Table 1.

Summary of NPM-ALK Interacting Proteins Identified by TAP LC-ESI MS/MS and Grouped Based on their Major Biological Functions

Protein Name (frequency, # of peptides)*
Apoptosis
PI3-kinase p85subunit beta (1,3)†; PI3-kinase p85subunit alpha (2,3)†; PI3-kinase p110 subunit beta (1,1)†; Death effector domain-containing protein (1,1); TNF receptor-associated fact3or 2 (1,1); 250 kd substrate of Akt (1,1); C-jun-amino-terminal kinase-interacting protein 4 (1,2); Vesicle-associated membrane protein-associated protein A (1,1); Cisplatin resistance-associated overexpressed protein (CROP) (1,2); Alpha-actinin-1 (1,3); Peroxiredoxin-2 (1,2); Protein kinase C inhibitor protein 1 (1,1); Seladin-1 (1,2); Thioredoxin-related transmembrane protein (1,1); Zinc finger FYVE domain-containing protein 1 (1,2); Cytochrome c oxidasepolypeptide II (2,1); Bcl-2-associated transcription factor 1 (2,7); Heat shock protein 60 (3,25)†; Protein LL5-beta (1,1); Zincfinger FYVE domain-containing protein 2 (1,1); Serine protease11 (2,1)
Signal transduction
SH3 domain protein 2B (1,3); JAK2 (1,1)†; SLIT-ROBO Rho GTPase-activating protein 1 (2,1); Ras-related protein Rab-10 (1,1); Ras-related protein Rab-2A (1,1); Ras-related protein Rab-14 (1,2); Ras-related protein Rab-7a (1,5); Ran GTPase-activating protein 1 (1,1); Ras-related protein Rab-6A (1,1); Ras-related protein Ral-A precursor (1,1); Ras-related protein Rab-19 (1,1); Ras-related protein Rab-21 (1,1); Ras-related protein Rab-1B (1,3); Ras GTPase-activating-like protein IQGAP1 (1,1); GPI transamidase (1,1); SH2/SH3adapter GRB2 (1,5)†; MAPkinase-activated protein kinase 1b (1,1); SAM68 (1,1); Insulin receptor substrate 1 (1,1)†; 5-hydroxytryptamine receptor 2A (1,1); IL-18 receptoraccessory protein (2,1); AMPK beta-1 chain (1,1); G patch domain-containing protein 8 (1,3); Conserved ERA-likeGTPase (1,1); PDZ-RhoGEF (1,1); Neurotrophic tyrosine kinase receptor type 1 (1,1); Rac3(1,2); ADP-ribosylation factor 6 (1,1); ADP-ribosylation factor-like protein 1 (1,1); ADP-ribosylation factor-like protein 3 (1,1); ADP-ribosylation factor 4 (1,1); Periodic tryptophan protein 2 homolog (1,1); Creatine kinase B-type (1,1); 14–3-3 protein theta (1,1); MARCKS-related protein (1,1); STIM1(1,3); Serine/threonine/tyrosinekinase 1 (1,1); SR-beta (1,1); Stonin-2 (1,1); Transmembrane protein 161A precursor (1,1); Kinesin-like protein KIF13B (1,1); UNR protein (1,1); A-Raf proto-oncogene serine/threonine-protein kinase (1,1); MEK kinase kinase 4 (1,1)†; MEK kinase 2 (1,1)†; ATPase family AAA domain-containing protein 3A (2,9); ATPase family AAA domain-containing protein 3B (1,1)
Biogenesis
Nucleoplasmin-3 (1,3); Acyl-CoA thioesterase 9 (1,2); Mitochondrial chaperone BCS1 (1,1); Methionine synthase reductase (1,1); Polyadenylate-binding protein 3 (1,1); Retinol dehydrogenase 11 (1,1); Oligosaccharyl transferase subunit STT3B (1,1); STT3-A (2,3); Phosphonoformate immuno-associated protein3 (1,1); NADH-cytochrome b5 reductase 3 (1,1); mPR (1,1); Medium-chain specific acyl-CoA dehydrogenase (1,1); E2K (1,1); Thermostable phenol sulfotransferase (2,2); HDL-bindingprotein (1,2); Glutamate carboxypeptidase 2 (1,1); Alpha-mannosidase 2 (1,1); 17-beta-hydroxysteroid dehydrogenase 4 (1,1); Dihydrolipoamide dehydrogenase (1,1); Peroxin-1 (1,1); Peroxiredoxin-6 (1,5); Adrenodoxin reductase (2,1); PMP70 (1,2); Protoporphyrinogen oxidase (1,1); Ribosome biogenesis protein BOP1 (1,1); Sra-1 (1,1); Dipeptidyl peptidase 9 (2,1); Mitochondrial malonyltransferase (2,2); Palladin (1,1); OSBP-related protein 11 (1,4); OSBP-related protein 10 (1,1); OSBP-related protein 9 (1,3); PRA1 family protein 3 (1,1); PRA1 family protein 2 (1,1); Collagen/fibrinogen domain-containing protein 3 (2,1); Adenine; phosphoribosyltransferase (1,3); Phosphoglucomutase-2 (1,1); NOC3-likeprotein (1,1); Synaptic vesicle membrane protein VAT-1 homolog (1,1); DPM1 synthase (1,2)
Proteasome degradation
26S proteasomeregulatory subunit S9 (1,1); E3 SUMO-protein ligase PIAS2 (1,1); E3 ubiquitin-protein ligase CNOT4 (1,1); BAG family molecular chaperone regulator 2 (1,2); Heat shock protein HSP 90-alpha (1,9); Ubiquitin-activating enzyme E1 (1,2); Ubiquitin carboxyl-terminal hydrolase 5 (1,1); Proteasome activator complex subunit 3 (1,1); Hsp90 co-chaperone Cdc37 (1,1); E3 ubiquitin-protein ligase (2,1); Ubiquitin-associated protein 2 (1,1); E3 ubiquitin-protein ligase UBR2 (1,1); E3 ubiquitin-protein ligase RNF216 (1,1); Sentrin/SUMO-specificprotease SENP1 (2,1); Ubiquitin-like product Chap1/Dsk2 (1,1); Proteasome regulatory particle non-ATPase 13 (1,1); SUMO-1-specific protease 3 (1,1); PAB-dependent poly(A)-specific ribonuclease subunit 2 (1,1); F-box only protein 28 (1,1); Heat shock 70 kd protein 1 (3,13)
Cell cycle
Fe65protein (1,1); WD repeat-containing protein 39 (1,1); ROD1 (1,1); FGFR2 (1,1); SHC-transforming protein 1 (2,4)†; Cyclin-dependent kinase 9 (1,1); Cell division cycle protein 20 homolog (1,1); 82Fip (2,15); Protein TBRG4 (1,1); E2-induced gene 3 protein (2,2); GTP-binding protein NGB (2,4); DHPprotein (1,1); Centromere protein J (1,1); Uncharacterized protein C2orf29 (1,1); TP53-target gene 5 protein (1,1); Interferon-related developmental regulator 1 (1,1); IFIT1 (1,1); Putative helicase MOV-10 (1,1); Cyclin G-associated kinase (2,4)†; Puromycin-sensitive aminopeptidase (1,1); La-related protein 7 (1,3); DLK (1,1); Adipocyte plasma membrane-associated protein (1,1); Tyrosine-protein kinase Lyn (1,1)†
DNA Repair
KU86 (1,1); KU70 (1,1); PCNA (2,5); FACT complex subunit SPT16 (1,1); DNA mismatch repair protein MSH2 (1,1); PARP-1 (2,2); DNA replication licensing factor MCM6 (2,4); Phosphorylation; Cell division cycle 2-related protein kinase 7 (1,1); PP2A-beta (1,1)†; Serine/threonine-protein kinase PCTAIRE-3 (1,1); Non-receptor tyrosine-protein kinase TNK1 (1,1); PRP4 kinase (1,1); Cyclin-T1 (2,3); mTOR (1,1)†; Phosphorylase kinasesubunit beta (1,1); PSK-C3 (1,1); Hisdomain-containing protein tyrosine phosphatase (1,2); Pyrophosphatase SID6–306 (1,1)
DNA and RNA processing
NFkB-repressing factor (1,2); Interleukin-1 receptor-associated kinase 1 (1,1); eIF-4G1 (1,4); TAFII-150 (1,1); Hic-2 (1,1); MBP-1 (3,14); CREB/ATF bZIP transcription factor (1,1); LanC-like protein 2 (1,1); Bromodomain adjacent to zinc finger domain protein 1B (1,1); Prohibitin-2 (2,2); Pre-mRNA-splicing factorSRP20 (1,1); Seryl-tRNA(Ser/Sec)synthetase (1,1); Transcription factor AP-1 (1,1)†; EIF-2A (1,1); snRNP-B (2,1); Arginine/serine-rich-splicing factor 14 (1,1); LIM domain-containing protein 1 (1,1); RNase inhibitor (1,1); Glycine–tRNA ligase (1,1); Alanine–tRNAligase (1,2); hRPB8 (1,1); RNase L inhibitor (1,3); PPAR-binding protein (1,1); TAFII-20/TAFII-15 (1,1); Chromosome-associated protein H (1,1); Pre-mRNA 3′-end-processing factor FIP1 (2,1); Proline–tRNA ligase (1,1); ATP-dependent RNA helicase DDX4 (1,9); S1 RNA-binding domain-containing protein 1 (1,1); CPSF 59 kDasubunit (1,2); Putative ribosomal RNA methyltransferase 1 (1,1); Nucleolar RNA helicase 2 (1,2); Splicing factor 45 (1,1); Bic-D 1 (1,1); Zinc finger and SCAN domain-containing protein 29 (1,1); Probable ATP-dependent RNA helicase DHX40 (1,1); Pumilio-2 (1,1); TBR-1(1,1); Zinc finger protein 768 (1,2); Exportin-5 (1,1); Probable helicase with zinc finger domain (1,4); Paraspeckle protein 1 (2,2); Zinc finger protein 503 (1,1)
Transport
AIP (1,1); Importin-8 (1,1); Nucleoprotein TPR (1,3); Rab-11 (1,2); E3 SUMO-protein ligase RanBP2 (1,1); Nup98 (2,3); Sec61 alpha-1 (1,1); mRNA export factor (1,1); hNup188 (1,2); eIF4Etransporter (1,1); Aladin (1,4); Transportin-1 (1,1); ATP-dependent RNA helicase DDX19A (1,1); Cyclin-M1 (1,1)†; SERCA3 (1,1); Probable cation-transporting ATPase 13A1 (1,1); Zinc transporter ZIP10 precursor (1,2); Kinesin-like protein KIF1B (1,1); Zeta-1 COP (1,1); Elongation factor G 1 (1,1); ERGIC-32 (1,1)
Others
Myomesin-1 (1,1); TP alpha (1,1); WD repeat-containing protein 62 (1,1); WD repeat-containing protein 6 (1,3); WD and tetratricopeptide repeats protein 1 (1,1); EF-hand domain-containing protein C17orf57 (2,1); Plastin-3 (1,2); MHC class I antigen Cw*7 (1,1); YTH domain family protein 3 (1,1); Hornerin (1,1); DSEL (1,1); Dermatan-sulfate epimerase-like protein precursor (2,2); Protein FAM10A5 (1,1); Tumor antigen BJ-HCC-21 (1,2); Synapse-associated protein 1 (1,1); Collagen alpha-1(XII) chain precursor (1,1); Protein EHM2 (1,1); Dynamin-3 (1,1); Neighbor of COX4 (1,1); FAST kinase domain-containing protein 5 (1,1)

^*Frequency refers to the number of times a protein was identified in three independent sample replicates (i.e., 2 means the protein was identified two times out of the three samples analyzed); # of peptides refers to the combined number of peptides identified for the protein in all three samples. 

^†Previously reported.