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Significant Genes List

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Table: Significant gene list. From Banerjee AG et al, 2005. Molecular Cancer Therapeutics –05-0033 Relative Probeset ID Gene Name Description Fold expression 12.042 206785_s_at KLRC2 " killer cell lectin-like receptor subfamily C, member 3" 11.713 210163_at CXCL11 chemokine (C-X-C motif) ligand 11 3.972 205569_at LAMP3 lysosomal-associated membrane protein 3 3.732 202269_x_at GBP1 " guanylate binding protein 1, interferon-inducible, 67kDa" 3.317 202270_at GBP1 " guanylate binding protein 1, interferon-inducible, 67kDa" 2.828 205488_at GZMA " granzyme A (granzyme 1, cytotoxic T-lymphocyte- associated serine esterase 3)" 2.789 205554_s_at DNASE1L3 deoxyribonuclease I-like 3 2.732 220026_at CLCA4 " chloride channel, calcium activated, family member 4" 2.585 212190_at SERPINE2 " serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2" 2.497 AFFX-HUMISGF3A STAT3 Stat3 protein /M97935_3_at 2.479 202953_at C1QB " complement component 1, q subcomponent, beta polypeptide" 2.395 201830_s_at NET1 neuroepithelial cell transforming gene 1 2.313 200798_x_at MCL1 myeloid cell leukemia sequence 1 (BCL2-related) 2.219 219117_s_at FKBP11 " FK506 binding protein 11, 19 kDa" 2.114 204620_s_at CSPG2 chondroitin sulfate proteoglycan 2 (versican) 2.071 202620_s_at PLOD2 " procollagen-lysine, 2- oxoglutarate 5-dioxygenase (lysine hydroxylase) 2" 2 208843_s_at GORASP2 " golgi reassembly stacking protein 2, 55kDa" 1.879 201669_s_at MARCKS myristoylated alanine-rich protein kinase C substrate 1.803 200782_at ANXA5 annexin A5 11.713 205916_at S100A7 S100 calcium binding protein A7 (psoriasin 1) 10.928 211430_s_at IGHG3 immunoglobulin heavy constant gamma 3 (G3m marker) 8.574 211906_s_at SERPINB4 " serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4" 8.515 1405_i_at CCL5 chemokine (C-C motif) ligand 5 8.225 209083_at CORO1A " coronin, actin binding protein, 1A" 6.233 34210_at CDW52 CDW52 antigen (CAMPATH-1 antigen) 6.021 211796_s_at TCRB "Homo sapiens T cell receptor beta chain BV20S1 BJ1-5 BC1 Table: Significant gene list. From Banerjee AG et al, 2005. Molecular Cancer Therapeutics –05-0033 mRNA, complete cds" 5.352 209126_x_at KRT6B keratin 6B 5.278 206666_at GZMK " granzyme K (serine protease, granzyme 3; tryptase II)" 5.098 209800_at KRT16 keratin 16 (focal non- epidermolytic palmoplantar keratoderma) 4.691 213975_s_at LYZ lysozyme (renal amyloidosis) 4.347 216834_at RGS1 regulator of G-protein signalling 1 4.347 209924_at CCL18 chemokine (C-C motif) ligand 18 (pulmonary and activation- regulated) 4.199 203915_at CXCL9 chemokine (C-X-C motif) ligand 9 4.141 212588_at PTPRC " protein tyrosine phosphatase, receptor type, C" 4.112 219947_at CLECSF6 " C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 6" 4.056 218469_at CKTSF1B1 " cysteine knot superfamily 1, BMP antagonist 1" 3.972 204533_at CXCL10 chemokine (C-X-C motif) ligand 10 3.758 209720_s_at SERPINB3 " serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3" 3.706 209795_at CD69 " CD69 antigen (p60, early T- cell activation antigen)" 3.58 208146_s_at CPVL " carboxypeptidase, vitellogenic-like" 3.555 219386_s_at BLAME SLAM family member 8 3.531 217028_at CXCR4 chemokine (C-X-C motif) receptor 4 3.531 205900_at KRT1 keratin 1 (epidermolytic hyperkeratosis) 3.482 201645_at TNC tenascin C (hexabrachion) 3.387 206211_at SELE selectin E (endothelial adhesion molecule 1) 3.34 32128_at CCL18 chemokine (C-C motif) ligand 18 (pulmonary and activation- regulated) 3.272 218468_s_at CKTSF1B1 " cysteine knot superfamily 1, BMP antagonist 1" 3.182 209969_s_at STAT1 " signal transducer and activator of transcription 1, 91kDa" 3.074 205419_at EBI2 Epstein-Barr virus induced gene 2 (lymphocyte-specific G protein-coupled receptor) 3.074 205831_at CD2 " CD2 antigen (p50), sheep red blood cell receptor" 3.074 205552_s_at OAS1 " 2',5'-oligoadenylate synthetase 1, 40/46kDa" 3.053 215536_at HLA-DQB2 " major histocompatibility complex, class II, DQ beta 2" Table: Significant gene list. From Banerjee AG et al, 2005. Molecular Cancer Therapeutics –05-0033 3.031 220330_s_at SAMSN1 " SAM domain, SH3 domain and nuclear localisation signals, 1" 3.01 209773_s_at RRM2 ribonucleotide reductase M2 polypeptide 2.99 209823_x_at HLA-DQB1 " major histocompatibility complex, class II, DQ beta 1" 2.969 209606_at PSCDBP " pleckstrin homology, Sec7 and coiled-coil domains, binding protein" 2.949 209719_x_at SERPINB3 " serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3" 2.949 213680_at KRT6B keratin 6B 2.908 208450_at LGALS2 " lectin, galactoside-binding, soluble, 2 (galectin 2)" 2.908 204614_at SERPINB2 " serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 2.908 219505_at CECR1 " cat eye syndrome chromosome region, candidate 1" 2.888 210020_x_at CALML3 calmodulin-like 3 2.77 221730_at COL5A2 " collagen, type V, alpha 2" 2.77 212998_x_at HLA-DQB2 " major histocompatibility complex, class II, DQ beta 2" 2.77 205595_at DSG3 desmoglein 3 (pemphigus vulgaris antigen) 2.732 211656_x_at HLA-DQB1 " major histocompatibility complex, class II, DQ beta 1" 2.713 206165_s_at CLCA2 " chloride channel, calcium activated, family member 2" 2.694 209218_at SQLE squalene epoxidase 2.694 208894_at HLA-DRA " major histocompatibility complex, class II, DR alpha" 2.676 213994_s_at SPON1 " spondin 1, (f-spondin) extracellular matrix protein" 2.657 201852_x_at COL3A1 " collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant)" 2.657 212236_x_at KRT17 keratin 17 2.657 201721_s_at LAPTM5 Lysosomal-associated multispanning membrane protein- 5 2.639 203213_at CDC2 " cell division cycle 2, G1 to S and G2 to M" 2.603 205668_at LY75 lymphocyte antigen 75 2.585 201890_at RRM2 ribonucleotide reductase M2 polypeptide 2.585 204563_at SELL selectin L (lymphocyte adhesion molecule 1) 2.585 212488_at COL5A1 " collagen, type V, alpha 1" 2.567 204952_at C4.4A GPI-anchored metastasis- associated protein homolog 2.567 204751_x_at DSC2 desmocollin 2 2.567 207173_x_at CDH11 " cadherin 11, type 2, OB- cadherin (osteoblast)" 2.532 213539_at CD3D " CD3D antigen, delta Table: Significant gene list. From Banerjee AG et al, 2005. Molecular Cancer Therapeutics –05-0033 polypeptide (TiT3 complex)" 2.532 205269_at LCP2 lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa) 2.532 211991_s_at HLA-DPA1 " major histocompatibility complex, class II, DP alpha 1" 2.514 209670_at TRA@ T cell receptor alpha locus 2.514 218986_s_at FLJ20035 FLJ20035 2.514 211748_x_at PTGDS prostaglandin D2 synthase 21kDa (brain) 2.497 200887_s_at STAT1 " signal transducer and activator of transcription 1, 91kDa" 2.497 212671_s_at HLA-DQA1 " major histocompatibility complex, class II, DQ alpha 1" 2.497 211654_x_at HLA-DQB1 " major histocompatibility complex, class II, DQ beta 1" 2.479 204655_at CCL5 chemokine (C-C motif) ligand 5 2.462 205157_s_at KRT17 keratin 17 2.462 202718_at IGFBP2 " insulin-like growth factor binding protein 2, 36kDa" 2.462 219995_s_at FLJ13841 FLJ13841 2.445 206164_at CLCA2 " chloride channel, calcium activated, family member 2" 2.428 201417_at SOX4 SRY (sex determining region Y)-box 4 2.428 202663_at WASPIP Wiskott-Aldrich syndrome protein interacting protein 2.412 212489_at COL5A1 " collagen, type V, alpha 1" 2.412 205483_s_at G1P2 " interferon, alpha-inducible protein (clone IFI-15K)" 2.395 203417_at MFAP2 microfibrillar-associated protein 2 2.378 213506_at F2RL1 coagulation factor II (thrombin) receptor-like 1 2.378 201739_at SGK serum/glucocorticoid regulated kinase 2.362 204469_at PTPRZ1 " protein tyrosine phosphatase, receptor-type, Z polypeptide 1" 2.362 204774_at EVI2A ecotropic viral integration site 2A 2.362 61734_at RCN3 " reticulocalbin 3, EF-hand calcium binding domain" 2.346 213537_at HLA-DPA1 " major histocompatibility complex, class II, DP alpha 1" 2.346 213193_x_at TRB@ T cell receptor beta locus 2.329 213293_s_at TRIM22 tripartite motif-containing 22 2.313 221059_s_at CHST6 carbohydrate (N- acetylglucosamine 6-O) sulfotransferase 6 2.313 204472_at GEM GTP binding protein overexpressed in skeletal muscle 2.313 208651_x_at CD24 CD24 antigen (small cell lung carcinoma cluster 4 antigen) 2.297 209436_at SPON1 " spondin 1, (f-spondin) extracellular matrix protein" Table: Significant gene list. From Banerjee AG et al, 2005. Molecular Cancer Therapeutics –05-0033 2.297 213603_s_at RAC2 " ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2)" 2.297 205081_at CRIP1 cysteine-rich protein 1 (intestinal) 2.282 202086_at MX1 " myxovirus (influenza virus) resistance 1, interferon- inducible protein p78 (mouse)" 2.282 209040_s_at PSMB8 " proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7)" 2.282 204962_s_at CENPA " centromere protein A, 17kDa" 2.266 214512_s_at PC4 (RNA pol activated RNA polymerase II II cofactor 4) transcription cofactor 4 2.266 204279_at PSMB9 " proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional protease 2)" 2.25 219918_s_at ASPM " asp (abnormal spindle)-like, microcephaly associated (Drosophila)" 2.25 212587_s_at PTPRC " protein tyrosine phosphatase, receptor type, C" 2.25 203325_s_at COL5A1 " collagen, type V, alpha 1" 2.235 209267_s_at BIGM103 " solute carrier family 39 (zinc transporter), member 8" 2.219 203502_at BPGM " 2,3-bisphosphoglycerate mutase" 2.219 202411_at IFI27 " interferon, alpha-inducible protein 27" 2.219 202546_at VAMP8 vesicle-associated
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  • Heterotrimeric Go Protein Links Wnt-Frizzled Signaling with Ankyrins to Regulate the Neuronal Microtubule Cytoskeleton Anne-Marie Lüchtenborg1,2, Gonzalo P

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    © 2014. Published by The Company of Biologists Ltd | Development (2014) 141, 3399-3409 doi:10.1242/dev.106773 RESEARCH ARTICLE Heterotrimeric Go protein links Wnt-Frizzled signaling with ankyrins to regulate the neuronal microtubule cytoskeleton Anne-Marie Lüchtenborg1,2, Gonzalo P. Solis1, Diane Egger-Adam2, Alexey Koval1, Chen Lin1,2, Maxime G. Blanchard1, Stephan Kellenberger1 and Vladimir L. Katanaev1,2,* ABSTRACT The evolutionarily conserved Wg pathway is important for Drosophila neuromuscular junctions (NMJs) represent a powerful numerous developmental programs and cellular processes (Logan model system with which to study glutamatergic synapse formation and Nusse, 2004). In the nervous system of Drosophila,Wg and remodeling. Several proteins have been implicated in these signaling is involved in the formation of neuromuscular junctions processes, including components of canonical Wingless (Drosophila (NMJs) (Packard et al., 2002; Miech et al., 2008). Being a Wnt1) signaling and the giant isoforms of the membrane-cytoskeleton glutamatergic synapse, the Drosophila NMJ provides a useful linker Ankyrin 2, but possible interconnections and cooperation experimental model with which to study mammalian central between these proteins were unknown. Here, we demonstrate that nervous system synapses, their formation and remodeling (Collins the heterotrimeric G protein Go functions as a transducer of Wingless- and DiAntonio, 2007). The Drosophila NMJ is a beads-on-a-string- Frizzled 2 signaling in the synapse. We identify Ankyrin 2 as a target like structure that is formed at the axon terminus and is composed of – – of Go signaling required for NMJ formation. Moreover, the Go-ankyrin distinct circular structures the synaptic boutons which contain interaction is conserved in the mammalian neurite outgrowth pathway.
  • Patient-Based Cross-Platform Comparison of Oligonucleotide Microarray Expression Profiles

    Patient-Based Cross-Platform Comparison of Oligonucleotide Microarray Expression Profiles

    Laboratory Investigation (2005) 85, 1024–1039 & 2005 USCAP, Inc All rights reserved 0023-6837/05 $30.00 www.laboratoryinvestigation.org Patient-based cross-platform comparison of oligonucleotide microarray expression profiles Joerg Schlingemann1,*, Negusse Habtemichael2,*, Carina Ittrich3, Grischa Toedt1, Heidi Kramer1, Markus Hambek4, Rainald Knecht4, Peter Lichter1, Roland Stauber2 and Meinhard Hahn1 1Division of Molecular Genetics, Deutsches Krebsforschungszentrum, Heidelberg, Germany; 2Chemotherapeutisches Forschungsinstitut Georg-Speyer-Haus, Frankfurt am Main, Germany; 3Central Unit Biostatistics, Deutsches Krebsforschungszentrum, Heidelberg, Germany and 4Department of Otorhinolaryngology, Universita¨tsklinik, Johann-Wolfgang-Goethe-Universita¨t Frankfurt, Frankfurt, Germany The comparison of gene expression measurements obtained with different technical approaches is of substantial interest in order to clarify whether interplatform differences may conceal biologically significant information. To address this concern, we analyzed gene expression in a set of head and neck squamous cell carcinoma patients, using both spotted oligonucleotide microarrays made from a large collection of 70-mer probes and commercial arrays produced by in situ synthesis of sets of multiple 25-mer oligonucleotides per gene. Expression measurements were compared for 4425 genes represented on both platforms, which revealed strong correlations between the corresponding data sets. Of note, a global tendency towards smaller absolute ratios was observed when
  • Cellular and Molecular Signatures in the Disease Tissue of Early

    Cellular and Molecular Signatures in the Disease Tissue of Early

    Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of