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Supporting Information for Proteomics DOI 10.1002/Pmic.200500648

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Supporting Information for Proteomics DOI 10.1002/pmic.200500648 Fiona M. McCarthy, Amanda M. Cooksey, Nan Wang, Susan M. Bridges, G. Todd Pharr and Shane C. Burgess Modeling a whole organ using proteomics: The avian bursa of Fabricius ª 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com Supporting Text: Determining Tissue Expression Patterns for Transcription Factors. We identified 107 transcription factors (TFs) from post-hatch bursas. Since the Transfac database (1) did not contain all of these TFs, we used PubMed literature searches to determine expression patterns for each. For each transcription factor, we searched PubMed for a combination of the protein and gene names, as determined by both NCBI and UniProt records. For example, Pax7 (gi:2576239; UniProt O42349) was searched as both PAX7 and Pax-7. In each case, articles were manually searched to confirm TF expression. We combined the TF names with the following terms to obtain reported tissue expression patterns: 1. Expression in the bursa. AND bursa* OR DT40 eg. (Pax7 OR “Pax-7”) AND (bursa* OR DT40) returned no items. 2. Expression in immune tissue. AND lymphocyte* OR leukocyte* OR “bone marrow” OR spleen OR “embryonic liver” OR hematopoietic eg. (Pax7 OR “Pax-7”) AND (lymphocyte* OR leukocyte* OR “bone marrow” OR spleen OR “embryonic liver” OR hematopoietic) returned 17 articles. 3. Expression during development. AND development OR embryo* eg. (Pax7 OR “Pax-7”) AND (development OR embryo*) returned 135 articles. 4. Expression in nervous tissue. AND neuron* OR nervous OR CNS OR retina* 1 eg. (Pax7 OR “Pax-7”) AND (neuron* OR nervous OR CNS OR retina*) returned 53 articles. 5. Expression in B-cells. For each TF identified from B-cells we also searched to determine if it had been previously reported specifically in B-cells using AND (B-cell* OR B-lymphocyte*) eg. (Pax7 OR “Pax-7”) AND (B-cell* OR B-lymphocyte*) returned 2 articles. REFERENCES 1. Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krull, M., Matys, V., Michael, H., Ohnhauser, R., et al. (2001) Nucleic Acids Res 29, 281-3. 2 FIGURE LEGENDS FOR SUPPORTING DATA Supporting Data: Fig 7. Bursal Membrane Proteins Grouped by Number of Transmembrane Domain. The number of transmembrane domains (TMD) for each membrane protein was determined either by their UniProt record or by using TMD prediction programs, as described (methods). Proteins classified by GO cellular component as membrane (GO:0016020) which do not contain TMDs are classified as membrane associated. Supporting Data: Fig 8. Bursal membrane proteins grouped by function. To determine function, bursal membrane proteins were annotated to the GO biological process ontology. The same GO terms are used to compare function of B-cell membrane proteins with stromal membrane proteins. Supporting Data: Fig 9. Bursal nuclear proteins grouped by function. The function of nuclear proteins was determined by annotating to GO biological process terms. A graphical representation of nuclear protein function in both B-cell and stroma is shown. 3 Supporting Data: Fig 7. membrane associated 1 TM 2 TM 3 TM 4 TM 5 TM 6 TM 7 TM 8-9 TM 10-11 TM 11-12 TM 14 TM 24 TM 4 Supporting Data: Fig 8. B-cells Stroma cell cycle/cell proliferation cell-cell signaling cell adhesion function unknown cell growth development apoptosis endocytosis immune response proteolysis and peptidolysis ion/proton transport signal transduction cell migration protein modification 5 Supporting Data: Fig 9. B-cells Stroma cell cycle/cell proliferation function unknown cell differentiation nuclear organization and biogenesis cell growth protein catabolism chromosome segregation protein modification chromatin modification RNA processing chromosome organization and biogenesis nuclear transport DNA metabolism signal transduction chromatin assembly or disassembly regulation of transcription, DNA-dependent 6 SUPPORTING DATA: TABLES Supporting Data: Table 3. AvDB Proteins Identified from the Post-hatch Bursa. Proteins and their gi accession numbers are listed along with their identified tissue compartment (B = B-cell; S = stroma; BS = both tissues). 7 Sample GI# Protein B 45382191 17.5 B 45384406 17-beta-hydroxysteroid dehydrogenase type IV B 1944138 2',5'-oligo adenylate synthetase A B 2981301 25-hydroxyvitamin D3 24-hydroxylase B 4033392 78 kDa glucose-regulated protein (GRP 78) B 6980689 A Chain A, Histone Octamer (CHICKen), Chromosomal Protein B 4566743 A3 adenosine receptor B 7512224 A41724 limb deformity (ld) protein (formin) B 280735 A60392 zinc finger protein Zfb B 3355757 ABC transporter protein; P-glycoprotein B 543753 Acetylcholinesterase (AChE) B 52138697 Acetylglucosaminyltransferase-like protein B 24637100 Aconitase B 4501881 Actin ; alpha skeletal muscle actin B 104520 Actin beta, cytosolic B 1168326 Actin, aortic smooth muscle (Alpha-actin) B 4501889 Actin, gamma 2 propeptide; actin, alpha-3 B 4501885 Actin; beta cytoskeletal actin B 131636 Adenylosuccinate lyase (Adenylosuccinase) B 114128 ADP-ribosylation factor 6 B 13430373 AF348088_1aryl hydrocarbon receptor nuclear translocator B 399020 AGRI_CHICK Agrin B 56744182 Akhirin B 45383031 Aldehyde dehydrogenase 1A1 B 14330324 Aldo-keto reductase B 47933930 Alpha 1-acid glycoprotein B 27657305 Alpha 3 glucosyltransferase B 63082 Alpha8 subunit of nicotinic acetylcholine receptor B 631001 Alpha-N-acetylgalactosaminidase B 131608 Amidophosphoribosyltransferase B 5689722 aminopeptidase B 45382361 Aminopeptidase Ey B 987866 AMPA receptor GluR4/D B 10120280 angiopoietin-2A B 114013 Apolipoprotein B B 2352033 Apoptosis associated protein (BAD homolog) B 2506217 Apoptosis regulator bcl-x B 1478410 Arginine vasotocin receptor, AVT receptor B 258405 Arginine-specific ADP-ribosyltransferase target protein B 104642 Aromatase cytochrome P450 19 B 19343352 Aryl hydrocarbon receptor ATA3_CHICK Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 B 18203648 (Calcium pump B 18028983 ATP-binding cassette transporter 1 B 113862 Atrial natriuretic factor (ANF) B 3551531 Avena B 10719897 Axin (Axis inhibition protein) B 12082811 B cell phosphoinositide 3-kinase adaptor B 28200457 Bcl-2 related anti-apoptotic protein (NR13) B 45382663 Bcl-2-related ovarian killer (BOK) 8 B 2147144 Beta 8 integrin B 1706654 Beta enolase (2-phospho-D-glycerate hydro-lyase) B 27734460 Beta-1,3-N-acetylglucosaminyltransferase radical fringe B 1352061 Beta-2-microglobulin B 33186751 Beta3-glucuronyltransferase B 63018 beta-actin B 45382773 Beta-synuclein B 30348610 BMP/retinoic acid-inducible neural-specific B 19568157 Breast cancer susceptibility protein B 996018 BRG1 protein B 996020 BRM protein B 19909956 Bruno-like RNA binding protein B 65324 brush border myosin IB B 86206 Ca2+transporting ATPase SERCA2a B 3023428 CADA_CHICK Cadherin-10 B 13431348 Cadherin-6 B 32967298 Calcineurin A alpha B 2493451 Calpain 2, large B 2493453 Calpain 3 large subunit B 38073296 Carbamyl phosphate synthetase 1 B 19071560 Carboxypeptidase Z B 42742275 cartilage associated protein B 46237616 Casein kinase 2, beta subunit B 3450875 Caspase-3 B 46487963 Cathelicidin B 11559418 Caudal-type homeodomain protein B 45384468 C-Delta-1 B 16930529 CDH1-D B 2462299 Cellular retinoic acid binding protein type I B 2737971 CFR-associated protein p70 [MASS=83 B 3660379 Chain D, Stigmatellin And Antimycin Bound Cytochrome Bc1 Complex B 15076564 ChB1 B 23452381 checkpoint 1 protein B 3318707 CHICKen B-Myb Dna Binding Domain B 2780916 CHICKen Src Tyrosine Kinase B 15341176 Choline acetyltransferase B 6644332 CHPPR/KIAA0009 protein B 25301665 Chromatin assembly factor-1 p48 subunit homolog, p46 B 45384402 Chromo-helicase-DNA-binding on the Z chromosome B 5725448 CHUNK-1 protein B 515105 Citrate Synthase B 22023892 class IV POU-domain transcription factor Brn-3.2 B 3036838 CNKx-2.3 B 2134315 Cnot protein B 13241978 CocoaCrisp B 104582 Cofilin B 26801170 Cohesin complex subunit B 27437030 colony stimulating factor 2 - human B 34305301 Connexin 32 B 20138050 CP26_CHICK Cytochrome P450 26 (Retinoic acid degradi B 912987 C-ret proto-oncogene product receptor tyrosine kinase 9 B 1236281 C-Serate-1 protein B 2313049 C-Serrate-2 B 19262916 Cytochrome P-450 B 29149953 cytochrome-c oxidase subunit III B 19571788 Cytokine receptor-beta B 6980692 D Chain D, Histone Octamer (CHICKen), Chromosomal Protein B 18643132 Dachshund 1 B 31322662 Death domain-containing TNFR23 B 14043015 Death receptor 6 B 7021380 Defender against cell death 1 B 4469173 Delta-9 desaturase B 7634804 Deltex 2 B 21320894 D-erythrulose reductase DGCR6 PROTEIN (DIGEORGE SYNDROME CRITICAL REGION 6 B 6685380 HOMOLOG B 45383700 diaphanous homolog 2 B 15778121 DNA ligase IV B 26983954 DNA polymerase kappa B 13959708 DNA topoisomerase II, B 45382811 DNA-dependent protein kinase catalytic subunit B 25513801 DR6 B 461969 DSL1_CHICK Dorsalin-1 (DSL-1) B 6065857 dynactin B 6478775 Dynamitin B 2494226 E2F1 TRANSCRIPTION FACTOR E2F1 (E2F-1) B 3417246 EAST protein B 31747199 ELAV-type RNA-binding protein 3 B 50953500 Ellis-van Creveld syndrome 2-like protein B 1079403 Embryo kinase 5 B 119359 Endoplasmin (Heat shock 108 kDa protein) (HSP108) B 2462302 Eph-like receptor tyrosine kinase B 1706627 Ephrin type-A receptor 5 B 1706677 Ephrin-A5 (EPH-related receptor tyrosine kinase ligand 7) B 41327732 Epidermal growth factor receptor b B 45382171 Estrogen receptor beta B 10178878 Eukaryote initiation factor 2 beta B 45382429 Ezrin B 115579 F-actin capping protein alpha-2 subunit B 9931640 Fas antigen B 9931642 Fas ligand receptor soluble
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    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