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Supplementary Table 1: Genes Affected by Anoikis. A, Ratio of Signal

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Supplementary Table 1: Genes affected by anoikis. a, ratio of signal intensity of nonanchored cells anchorage dependent cells (CasKoSrc) over anchored cells; b, induced by Src transformation of Cx43KO cells; c, decreased by Src transformation of Cx43Ko cells; *, induced by normalization of Src transformed cells by neighboring nontransformed cells. Gene Symbol Probe Set Fold Changea Gene Name increased Selenbp1 1450699_at 23.22 selenium binding protein 1 Dscr1l1 1450243_a_at 10.77 Down syndrome critical region gene 1-like 1 Dscr1l1 1421425_a_at 4.29 Down syndrome critical region gene 1-like 1 Ttyh1 1426617_a_at 6.70 tweety homolog 1 (Drosophila) 5730521E12Rik 1419065_at 6.16 RIKEN cDNA 5730521E12 gene c 6330406I15Rik 1452244_at 5.87 RIKEN cDNA 6330406I15 gene AF067063 1425160_at 5.73 clone L2 uniform group of 2-cell-stage gene family mRNA Morc 1419418_a_at 5.55 microrchidia c Gpr56 1421118_a_at 5.43 G protein-coupled receptor 56 Pax6 1452526_a_at 5.06 paired box gene 6 Tgfbi 1415871_at 3.73 transforming growth factor beta induced Adarb1 1434932_at 3.70 adenosine deaminase RNA-specific B1 Ddx3y 1452077_at 3.30 DEAD (Asp-Glu-Ala-Asp) box polypeptide 3 Y-linked b Ampd3 1422573_at 3.20 AMP deaminase 3 Gli2 1459211_at 3.07 GLI-Kruppel family member GLI2 Selenbp2 1417580_s_at 2.96 selenium binding protein 2 Adamts1 1450716_at 2.80 a disintegrin-like and metalloprotease with thrombospondin type 1 motif 1 Dusp15 1426189_at 2.70 dual specificity phosphatase-like 15 Dpep3 1429035_at 2.60 dipeptidase 3 Sepp1 1452141_a_at 2.57 selenoprotein P plasma 1 Car9 1427013_at 2.49 carbonic anhydrase 9 H2-T23 1449556_at 2.49 histocompatibility 2 T region locus 23 b Emb 1415857_at 2.46 embigin Acas2l 1437582_at 2.42 acetyl-Coenzyme A synthetase 2 (AMP forming)-like Igh-6 1452574_x_at 2.38 immunoglobulin heavy chain 6 (heavy chain of IgM) Vig1-pending 1421008_at 2.36 viral hemorrhagic septicemia virus (VHSV) induced gene 1 Gng11 1448942_at 2.25 guanine nucleotide binding protein (G protein) gamma 11 C630002M10Rik 1422587_at 2.24 RIKEN cDNA C630002M10 gene Matn2 1419442_at 2.23 matrilin 2 Adamts4 1452595_at 2.22 a disintegrin-like and metalloprotease with thrombospondin type 1 motif 4 c Cdkn1b 1419497_at 2.20 cyclin-dependent kinase inhibitor 1B (P27) Slc40a1 1417061_at 2.19 solute carrier family 40 (iron-regulated transporter) member 1 Col6a3 1424131_at 2.18 procollagen type VI alpha 3 *c Vcam1 1415989_at 2.11 vascular cell adhesion molecule 1 Tafa5-pending 1419490_at 2.09 TAFA5 protein Bcl2l11 1435448_at 2.08 BCL2-like 11 (apoptosis facilitator) Edil3 1433474_at 2.06 EGF-like repeats and discordin I-like domains 3 2310022G12Rik 1424960_at 2.03 RIKEN cDNA 2310022G12 gene decreased A530090O15Rik 1424880_at -4.36 RIKEN cDNA A530090O15 gene Idi1 1423804_a_at -4.15 isopentenyl-diphosphate delta isomerase Idi1 1451122_at -2.97 isopentenyl-diphosphate delta isomerase Met 1422990_at -3.97 met proto-oncogene b Nol5a 1455035_s_at -3.83 nucleolar protein 5A Siva-pending 1418377_a_at -3.80 Cd27 binding protein (Hindu God of destruction) Psmc4 1416290_a_at -3.78 prosome macropain 4 c 1110020L19Rik 1424277_at -3.78 RIKEN cDNA 1110020L19 gene c Chc1l 1431017_at -3.69 chromosome condensation 1-like c 1110018O08Rik 1428882_at -3.44 RIKEN cDNA 1110018O08 gene Loxl3 1436269_s_at -3.22 lysyl oxidase-like 3 Sema3a 1449865_at -3.21 semaphorin 3A b C78541 1423453_at -3.08 expressed sequence C78541 Hip1 1424755_at -3.03 huntingtin interacting protein 1 Abcg5 1419393_at -2.88 ATP-binding cassette G5 Fabp5 1416022_at -2.86 fatty acid binding protein 5 Fabp5 1416021_a_at -2.32 fatty acid binding protein 5 Alg12 1424818_at -2.75 asparagine-linked glycosylation 12 homolog Sc4mol 1423078_a_at -2.74 sterol-C4-methyl oxidase-like b Ppan 1423703_at -2.65 peter pan homolog (Drosophila) Rangap1 1423749_s_at -2.56 RAN GTPase activating protein 1 c Hmgcs1 1433443_a_at -2.54 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 c Hmgcs1 1433446_at -2.10 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 Fdps 1423418_at -2.49 farnesyl diphosphate synthetase Ptgs2 1417262_at -2.45 prostaglandin-endoperoxide synthase 2 c Tpd52l1 1418412_at -2.39 tumor protein D52-like 1 b Ldlr 1421821_at -2.25 low density lipoprotein receptor Psat1 1454607_s_at -2.23 phosphoserine aminotransferase 1 b 2010317E03Rik 1416939_at -2.21 RIKEN cDNA 2010317E03 gene 1110025L05Rik 1434543_a_at -2.15 RIKEN cDNA 1110025L05 gene BE949497 1460713_at -2.12 EST BE949497 0610012A19Rik 1424907_a_at -2.11 RIKEN cDNA 0610012A19 gene b C730024G01Rik 1423577_at -2.11 RIKEN cDNA C730024G01 gene b Srm 1421260_a_at -2.10 spermidine synthase b Akr1b3 1456590_x_at -2.08 aldo-keto reductase family 1, member B3 (aldose reductase) b D11Ertd175e 1416605_at -2.07 DNA segment Chr 11 ERATO Doi 175 expressed BC004738 1451895_a_at -2.03 Mus Musculus mRNA similar to dual specificity phosphatase 9 b Asf1b 1423714_at -2.02 ASF1 anti-silencing function 1 homolog B (S. cerevisiae) 2 Supplementary Table 2: Genes affected by anchorage independence. a, ratio of signal intensity of anchorage independent cells (CasF253Src) over anchorage dependent cells (CasKoSrc); b, induced by Src transformation of Cx43KO cells; c, decreased by Src transformation of Cx43Ko cells. Gene Symbol Probe Set Fold Changea Gene Name increased Igfbp3 1423062_at 36.30 insulin-like growth factor binding protein 3 b Areg 1421134_at 13.15 amphiregulin Dkk2 1420512_at 12.50 dickkopf homolog 2 (Xenopus laevis) 9130004C02Rik 1435042_at 12.30 RIKEN cDNA 9130004C02 gene b Fkbp11 1417267_s_at 9.86 FK506 binding protein 11 c Sox2 1416967_at 8.77 SRY-box containing gene 2 Odz3 1449315_at 7.29 odd Oz/ten-m homolog 3 (Drosophila) Steap 1424938_at 5.21 six transmembrane epithelial antigen of the prostate Il1rl1 1422317_a_at 5.15 interleukin 1 receptor-like 1 Il1rl1 1425145_at 4.12 interleukin 1 receptor-like 1 Msln 1460238_at 4.17 mesothelin Ednra 1451691_at 4.00 endothelin receptor type A c Timp3 1449334_at 3.39 tissue inhibitor of metalloproteinase 3 c Timp3 1449335_at 3.19 tissue inhibitor of metalloproteinase 3 c Timp3 1419089_at 2.95 tissue inhibitor of metalloproteinase 3 Timp3 1419088_at 2.18 tissue inhibitor of metalloproteinase 3 c Fbn1 1460208_at 2.76 fibrillin 1 Ahr 1422631_at 2.73 aryl-hydrocarbon receptor c Osbpl6 1456495_s_at 2.60 oxysterol binding protein-like 6 Akr1c18 1419136_at 2.54 aldo-keto reductase family 1 member C18 b Gfra1 1421973_at 2.48 glial cell line derived neurotrophic factor family receptor alpha 1 b Mmd 1423489_at 2.41 monocyte to macrophage differentiation-associated Clca2 1460259_s_at 2.35 chloride channel calcium activated 2 c A630095P14Rik 1437642_at 2.31 RIKEN cDNA A630095P14 gene Alcam 1426301_at 2.29 activated leukocyte cell adhesion molecule Clca1 1417852_x_at 2.29 chloride channel calcium activated 1 Ptgs2 1417262_at 2.20 prostaglandin-endoperoxide synthase 2 Phex 1421979_at 2.12 phosphate regulating gene homologies to endopeptidases on X chromosome B430320C24Rik 1448024_at 2.07 RIKEN cDNA B430320C24 gene Cth 1426243_at 2.03 cystathionase (cystathionine gamma-lyase) decreased Epha3 1425575_at -176.40 Eph receptor A3 Asb4 1423422_at -10.25 ankyrin repeat and SOCS box-containing protein 4 Asb4 1433919_at -7.29 ankyrin repeat and SOCS box-containing protein 4 b Emb 1415857_at -7.27 embigin 3 2310015I10Rik 1424921_at -4.95 RIKEN cDNA 2310015I10 gene Nid1 1448469_at -4.69 nidogen 1 Nid1 1416808_at -4.03 nidogen 1 Dkk3 1448669_at -4.23 dickkopf homolog 3 (Xenopus laevis) Dkk3 1417312_at -4.13 dickkopf homolog 3 (Xenopus laevis) 2610028F08Rik 1455893_at -4.23 RIKEN cDNA 2610028F08 gene Ctla2a 1448471_a_at -3.94 cytotoxic T lymphocyte-associated protein 2 alpha Ctla2a 1416811_s_at -2.73 cytotoxic T lymphocyte-associated protein 2 alpha Tafa5-pending 1419490_at -3.91 TAFA5 protein b Atox1 1460640_at -3.83 antioxidant protein 1 Tm4sf2 1448737_at -3.52 transmembrane 4 superfamily member 2 Tm4sf2 1417502_at -2.95 transmembrane 4 superfamily member 2 1110028G01Rik 1427201_at -3.14 RIKEN cDNA 1110028G01 gene Txnip 1415996_at -2.82 thioredoxin interacting protein Adamts4 1455965_at -2.47 a disintegrin-like and metalloprotease with thrombospondin type 1 motif 4 c Nedd9 1437132_x_at -2.37 neural precursor cell expressed, developmentally down-regulated gene 9 Dncic1 1416361_a_at -2.34 dynein cytoplasmic intermediate chain 1 c Tgfb2 1423250_a_at -2.31 transforming growth factor beta 2 1810009M01Rik 1418004_a_at -2.04 RIKEN cDNA 1810009M01 gene 4 Supplementary Table 3: Genes affected by migration. a, ratio of signal intensity of anchorage independent migratory cells (CasWtSrc) over anchorage independent nonmigratory cells (CasF253Src); b, induced by Src transformation of Cx43KO cells; c, decreased by Src transformation of Cx43Ko cells; *, induced by normalization of Src transformed cells by neighboring nontransformed cells. Gene Symbol Probe Set Fold Changea Gene Name increased c Sox2 1416967_at 10.27 SRY-box containing gene 2 c Slit2 1424659_at 4.85 Slit2 c Odz3 1449315_at 4.81 odd Oz/ten-m homolog 3 (Drosophila) b Areg 1421134_at 3.68 amphiregulin Akr1c18 1419136_at 3.33 aldo-keto reductase family 1 member C18 b Gfra1 1421973_at 3.18 glial cell line derived neurotrophic factor family receptor alpha 1 Ptgs1 1423414_at 2.93 prostaglandin-endoperoxide synthase 1 AI851155 1448845_at 2.83 expressed sequence AI851155 Dkk2 1420512_at 2.70 dickkopf homolog 2 (Xenopus laevis) BB128963 1452288_at 2.68 expressed sequence BB128963 Ahr 1422631_at 2.68 aryl-hydrocarbon receptor Pkp4 1452209_at 2.51 plakophilin 4 Il1rl1 1422317_a_at 2.33 interleukin 1 receptor-like 1 Il1rl1 1425145_at
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  • A Role for Glial Cell–Derived Neurotrophic Factor–Induced Expression by Inflammatory Cytokines and RET/GFRA1 Receptor Up-Regulation in Breast Cancer

    A Role for Glial Cell–Derived Neurotrophic Factor–Induced Expression by Inflammatory Cytokines and RET/GFRA1 Receptor Up-Regulation in Breast Cancer

    Research Article A Role for Glial Cell–Derived Neurotrophic Factor–Induced Expression by Inflammatory Cytokines and RET/GFRA1 Receptor Up-regulation in Breast Cancer Selma Esseghir,1 S. Katrina Todd,1 Toby Hunt,2 Richard Poulsom,2 Ivan Plaza-Menacho,1 Jorge S. Reis-Filho,1 and Clare M. Isacke1 1Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research and 2In Situ Hybridisation Service and Histopathology Unit, Cancer Research UK-London Research Institute, London, United Kingdom Abstract system homeostasis and the inflammatory response (3, 4) and in By screening a tissue microarray of invasive breast tumors, we tumor progression (5). The neurotrophic factor glial cell–derived have shown that the receptor tyrosine kinase RET (REar- neurotrophic factor (GDNF) was first identified for its trophic ranged during Transfection) and its coreceptor GFRA1(GDNF activity on midbrain dopaminergic neurons; however, GDNF has receptor family A-1) are overexpressed in a subset of estrogen subsequently been shown to have broader effects in regulating receptor–positive tumors. Germ line–activating oncogenic growth, survival, and migration of neurons in the brain, spinal cord, mutations in RET allow this receptor to signal independently and periphery as well as having an essential role in the growth and A branching of the ureteric buds of the developing kidney (6, 7). Mice of GFR 1and its ligand glial cell–derived neurotrophic factor Gdnf (GDNF) to promote a spectrum of endocrine neoplasias. with a homozygous deletion of die shortly after birth due to However, it is not known whether tumor progression can also severe defects in renal differentiation and the absence of an enteric nervous system (8, 9).
  • Identification of Putative Causal Loci in Whole-Genome

    Identification of Putative Causal Loci in Whole-Genome

    ARTICLE https://doi.org/10.1038/s41467-021-22889-4 OPEN Identification of putative causal loci in whole- genome sequencing data via knockoff statistics ✉ Zihuai He 1,2 , Linxi Liu 3, Chen Wang 4, Yann Le Guen 1, Justin Lee2, Stephanie Gogarten 5, Fred Lu6, Stephen Montgomery 7,8, Hua Tang 6,7, Edwin K. Silverman9, Michael H. Cho 9, Michael Greicius1 & ✉ Iuliana Ionita-Laza4 The analysis of whole-genome sequencing studies is challenging due to the large number of 1234567890():,; rare variants in noncoding regions and the lack of natural units for testing. We propose a statistical method to detect and localize rare and common risk variants in whole-genome sequencing studies based on a recently developed knockoff framework. It can (1) prioritize causal variants over associations due to linkage disequilibrium thereby improving interpret- ability; (2) help distinguish the signal due to rare variants from shadow effects of significant common variants nearby; (3) integrate multiple knockoffs for improved power, stability, and reproducibility; and (4) flexibly incorporate state-of-the-art and future association tests to achieve the benefits proposed here. In applications to whole-genome sequencing data from the Alzheimer’s Disease Sequencing Project (ADSP) and COPDGene samples from NHLBI Trans-Omics for Precision Medicine (TOPMed) Program we show that our method com- pared with conventional association tests can lead to substantially more discoveries. 1 Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA. 2 Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA, USA. 3 Department of Statistics, Columbia University, New York, NY, USA. 4 Department of Biostatistics, Columbia University, New York, NY, USA.