       
Cytoskeleton proteins (5.1)       
  GB11965 Group8.46 Mhc-PB CG17927 W(0.36) Myosin tail
       Myosin head (motor domain)
  GB17681 Group7.42 Act5C-PB CG4027 W(0.38) Actin
  GB16881 Group6.3 up-PG CG7107 W(0.30) --
  GB17469 Group4.23 shot-PG CG18076 W(0.42) Spectrin repeat
       Growth-Arrest-Specific Protein 2 Domain
       Plectin repeat
       EF hand
  GB19016 Group1.21 lva-PC CG6450 W(0.52) --
  GB10337 Group4.18 Ank2-PB CG7462 W(0.61) Ankyrin repeat
       ZU5 domain
       Death domain
Transcription associated prot. (5.2)       
  GB15645 Group11.31 NFAT-PA CG11172 W(0.71) Rel homology domain (RHD)
       IPT/TIG domain
  GB16648 Group9.18 usp-PA CG4380 W(0.20) Ligand-binding domain of nuclear hormone receptor
       Zinc finger, C4 type (two domains)
  GB19023 Group2.33 Hcf-PD CG1710 W(0.42) Kelch motif
       Fibronectin type III domain
Other proteins (5.3)       
  GB10771 GroupUn.3863 Jheh1-PA CG15101 W(0.46) Epoxide hydrolase N terminus
       alpha/beta hydrolase fold
  GB11059 Group8.20 RfaBp-PA CG11064 W(0.49) Lipoprotein amino terminal region
       von Willebrand factor type D domain
       Domain of Unknown Function (DUF1081)
  GB17439 Group3.31 Scs-fp-PC CG17246 W(0.59) FAD binding domain
       Fumarate reductase/succinate dehydrogenase flavoprotein C-terminal domain
  GB16882 Group16.12 wal-PA CG8996 Q(0.51) Electron transfer flavoprotein FAD-binding
       Electron transfer flavoprotein domain
  GB12827 GroupUn.5348 Dox-A2-PA CG10484 Q(0.42) PCI domain
  GB10658 Group14.24 l(3)neo18-PA CG9762 W(0.70) --
JH responsive (6)       
Metabolic enzymes (6.1)       
  GB19085 Group13.10 CG9009-PA CG9009 Q(1.10) AM P-binding enzyme
  GB16747 Group4.23 CG17323-PA CG17323 Q(0.46) UDP-glucoronosyl and UDP-glucosyl transferase
  GB15619 Group2.43 CG8036-PC CG8036 Q(0.33) Transketolase, thiamine diphosphate binding domain
       Transketolase, pyridine binding domain
       Transketolase, C-terminal domain
  GB13982 Group13.10 Faa-PA CG14993 W(0.34) Fumarylacetoacetate (FAA) hydrolase family
  GB14870 Group13.13 CG31472-PB CG31472 W(0.38) Pyridoxamine 5'-phosphate oxidase
  GB13626 GroupUn.593 CG6206-PB CG6206 W(0.40) Glycosyl hydrolases family 38 N-terminal domain
       Glycosyl hydrolases family 38 C-terminal domain
  GB19030 Group15.25 CG10638-PA CG10638 W(0.60) Aldo/keto reductase family
  GB19460 Group1.18 Ald-PB CG6058 W(0.86) Fructose-bisphosphate aldolase class-I
  GB17864 GroupUn.36 CG7920-PA CG7920 W(0.90) Acetyl-CoA hydrolase/transferase
  GB13401 Group6.55 CG9629-PA CG9629 W(1.70) Aldehyde dehydrogenase family
Carrier activity (6.2)       
  GB14751 Group2.38 Tsp5D-PA CG4690 W(0.44) Tetraspanin family
  GB12135 Group1.65 CG1213-PC CG1213 Q(0.76) Sugar (and other) transporter
       Major Facilitator Superfamily
  GB13781 Group15.34 CG33528-PC CG33528 Q(0.58) Major Facilitator Superfamily
  GB17499 Group7.37 sesB-PC CG16944 Q(0.57) Mitochondrial carrier protein
Protein binding (6.3)       
  GB13815 Group11.41 Cdep-PC CG31536 Q(0.72) FERM domain (Band 4.1 family)
       PH domain
  GB18087 Group1.59 Nacalpha-PC CG8759 Q(0.47) NAC domain
  GB10836 Group2.22 Hsc70Cb-PC CG6603 Q(0.44) Hsp70 protein
  GB19860 Group1.82 Hsc70-5-PA CG8542 Q(0.42) Hsp70 protein
  GB18197 Group16.15 CAP-PC CG18408 Q(0.53) SH3 domain
  GB10587 Group13.6 Cct5-PA CG8439 Q(0.31) TCP-1/cpn60 chaperonin family
Nucleic acid binding (6.4)       
  GB15755 Group5.12 RpS11-PC CG8857 Q(0.61) Ribosomal protein S17
  GB15503 Group15.29 RpL4-PA CG5502 Q(0.39) Ribosomal protein L4/L1 family
  GB20034 GroupUn.1172 CG8108-PB CG8108 Q(0.32) --
Other proteins (6.5)       
  GB12348 Group12.16 CG31952-PA CG31952 Q(0.91) --
  GB14145 Group3.14 uzip-PA CG3533 Q(0.49) --
  GB19075 Group5.26 CG3153-PA CG3153 Q(0.28) ML domain
  GB19923 Group16.6 Cp1-PC CG6692 W(0.42) Papain family cysteine protease
       Cathepsin propeptide inhibitor domain (I29)
  GB11059 Group8.20 RfaBp-PA CG11064 W(0.74) Lipoprotein amino terminal region
       von Willebrand factor type D domain
       Domain of Unknown Function (DUF1081)
  GB18626 GroupUn.41 Ccp84Ad-PA CG2341 Q(1.53) Insect cuticle protein
Hormone + caste (7)       
JH24htreat+QL4 GB19085 Group13.10 CG9009-PA CG9009 Q(1.1) AMP-binding enzyme
JH24htreat+QL4 GB10836 Group2.22 Hsc70Cb-PC CG6603 Q(0.44) Hsp70 protein
JH24htreat+QL4 GB19860 Group1.82 Hsc70-5-PA CG8542 Q(0.42) Hsp70 protein
JH24htreat+QL4 GB15503 Group15.29 RpL4-PA CG5502 Q(0.39) Ribosomal protein L4/L1 family
JH24htreat+QL4 GB15619 Group2.43 CG8036-PC CG8036 Q(0.33) Transketolase, thiamine diphosphate binding domain
       Transketolase, pyridine binding domain
       Transketolase, C-terminal domain
JH24htreat+QL4 GB10587 Group13.6 Cct5-PA CG8439 Q(0.31) TCP-1/cpn60 chaperonin family
JH24hcontrol+WL4 GB13401 Group6.55 CG9629-PA CG9629 W(1.70) Aldehyde dehydrogenase family
JH24hcontrol+WL4+WS2 GB16686 Group15.25 no similarity   W(0.96) --
JH24hcontrol+WL4 GB16631 Group16.12 no reciprocal   W(0.74) Leucine Rich Repeat
JH24hcontrol+WL4 GB11059 Group8.20 RfaBp-PA CG11064 W(0.44) Lipoprotein amino terminal region
       von Willebrand factor type D domain
       Domain of Unknown Function (DUF1081)
  1. M = log2 of the gene expression differences between developing queen and worker samples (based on microarray experiments). W = worker, Q = queen