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SI Appendix Overrepresented and Underrepresented Gene Ontology (GO) Terms

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SI Appendix Overrepresented and Underrepresented Gene Ontology (GO) Terms To explore the biological functions of the sets of genes identified by our analysis we examined each gene set for overrepresented and underrepresented Gene Ontology (GO) terms using the Generic GO Term Finder at http://go.princeton.edu/cgi‐bin/GOTermFinder. The results from this analysis are summarized in tables S1‐S4 containing the enriched GO terms with the corresponding Bonferroni corrected p‐values. The legend for the header of the tables is: N Set – Number of genes in the our gene set with the corresponding GO term (first column) N Tot – Number of genes in the genome with the corresponding GO term (first column) p val – Bonferroni corrected probability for finding the observed N Set number or greater number of genes with the corresponding GO term if the genes were sampled from the genome randomly. The probability is computed from the hypergeometric distribution and corrected for multiple hypotheses testing. The Swiss‐Prot identifiers corresponding to the genes from each set can be found in the accompanying word document, Supp_Info_GO_GeneSets.doc. The genes are listed in accordance to the enriched GO terms in the default format of the Generic GO Term Finder. The total number of Swiss‐Prot identifiers used by the GO Term Finder for computing p‐values is 38594. 1.1 Genes coupled more strongly in non‐cancer cells, ΔC> 1 The total number of Swiss‐Prot identifiers corresponding to the gene set and used for computing the p‐values is 846. Table S1 GO ID Term p val N Set N Tot GO:0032501 multicellular organismal process 8.E-24 200 4721 GO:0032502 developmental process 6.E-13 163 4393 GO:0048856 anatomical structure development 9.E-13 120 2822 GO:0009605 response to external stimulus 5.E-12 59 929 GO:0006936 muscle contraction 5.E-12 27 200 GO:0048731 system development 1.E-11 108 2497 GO:0003012 muscle system process 2.E-11 27 209 GO:0006941 striated muscle contraction 3.E-11 17 70 GO:0003008 system process 4.E-11 83 1701 GO:0048513 organ development 4.E-11 87 1832 GO:0007275 multicellular organismal development 5.E-11 126 3206 GO:0007267 cell-cell signaling 3.E-08 46 758 GO:0065008 regulation of biological quality 6.E-08 76 1720 GO:0007154 cell communication 1.E-07 190 6205 GO:0006952 defense response 1.E-07 43 712 GO:0051239 regulation of multicellular organismal process 3.E-07 43 732 regulation of multicellular organismal process GO:0051239 & multicellular organismal process 3.E-07 43 732 GO:0006935 chemotaxis 6.E-07 20 179 GO:0042330 taxis 6.E-07 20 179 GO:0050896 response to stimulus 1.E-06 138 4213 GO:0048518 positive regulation of biological process 3.E-06 74 1814 GO:0007155 cell adhesion 4.E-06 53 1103 GO:0022610 biological adhesion 4.E-06 53 1103 positive regulation of response to external GO:0032103 stimulus 4.E-06 11 50 GO:0007165 signal transduction 5.E-06 171 5693 GO:0006950 response to stress 3.E-05 74 1916 GO:0008283 cell proliferation 4.E-05 51 1118 GO:0048522 positive regulation of cellular process 4.E-05 66 1636 GO:0048869 cellular developmental process 5.E-05 74 1935 GO:0030154 cell differentiation 5.E-05 69 1753 GO:0042221 response to chemical stimulus 5.E-05 45 933 GO:0007626 locomotory behavior 6.E-05 22 279 GO:0040011 locomotion 7.E-05 33 576 GO:0009611 response to wounding 8.E-05 32 550 GO:0051704 multi-organism process 9.E-05 36 671 GO:0009653 anatomical structure morphogenesis 1.E-04 60 1461 GO:0007166 cell surface receptor linked signal transduction 1.E-04 94 2731 GO:0003013 circulatory system process 2.E-04 20 248 GO:0008015 blood circulation 2.E-04 20 248 GO:0003015 heart process 2.E-04 12 87 GO:0060047 heart contraction 2.E-04 12 87 GO:0032101 regulation of response to external stimulus 3.E-04 13 109 regulation of response to external stimulus & GO:0032101 response to external stimulus 3.E-04 13 109 GO:0006968 cellular defense response 3.E-04 10 60 GO:0007517 muscle development 6.E-04 21 295 GO:0003009 skeletal muscle contraction 9.E-04 5 10 GO:0050900 leukocyte migration 9.E-04 10 67 GO:0019932 second-messenger-mediated signaling 1.E-03 21 309 GO:0007610 behavior 1.E-03 27 476 regulation of developmental process & GO:0050793 developmental process 2.E-03 50 1228 GO:0048519 negative regulation of biological process 2.E-03 66 1813 GO:0050793 regulation of developmental process 2.E-03 50 1230 GO:0009887 organ morphogenesis 2.E-03 34 693 GO:0042592 homeostatic process 3.E-03 40 910 GO:0042127 regulation of cell proliferation 4.E-03 35 751 GO:0051707 response to other organism 4.E-03 18 252 GO:0006928 cell motion 4.E-03 31 626 GO:0051674 localization of cell 4.E-03 31 626 regulation of cell proliferation & cell GO:0042127 proliferation 5.E-03 33 696 GO:0030855 epithelial cell differentiation 5.E-03 10 80 GO:0006874 cellular calcium ion homeostasis 5.E-03 14 161 GO:0012501 programmed cell death 6.E-03 46 1144 GO:0002376 immune system process 6.E-03 63 1775 GO:0055074 calcium ion homeostasis 6.E-03 14 164 GO:0048584 positive regulation of response to stimulus 7.E-03 15 188 GO:0008219 cell death 1.E-02 47 1204 1.1 Genes Receptors nuclear receptor co‐repressor 1 C20orf191 insulin‐like growth factor 2 receptor IGF2R interferon gamma receptor 2 (interferon gamma transducer 1) IFNGR2 epidermal growth factor receptor EGFR diazepam binding inhibitor (GABA receptor modulator, acyl‐Coenzyme A binding protein) DBI protein tyrosine phosphatase, non‐receptor type 1PTPN1 integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) ITGB2 tumor necrosis factor receptor superfamily, member 1B TNFRSF1B sortilin‐related receptor, L(DLR class) A repeats‐containing SORL1 Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A colony stimulating factor 3 receptor (granulocyte) CSF3R fibroblast growth factor receptor 2FGFR2 Fc fragment of IgG, low affinity IIIa, receptor (CD16a) FCGR3A /// FCGR3B Fc fragment of IgG, low affinity IIIb, receptor (CD16b) FCGR3B Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide FCER1G fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism) FGFR3 folate receptor 1 (adult) FOLR1 Fas (TNF receptor superfamily, member 6) FAS interferon (alpha, beta and omega) receptor 2IFNAR2 toll‐like receptor 2TLR2 chemokine (C‐C motif) receptor 1 CCR1 formyl peptide receptor 1FPR1 interleukin 2 receptor, beta IL2RB adenosine A1 receptor ADORA1 ryanodine receptor 1 (skeletal) RYR1 protein tyrosine phosphatase, non‐receptor type 14 PTPN14 integrin, alpha M (complement component 3 receptor 3 subunit) ITGAM interleukin 7 receptor IL7R chemokine (C‐X3‐C motif) receptor 1CX3CR1 interleukin 6 receptor IL6R G protein‐coupled receptor 64 GPR64 protein tyrosine phosphatase, receptor type, RPTPRR growth factor receptor‐bound protein 14GRB14 platelet‐activating factor receptor PTAFR nuclear receptor subfamily 0, group B, member 1NR0B1 tumor necrosis factor receptor superfamily, member 8TNFRSF8 leukocyte immunoglobulin‐like receptor, subfamily A (without TM domain), member 3LILRA3 anti‐Mullerian hormone receptor, type IIAMHR2 protein tyrosine phosphatase, receptor type, alpha 2 PPFIA2 interleukin 8 receptor, beta IL8RB hepatitis A virus cellular receptor 1HAVCR1 colony stimulating factor 2 receptor, alpha, low‐affinity (granulocyte‐macrophage) CSF2RA neuropeptide Y receptor Y5 NPY5R leukocyte‐associated immunoglobulin‐like receptor 2LAIR2 egf‐like module containing, mucin‐like, hormone receptor‐like 2EMR2 chemokine‐like receptor 1CMKLR1 cannabinoid receptor 1 (brain) CNR1 angiotensin II receptor, type 1AGTR1 arginine vasopressin receptor 1B AVPR1B killer cell immunoglobulin‐like receptor, two domains, long cytoplasmic tail, 4KIR2DL4 G protein‐coupled receptor 15 GPR15 leukocyte receptor cluster (LRC) member 4 LENG4 interleukin 10 receptor, beta IL10RB G protein‐coupled receptor kinase interactor 2GIT2 integrin, alpha X (complement component 3 receptor 4 subunit) ITGAX protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), alpha 1 PPFIA1 colony stimulating factor 2 receptor, alpha, low‐affinity (granulocyte‐macrophage) CSF2RA cholecystokinin B receptor CCKBR glutamate receptor, ionotropic, N‐methyl D‐aspartate 2CGRIN2C protein tyrosine phosphatase, receptor type, RPTPRR growth factor receptor‐bound protein 7GRB7 natural cytotoxicity triggering receptor 3NCR3 T cell receptor beta variable 19 TRBV19 T cell receptor beta constant 1TRBC1 aryl hydrocarbon receptor nuclear translocator‐like ARNTL fibroblast growth factor receptor 1 (fms‐related tyrosine kinase 2, Pfeiffer syndrome) FGFR1 Fc fragment of IgG, low affinity IIc, receptor for (CD32) FCGR2C leukocyte receptor cluster (LRC) member 4 LENG4 diazepam binding inhibitor (GABA receptor modulator, acyl‐Coenzyme A binding protein) DBI leukocyte immunoglobulin‐like receptor, subfamily B, member 3LILRB3 killer cell immunoglobulin‐like receptor, two domains, long cytoplasmic tail, 4KIR2DL4 pre T‐cell antigen receptor alphaPTCRA colony stimulating factor 2 receptor, alpha, low‐affinity (granulocyte‐macrophage) CSF2RA protein tyrosine phosphatase, receptor type, UPTPRU natural cytotoxicity triggering receptor 3NCR3 met proto‐oncogene (hepatocyte growth factor receptor) MET interferon gamma receptor 1IFNGR1 EPH receptor B1 EPHB1 protein tyrosine phosphatase, non‐receptor type 18 (brain‐derived) PTPN18 killer cell lectin‐like receptor subfamily B, member 1KLRB1 protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4 PPFIA4 neurotrophic tyrosine kinase, receptor, type 3NTRK3 G protein‐coupled receptor
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  • Celsr1-3 Cadherins in PCP and Brain Development

    Celsr1-3 Cadherins in PCP and Brain Development

    CHAPTER SEVEN Celsr1–3 Cadherins in PCP and Brain Development Camille Boutin, André M. Goffinet1, Fadel Tissir1 Institute of Neuroscience, Developmental Neurobiology, Universite´ Catholique de Louvain, Brussels, Belgium 1Corresponding authors: Equal contribution. e-mail address: [email protected]; andre. [email protected] Contents 1. Celsr1–3 Expression Patterns 164 2. Celsr1: A Major Player in Vertebrate PCP 165 3. Celsr2 and 3 in Ciliogenesis 169 4. Celsr1–3 in Neuronal Migration 171 5. Celsr2 and Celsr3 in Brain Wiring 174 5.1 Motifs of Celsr important for their functions 176 References 179 Abstract Cadherin EGF LAG seven-pass G-type receptors 1, 2, and 3 (Celsr1–3) form a family of three atypical cadherins with multiple functions in epithelia and in the nervous system. During the past decade, evidence has accumulated for important and distinct roles of Celsr1–3 in planar cell polarity (PCP) and brain development and maintenance. Although the role of Celsr in PCP is conserved from flies to mammals, other functions may be more distantly related, with Celsr working only with one or a subset of the classical PCP partners. Here, we review the literature on Celsr in PCP and neural devel- opment, point to several remaining questions, and consider future challenges and possible research trends. Celsr1–3 genes encode atypical cadherins of more than 3000 amino acids ( Fig. 7.1). Their large ectodomain is composed of nine N-terminal cadherin repeats (typical cadherins have five repeats), six epidermal growth factor (EGF)-like domains, two laminin G repeats, one hormone receptor motif (HRM), and a G-protein-coupled receptor proteolytic site (GPS).