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PNAS 07-04849-SI Table 3. 6-18-2007

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Table 5. β-arrestin 2-interacting proteins under nonstimulated (-) condition IPI accession Swiss- Number of Prot Gene symbol Protein name experiments accession number number detected Signal transduction Adaptor proteins IPI00027355 P32121 ARRB2 β-arrestin 2 6 IPI00293857 P49407 ARRB1 β-arrestin 1 6 IPI00021353 P10523 SAG S-arrestin (Retinal S-antigen) (48 kDa protein) (S-AG) (Rod photoreceptor arrestin) 2 IPI00003917 P36575 ARR3 X-arrestin (Arrestin-C) (Cone arrestin) (cArr) (Retinal cone arrestin-3) (C-arrestin) 2 IPI00216318 P31946 YWHAB 14-3-3 β/α (14-3-3 protein beta/alpha) (Protein kinase C inhibitor protein 1) (KCIP-1) (Protein 1054) 2 IPI00220642 P61981 YWHAG 14-3-3 γ (14-3-3 protein gamma) (Protein kinase C inhibitor protein 1) (KCIP-1) 2 IPI00018146 P27348 YWHAQ 14-3-3 θ (14-3-3 protein tau) (14-3-3 protein theta) (14-3-3 protein T-cell) (HS1 protein) 2 IPI00216319 Q04917 YWHAH 14-3-3 η (14-3-3 protein eta) (Protein AS1) 2 IPI00000816 P62258 YWHAE 14-3-3 ε (14-3-3 protein epsilon) (14-3-3E) 2 Protein kinases IPI00027251 Q15208 STK38 STK38 (Serine/threonine-protein kinase 38) (NDR1 protein kinase) (Nuclear Dbf2-related kinase 1) 4 SCY1-like 2 (SCY1-like 2 protein) (coated vesicle-associated kinase of 104 kDa) (Eukaryotic protein IPI00396218 Q6P3W7 SCYL2 2 kinase family protein) (CDNA FLJ10074 fis, clone HEMBA1001744, weakly similar to SCY1 IPI00013835 Q13574 DGKZ DGK ζ (Diacylglycerol kinase zeta) (Diglyceride kinase zeta) (DGK-zeta) (DAG kinase zeta) 2 DGK ε (Diacylglycerol kinase epsilon) (Diglyceride kinase epsilon) (DGK-epsilon) (DAG kinase IPI00003293 P52429 DGKE 2 epsilon) Casein kinase II (casein kinase II alpha 1 subunit) (protein kinase CK2) (CK2 catalytic subunit alpha) IPI00472911 P68400 CSNK2A1 2 (casein kinase II alpha subunit) (casein kinase II-alpha subunit) (Casein kinase II alpha 1 subunit isoform ERK-2 (Mitogen-activated protein kinase 1) (Extracellular signal-regulated kinase 2) (Mitogen-activated IPI00003479 P28482 MAPK1 2 protein kinase 2) (MAP kinase 2) (MAPK 2) (p42-MAPK) (ERT1) IPI00172636 Q8N553 CAMK2D CaM kinase II delta (Calcium/calmodulin-dependent protein kinase (CaM kinase) II delta) 2 Cell division cycle 2-like protein kinase 5 (CDC2-related protein kinase 5) (Cholinesterase-related cell IPI00029162 Q14004 CDC2L5 2 division controller) IPI00023503 Q00526 CDK3 Cell division protein kinase 3 2 Cell division protein kinase 7 (CDK-activating kinase) (CAK) (TFIIH basal transcription factor complex IPI00000685 P50613 CDK7 2 kinase subunit) (39 kDa protein kinase) (P39 Mo15) (STK1) (CAK1) IPI00167096 Q8N752 CSNK1A1L CK1 (Casein kinase I isoform alpha-like) (CKI-alpha-like) 2 IPI00163851 Q9P2K8 EIF2AK4 GCN2 eIF2α kinase (Eukaryotic translation initiation factor 2-alpha kinase 4) (GCN2-like protein) 2 Phosphatases IPI00020950 P35813 PPM1A PP2Cα (Protein phosphatase 2C isoform alpha) (PP2C-alpha) (IA) (Protein phosphatase 1A) 3 IPI00026612 O75688 PPM1B PP2Cβ (Protein phosphatase 2C isoform beta) (PP2C-beta) 3 PP2A, subunit A, PR65-α (Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha IPI00554737 P30153 PPP2R1A isoform) (PP2A, subunit A, PR65-alpha isoform) (PP2A, subunit A, R1-alpha isoform) (Medium tumor 2 antigen-associated 61 kDa protein) Protein phosphatase 1 regulatory subunit 12A (Myosin phosphatase-targeting subunit 1) (Myosin IPI00183002 O14974 PPP1R12A 2 phosphatase target subunit 1) (Protein phosphatase myosin-binding subunit) Trafficking IPI00216393 P09496 CLTA Clathrin light chain A 2 IPI00216472 P09497 CLTB Clathrin light chain B 2 AP-2 α1 (AP-2 complex subunit alpha-1) (Adapter-related protein complex 2 alpha- 1 subunit) (Alpha- IPI00304577 O95782 AP2A1 adaptin A) (Adaptor protein complex AP-2 alpha-1 subunit) (Clathrin assembly protein complex 2 alpha-A 2 large chain) (100 kDa coated vesicle protein A) (Plasma membrane adaptor HA2/AP2 adaptin alpha A AP-2 β1 (AP-2 complex subunit beta-1) (Adapter-related protein complex 2 beta-1 subunit) (Beta-adaptin) IPI00784156 P63010 AP2B1 (Plasma membrane adaptor HA2/AP2 adaptin beta subunit) (Clathrin assembly protein complex 2 beta 2 large chain) (AP105B) Gaf-1 (Rab11 family-interacting protein 5) (Rab11-FIP5) (Rab11-interacting protein Rip11) (Gamma- IPI00022033 Q9BXF6 RAB11FIP5 2 SNAP-associated factor 1) (Phosphoprotein pp75) VPS35 (Vesicle protein sorting 35) (Vacuolar protein sorting-associated protein 35) (hVPS35) (Maternal- IPI00018931 Q96QK1 VPS35 2 embryonic 3) IPI00018452 Q99829 CPNE1 Copine-1 (copine i) 2 AP-3 δ1 (Delta-adaptin) (AP-3 complex subunit delta-1) (Adapter-related protein complex 3 subunit IPI00411453 O14617 AP3D1 3 delta-1) (Delta-adaptin 3) (AP-3 complex subunit delta) G protein- and small GTPase-related α-Pix (Alpha-Pix) (Rho guanine nucleotide exchange factor 6) (Rac/Cdc42 guanine nucleotide exchange IPI00014256 Q15052 ARHGEF6 2 factor 6) (PAK-interacting exchange factor alpha) (COOL-2) IPI00294879 P46060 RANGAP1 Ran GTPase-activating protein 1 2 IPI00169307 Q8NI19 ARHGAP21 Rho GTPase activating protein 10 2 IPI00179890 Q9UN86 G3BP2 Ras-GTPase-activating protein-binding protein 2 (GAP SH3-domain-binding protein 2) (G3BP-2) 2 Other signaling proteins IPI00075248 P62158 CALM1 Calmodulin (CaM) 3 Annexin II (Annexin A2) (Lipocortin II) (Calpactin I heavy chain) (Chromobindin-8) (p36) (Protein I) IPI00455315 P07355 ANXA2 2 (Placental anticoagulant protein IV) (PAP-IV) Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 (TGF-beta-activated kinase 1- IPI00019459 Q15750 TAB1 2 binding protein 1) (TAK1-binding protein 1) I κ-B kinase α (Inhibitor of nuclear factor kappa-B kinase subunit alpha) (I kappa-B kinase alpha) (IkBKA) IPI00005104 O15111 IKKA (IKK-alpha) (IKK-A) (IkappaB kinase) (I-kappa-B kinase 1) (IKK1) (Conserved helix-loop- helix ubiquitous 2 kinase) (Nuclear factor NF-kappa-B inhibitor IPI00215948 P35221 CTNNA1 Catenin α-1 (Catenin alpha-1) (Cadherin-associated protein) (Alpha E-catenin) (NY- REN-13 antigen) 2 Catenin δ-1 (Catenin delta-1) (p120 catenin) (p120(ctn)) (Cadherin-associated Src substrate) (CAS) IPI00182469 O60716 CTNND1 2 (p120(cas)) IPI00414286 O75056 SDC3 Syndecan-3 (SYND3) 2 IPI00018522 Q99873 PRMT1 PRMT1 (Protein arginine N-methyltransferase 1) (Interferon receptor 1-bound protein 4) 2 IPI00646469 Q4G100 WDR26 WDR26 (WDR26 protein) (Myocardial ischemic preconditioning upregulated protein 2) 2 Nucleic acid binding DNA binding, chromatin structure and cell cycle regualtion IPI00217469 Q02539 HIST1H1A Histone H1.1 (H1 histone family, member 1) 2 IPI00021924 Q92522 H1FX Histone H1x 2 IPI00216730 Q8IUE6 HIST2H2AB Histone H2A (Histone H2A type 2-B) 2 Ku70 (ATP-dependent DNA helicase 2 subunit 1) (ATP-dependent DNA helicase II 70 kDa subunit) IPI00644712 P12956 XRCC6 (Lupus Ku autoantigen protein p70) (70 kDa subunit of Ku antigen) (Thyroid-lupus autoantigen) (TLAA) 2 (CTC box- binding factor 75 kDa subunit) (CTCBF) (CTC75) (DNA-repair protein XRCC6) IPI00289601 Q92769 HDAC2 HDAC2 (histone deacetylase 2) (hd2) 2 IPI00152785 P23527 HIST1H2BO Histone H2B (Histone H2B type 1-O) (H2B.n) (H2B/n) (H2B.2) 2 Ku80 (ATP-dependent DNA helicase 2 subunit 2) (ATP-dependent DNA helicase II 80 kDa subunit) (Lupus Ku autoantigen protein p86) (Ku86) (Ku80) (86 kDa subunit of Ku antigen) (Thyroid-lupus IPI00220834 P13010 XRCC5 2 autoantigen) (TLAA) (CTC box-binding factor 85 kDa subunit) (CTCBF) (CTC85) (Nuclear factor IV) (DNA-repair protein XRCC5) IPI00292135 Q14739 LBR Lamin-B receptor (Integral nuclear envelope inner membrane protein) (LMN2R) 2 MCM3 (DNA replication licensing factor MCM3) (DNA polymerase alpha holoenzyme-associated protein IPI00013214 P25205 MCM3 2 P1) (RLF subunit beta) (P102 protein) (P1-MCM3) Transcription factor and transcription regulatory protein Nopp 140 (Nucleolar phosphoprotein p130) (Nucleolar 130 kDa protein) (140 kDa nucleolar IPI00292387 Q14978 NOLC1 4 phosphoprotein) (Nucleolar and coiled-body phosphoprotein 1) IPI00298696 Q13428 TCOF1 Treacle (Treacher collins franceschetti syndrome 1) 6 JBP1 (Protein arginine N-methyltransferase 5) (Shk1 kinase-binding protein 1 homolog) (SKB1Hs) IPI00441473 O14744 PRMT5 3 (Jak-binding protein 1) (72 kDa ICln-binding protein) IPI00549248 P06748 NPM1 Nucleophosmin (NPM) (Nucleolar phosphoprotein B23) (Numatrin) (Nucleolar protein NO38) 3 IPI00029631 P84090 ERH ERH (Enhancer of rudimentary homolog) 2 TIF 1B (Transcription intermediary factor 1-beta) (TIF1-beta) (Tripartite motif-containing protein 28) IPI00438229 Q13263 TRIM28 (Nuclear corepressor KAP-1) (KRAB- associated protein 1) (KAP-1) (KRAB-interacting protein 1) (KRIP-1) 3 (RING finger protein 96) YB-1 (Y-box transcription factor) (Nuclease sensitive element-binding protein 1) (Y-box-binding IPI00031812 P67809 YBX1 protein 1) (Y-box transcription factor) (CCAAT-binding transcription factor I subunit A) (CBF-A) 2 (Enhancer factor I subunit A) (EFI-A) (DNA-binding protein B) (DBPB) LEO1 (RNA polymerase-associated protein LEO1) (Replicative senescence down- regulated leo1-like IPI00103090 Q8WVC0 LEO1 2 protein) Tho4 (THO complex subunit 4) (Ally of AML-1 and LEF-1) (Transcriptional coactivator Aly/REF) IPI00328840 Q86V81 THOC4 2 (bZIP-enhancing factor BEF) ZNF265 (Zinc finger protein 265) (Zinc finger Ran-binding domain-containing protein 2) (Zinc IPI00029400 O95218 ZNF265 3 finger, splicing) Trap150 (Thyroid hormone receptor-associated protein 3) (Thyroid hormone receptor-associated IPI00104050 Q9Y2W1 THRAP3 5 protein complex 150 kDa component) IPI00013788 O43719 HTATSF1 TATSF1 (Tat-SF1) (HIV Tat-specific factor 1) 5 IPI00031960 O95602 POLR1A RPA194
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  • Downloaded from the TCGA Data Portal ( Data.Nci.Nih.Gov/Tcga/) (Supplemental Table S1)

    Downloaded from the TCGA Data Portal ( Data.Nci.Nih.Gov/Tcga/) (Supplemental Table S1)

    bioRxiv preprint doi: https://doi.org/10.1101/023010; this version posted February 11, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks Endre Sebestyén1,*, Babita Singh1,*, Belén Miñana1,2, Amadís Pagès1, Francesca Mateo3, Miguel Angel Pujana3, Juan Valcárcel1,2,4, Eduardo Eyras1,4,5 1Universitat Pompeu Fabra, Dr. Aiguader 88, E08003 Barcelona, Spain 2Centre for Genomic Regulation, Dr. Aiguader 88, E08003 Barcelona, Spain 3Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), E08908 L’Hospitalet del Llobregat, Spain. 4Catalan Institution for Research and Advanced Studies, Passeig Lluís Companys 23, E08010 Barcelona, Spain *Equal contribution 5Correspondence to: [email protected] Keywords: alternative splicing, RNA binding proteins, splicing networks, cancer 1 bioRxiv preprint doi: https://doi.org/10.1101/023010; this version posted February 11, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Alternative splicing is regulated by multiple RNA-binding proteins and influences the expression of most eukaryotic genes. However, the role of this process in human disease, and particularly in cancer, is only starting to be unveiled.