Table 1 Summary of the C9orf72 and SMCR8 protein interactomes and selected functional categories
Gene Name | Protein Name | Total # Spectra | |
|---|---|---|---|
RNase | |||
- | + | ||
A. C9orf72-FL | |||
 C9orf72 | chromosome 9 open reading frame 72 | 108 | 103 |
TOP 20 C9orf72-INTERACTING PROTEINS | |||
  SMCR8 | Smith-Magenis syndrome chromosome region, candidate 8 | 165 | 217 |
  WDR41 | WD repeat domain 41 | 69 | 85 |
  FLG2 | filaggrin family member 2 | 33 | 6 |
  LRPPRC | leucine rich pentatricopeptide repeat containing | 23 | 25 |
  IARS | isoleucyl-tRNA synthetase | 21 | 22 |
  SERPINB3 | serpin family B member 3 | 21 | 0 |
  CALML5 | calmodulin like 5 | 20 | 0 |
  HADHA | hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase, alpha subunit | 18 | 14 |
  CDSN | corneodesmosin | 17 | 8 |
  EEF2 | eukaryotic translation elongation factor 2 | 15 | 18 |
  FABP5 | fatty acid binding protein 5 | 15 | 0 |
  COPB1 | coatomer protein complex subunit beta 1 | 14 | 14 |
  DSC1 | desmocollin 1 | 14 | 15 |
  U2AF2 | U2 small nuclear RNA auxiliary factor 2 | 14 | 6 |
  LUC7L3 | LUC7 like 3 pre-mRNA splicing factor | 13 | 4 |
  EIF2S3 | eukaryotic translation initiation factor 2 subunit gamma | 12 | 10 |
  HNRNPH2 | heterogeneous nuclear ribonucleoprotein H2 | 12 | 9 |
  KHDRBS1 | KH RNA binding domain containing, signal transduction associated 1 | 12 | 6 |
  PSMC2 | proteasome 26S subunit, ATPase 2 | 12 | 25 |
B. FL-SMCR8 | |||
 SMCR8 | Smith-Magenis syndrome chromosome region, candidate 8 | 1135 | 1182 |
TOP 25 SMCR8-INTERACTING PROTEINS | |||
  DNAJA1 | DnaJ heat shock protein family member A1 | 70 | 76 |
  GTF2I | general transcription factor IIi | 55 | 61 |
  CAD | carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase | 62 | 48 |
  ATP1A1 | ATPase Na+/K+ transporting subunit alpha 1 | 38 | 46 |
  EPRS | glutamyl-prolyl-tRNA synthetase | 36 | 40 |
  MAGED1 | MAGE family member D1 | 26 | 33 |
  WDR41 | WD repeat domain 41 | 32 | 33 |
  DNAJC7 | DnaJ heat shock protein family member C7 | 30 | 32 |
  SLC25A3 | solute carrier family 25 member 3 | 22 | 32 |
  STUB1 | STIP1 homology and U-box containing protein 1 | 30 | 31 |
  GCN1 | GCN1, eIF2 alpha kinase activator homolog | 37 | 30 |
  DDB1 | damage specific DNA binding protein 1 | 31 | 29 |
  DYNC1H1 | dynein cytoplasmic 1 heavy chain 1 | 38 | 29 |
  CHD4 | chromodomain helicase DNA binding protein 4 | 13 | 28 |
  SLC25A11 | solute carrier family 25 member 11 | 14 | 28 |
  RANBP2 | RAN binding protein 2 | 29 | 25 |
  RUVBL2 | RuvB like AAA ATPase 2 | 30 | 25 |
  ATP2A2 | ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 | 19 | 22 |
  DNAJA3 | DnaJ heat shock protein family member A3 | 19 | 22 |
  IARS | isoleucyl-tRNA synthetase | 18 | 22 |
  STIP1 | stress induced phosphoprotein 1 | 37 | 22 |
  COPA | coatomer protein complex subunit alpha | 23 | 20 |
  HUWE1 | HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase | 29 | 20 |
  AIFM1 | apoptosis inducing factor, mitochondria associated 1 | 18 | 18 |
  C9orf72 | chromosome 9 open reading frame 72 | 15 | 18 |
AMINOACYL-tRNA SYNTHESIS | |||
  EPRS | glutamyl-prolyl-tRNA synthetase | 40 | 13 |
  IARS | isoleucyl-tRNA synthetase | 18 | 22 |
  DARS | aspartyl-tRNA synthetase | 11 | 8 |
  MARS | methionyl-tRNA synthetase | 10 | 6 |
  RARS | arginyl-tRNA synthetase | 9 | 8 |
  LARS | leucyl-tRNA synthetase | 9 | 14 |
  QARS | glutaminyl-tRNA synthetase | 8 | 7 |
  TARS2 | threonyl-tRNA synthetase 2, mitochondrial (putative) | 6 | 4 |
  TARS | threonyl-tRNA synthetase | 4 | 0 |
  FARSA | phenylalanyl-tRNA synthetase alpha subunit | 0 | 6 |
CELL CYCLE | |||
  SMC3 | structural maintenance of chromosomes 3 | 12 | 8 |
  CDK4 | cyclin dependent kinase 4 | 5 | 0 |
  PCNA | proliferating cell nuclear antigen | 5 | 4 |
  MCM7 | minichromosome maintenance complex component 7 | 4 | 6 |
  YWHAZ | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta | 4 | 9 |
  RAD21 | RAD21 cohesin complex component | 3 | 0 |
  CDC7 | cell division cycle 7 | 3 | 0 |
  PLK1 | polo like kinase 1 | 3 | 9 |
  PPP6C | protein phosphatase 6 catalytic subunit | 3 | 0 |
  CDKN2A | cyclin dependent kinase inhibitor 2A | 0 | 3 |
  MCM2 | minichromosome maintenance complex component 2 | 0 | 4 |
  MCM5 | minichromosome maintenance complex component 5 | 0 | 4 |
  SMC1A | structural maintenance of chromosomes 1A | 0 | 4 |
HEAT SHOCK PROTEINS / CHAPERONES | |||
  DNAJA1 | DnaJ heat shock protein family member A1 | 70 | 76 |
  DNAJC7 | DnaJ heat shock protein family member C7 | 30 | 32 |
  DNAJA3 | DnaJ heat shock protein family member A3 | 19 | 22 |
  DNAJA3 | DnaJ heat shock protein family member A3 | 19 | 22 |
  HSPH1 | heat shock protein family H member 1 | 19 | 8 |
  BAG5 | BCL2 associated athanogene 5 | 18 | 11 |
  DNAJA2 | DnaJ heat shock protein family member A2 | 15 | 16 |
  BAG2 | BCL2 associated athanogene 2 | 11 | 16 |
  BAG6 | BCL2 associated athanogene 6 | 11 | 8 |
  SERPINH1 | serpin family H member 1 | 11 | 0 |
  HSPB1 | heat shock protein family B member 1 | 10 | 9 |
  MDN1 | midasin AAA ATPase 1 | 10 | 14 |
  FKBP8 | FK506 binding protein 8 | 8 | 0 |
  DNAJB6 | DnaJ heat shock protein family member B6 | 6 | 4 |
  PFDN2 | prefoldin subunit 2 | 5 | 4 |
  DNAJB1 | DnaJ heat shock protein family member B1 | 4 | 0 |
  HSPA4 | heat shock protein family A member 4 | 4 | 3 |
  HSPA4 | heat shock protein family A member 4 | 4 | 3 |
  RBBP7 | RB binding protein 7, chromatin remodeling factor | 3 | 4 |
  SERPINB3 | serpin family B member 3 | 3 | 0 |
  BAG3 | BCL2 associated athanogene 3 | 2 | 3 |
  UNC45A | unc-45 myosin chaperone A | 2 | 5 |
  DNAJB11 | DnaJ heat shock protein family member B11 | 0 | 6 |
  DNAJC10 | DnaJ heat shock protein family member C10 | 0 | 5 |
  PARK7 | Parkinsonism associated deglycase | 0 | 4 |
MISMATCH REPAIR | |||
  RFC3 | replication factor C subunit 3 | 5 | 0 |
  SSBP1 | single stranded DNA binding protein 1 | 5 | 0 |
  MSH6 | mutS homolog 6(MSH6) | 5 | 5 |
  POLD3 | DNA polymerase delta 3, accessory subunit | 2 | 3 |
  PCNA | proliferating cell nuclear antigen | 0 | 4 |
  POLD1 | DNA polymerase delta 1, catalytic subunit | 0 | 3 |
PHAGOSOME/AUTOPHAGY | |||
  DYNC1H1 | dynein cytoplasmic 1 heavy chain 1 | 38 | 29 |
  SEC16A | SEC16 homolog A, endoplasmic reticulum export factor | 14 | 12 |
  TUBB4A | tubulin beta 4A class IVa | 11 | 10 |
  IRS4 | insulin receptor substrate 4 | 10 | 13 |
  TUBB3 | tubulin beta 3 class III | 9 | 13 |
  TUBB6 | tubulin beta 6 class V | 9 | 18 |
  PPP2R1A | protein phosphatase 2 scaffold subunit Aalpha | 7 | 5 |
  CDK5 | cyclin dependent kinase 5 | 7 | 0 |
  SEC61B | Sec61 translocon beta subunit | 6 | 0 |
  HLA-A | major histocompatibility complex, class I, A | 5 | 5 |
  ANKRD28 | aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase | 5 | 5 |
  RAB1B | RAB1B, member RAS oncogene family | 5 | 0 |
  SLC3A2 | solute carrier family 3 member 2 | 4 | 8 |
  SEC24C | SEC24 homolog C, COPII coat complex component | 4 | 3 |
  TFRC | transferrin receptor | 4 | 0 |
  AP3M1 | adaptor related proteincomplex 3 Mu 1 subunit | 3 | 0 |
  PPP6C | protein phosphatase 6 catalytic subunit | 3 | 0 |
  BAG3 | BCL2 associated athanogene 3 | 2 | 3 |
  WDR5 | WD repeat domain 5 | 0 | 5 |
  YME1L1 | YME1 like 1 ATPase | 0 | 4 |
  KEAP1 | kelch like ECH associated protein 1 | 0 | 4 |
  DYNC1I2 | dynein cytoplasmic 1 intermediate chain 2 | 0 | 4 |
  CDKN2A | cyclin dependent kinase inhibitor 2A | 0 | 3 |
  HLA-B | major histocompatibility complex, class I, B | 0 | 3 |
PROTEIN PROCESSING IN THE ENDOPLASMIC RETICULUM | |||
  DNAJA1 | DnaJ heat shock protein family (Hsp40) member A1 | 70 | 76 |
  STUB1 | STIP1 homology and U-box containing protein 1 | 30 | 31 |
  HSPH1 | heat shock protein family H (Hsp110) member 1 | 19 | 8 |
  DNAJA2 | DnaJ heat shock protein family (Hsp40) member A2 | 15 | 16 |
  BAG2 | BCL2 associated athanogene 2 | 11 | 16 |
  SEC61B | Sec61 translocon beta subunit | 6 | 0 |
  RPN1 | ribophorin I | 5 | 3 |
  TXNDC5 | thioredoxin domain containing 5 | 5 | 2 |
  DNAJB1 | DnaJ heat shock protein family (Hsp40) member B1 | 4 | 0 |
  SEC24C | SEC24 homolog C, COPII coat complex component | 4 | 3 |
  DDOST | dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kD subunit | 3 | 4 |
  SSR4 | signal sequence receptor subunit 4 | 2 | 3 |
  DNAJB11 | DnaJ heat shock protein family (Hsp40) member B11 | 0 | 6 |
  DNAJC10 | DnaJ heat shock protein family (Hsp40) member C10 | 0 | 5 |
  RRBP1 | ribosome binding protein 1 | 0 | 3 |
PROTEOSOME | |||
  PSMC2 | proteasome 26S subunit, ATPase 2 | 22 | 18 |
  PSMD2 | proteasome 26S subunit, non-ATPase 2 | 18 | 10 |
  PSMA7 | proteasome subunit alpha 7 | 17 | 16 |
  PSMD11 | proteasome 26S subunit, non-ATPase 11 | 14 | 9 |
  PSMC3 | proteasome 26S subunit, ATPase 3 | 12 | 9 |
  PSMD3 | proteasome 26S subunit, non-ATPase 3 | 12 | 8 |
  PSMA5 | proteasome subunit alpha 5 | 11 | 6 |
  PSMC5 | proteasome 26S Subunit, ATPase 5 | 10 | 10 |
  PSME3 | proteasome activator subunit 3 | 10 | 11 |
  PSMA6 | proteasome subunit alpha 6 | 9 | 0 |
  PSMD6 | proteasome 26S subunit, non-ATPase 6 | 9 | 7 |
  PSMA3 | proteasome subunit alpha 3 | 8 | 3 |
  PSMD1 | proteasome 26S subunit, non-ATPase 1 | 8 | 8 |
  PSMA1 | proteasome subunit alpha 1 | 7 | 7 |
  PSMB1 | proteasome subunit beta 1 | 7 | 7 |
  PSMB5 | proteasome subunit beta 5 | 6 | 6 |
  PSMC1 | proteasome 26S subunit, ATPase 1 | 6 | 6 |
  PSMB2 | proteasome subunit beta 2 | 5 | 5 |
  PSMB6 | proteasome subunit beta 6 | 5 | 5 |
  PSMC4 | proteasome 26S subunit, ATPase 4 | 5 | 0 |
  PSMC6 | proteasome 26S subunit, ATPase 6 | 5 | 6 |
  PSMD12 | proteasome 26S subunit, non-ATPase 12 | 4 | 2 |
  PSMD7 | proteasome 26S subunit, non-ATPase 7 | 3 | 0 |
  PSMD13 | proteasome 26S subunit, non-ATPase 13 | 0 | 3 |
  PSMD14 | proteasome 26S subunit, non-ATPase 14 | 0 | 3 |
  PSMD8 | proteasome 26S subunit, non-ATPase 8 | 0 | 6 |
RNA TRANSPORT | |||
  RANBP2 | RAN binding protein 2 | 29 | 25 |
  XPO1 | exportin 1 | 13 | 13 |
  NUP93 | nucleoporin 93 | 11 | 10 |
  NUP133 | nucleoporin 133 | 10 | 15 |
  THOC2 | THO complex 2 | 9 | 6 |
  RANGAP1 | Ran GTPase activating protein 1 | 8 | 11 |
  KPNB1 | karyopherin subunit beta 1 | 7 | 5 |
  KPNA2 | karyopherin subunit alpha 2 | 6 | 4 |
  EIF4A1 | eukaryotic translation initiation factor 4A1 | 5 | 4 |
  EIF4G1 | eukaryotic translation initiation factor 4 gamma 1 | 5 | 4 |
  NUP155 | nucleoporin 155 | 4 | 6 |
  NUP210 | nucleoporin 210 | 4 | 0 |
  EIF3F | eukaryotic translation initiation factor 3 subunit F | 3 | 3 |
  FXR2 | FMR1 autosomal homolog 2 | 3 | 0 |
  NUP160 | nucleoporin 160 | 3 | 4 |
  NUP205 | nucleoporin 205 | 3 | 4 |
  EIF3E | eukaryotic translation initiation factor 3 subunit E | 2 | 4 |
  FMR1 | fragile X mental retardation 1 | 2 | 0 |
  NUP98 | nucleoporin 98 | 2 | 5 |
  NUP153 | nucleoporin 153 | 0 | 5 |
  THOC3 | THO complex 3 | 0 | 4 |
  XPOT | exportin for tRNA | 0 | 4 |
UBIQUITINATION / SUMOYLATION | |||
  STUB1 | STIP1 homology and U-box containing protein 1 | 30 | 31 |
  HUWE1 | HECT, UBA and WWE domain containing 1, E3 ubiquitin ligase | 29 | 20 |
  RANBP2 | RAN binding protein 2, E3 SUMO ligase | 29 | 25 |
  RNF40 | ring finger protein 40, E3 ubiquitin ligase | 4 | 10 |
  USP7 | ubiquitin specific peptidase 7 | 4 | 9 |
  USP9X | ubiquitin specific peptidase 9, X-linked | 4 | 5 |
  RNF2 | ring finger protein 2, , E3 ubiquitin protein ligase | 3 | 0 |
  UBR5 | ubiquitin protein ligase E3 component n-recognin 5 | 3 | 12 |
  USP15 | ubiquitin specific peptidase 15 | 3 | 0 |
  SUMO3 | small ubiquitin-like modifier 3 | 0 | 3 |
  MKRN2 | makorin ring finger protein 2, E3 ubiquitin ligase | 0 | 3 |