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SUPPLEMENTAL TABLE 1. Annotation of Top PAM Classifiers

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SUPPLEMENTAL TABLE 1. Annotation of Top PAM Classifiers SUPPLEMENTAL TABLE 1. Annotation of top PAM classifiers Affy ID Entrez Gene ID Gene SAM ranka Gene ontology and other literature 204891_s_at 3932 Lymphocyte-specific protein 8 Function: ATPase binding; CD4 receptor binding; CD8 receptor tyrosine kinase (LCK) binding; SH2 domain binding; glycoprotein binding; nucleotide binding; phosphoinositide 3-kinase binding; protein C-terminus binding; protein kinase binding; protein serine/ threonine phosphatase activity; protein-tyrosine kinase activity; transferase activity Process: Ras protein signal transduction; T-cell differentiation; caspase activation; hemopoiesis; induction of apoptosis; intracellular signaling cascade; positive regulation of T-cell activation; positive regulation of T-cell receptor signaling pathway; positive regulation of T-cell receptor signaling pathway; protein amino acid phosphorylation; protein amino acid phosphorylation; regulation of lymphocyte activation; regulation of progression through cell cycle; release of sequestered calcium ion into cytosol; response to drug; response to drug; zinc ion homeostasis Component: lipid raft; pericentriolar material 200982_s_at 309 Annexin A6 (ANXA6) 9 Function: calcium ion binding; calcium-dependent phospholipid binding; catalytic activity; protein binding Literature: Asthmatic vs non-asthmatic mouse lung proteomic screen (Houtman et al. 1); KO mice are normal (Hawkins et al. 2); Annexins in lung epithelia (Mayran et al. 3); Potential Interaction between Annexin VI and a 56-kDa Protein Kinase in T Cells (Dubois et al. 4); Annexin VI is required for budding of clathrin-coated pits (Lin et al. 5) 210915_x_at 28568 T-cell receptor beta variable 10 Component: integral to membrane; membrane 213193_x_at19 (TRBV19) 17 214022_s_at 8519 Interferon-induced 12 Function: protein binding; receptor signaling protein activity 201601_x_attransmembrane protein 1 54 Process: cell surface receptor linked signal transduction; (9–27) (IFITM1) immune response; negative regulation of cell proliferation; regulation of progression through cell cycle; response to biotic stimulus Component: integral to membrane; plasma membrane 205758_at 925 CD8 antigen, alpha 13 Function: MHC class I protein binding; coreceptor activity; polypeptide (p32) (CD8A) protein binding Process: T-cell activation; antigen presentation; cellular defense response (sensu Vertebrata); transmembrane receptor protein tyrosine kinase signaling pathway Component: T-cell receptor complex; integral to plasma membrane; membrane 201669_s_at 4082 Myristoylated alanine-rich 16 Function: actin filament binding; calmodulin binding 201670_s_atprotein kinase C substrate 46 Process: cell motility (MARCKS) Component: actin cytoskeleton; plasma membrane Literature: A peptide against the N-Terminus of MARCKS inhibits degranulation of human leukocytes in vitro (Takashi et al. 6); Treatment of airway mucus hypersecretion (Rogers and Barnes7); MARCKS protein is a key molecule regulating mucin secretion by human airway epithelial cells in vitro (Li et al.) 205114_s_at 414062 Chemokine (C-C motif) 19 Function: chemokine activity ligand 3 (CCL3) Process: immune response Component: extracellular region 213241_at 10154 Plexin C1 (PLXNC1) 20 Function: receptor activity; receptor binding Process: cell adhesion; development Component: integral to membrane; plasma membrane Literature: Unknown immunologic function – Plexin C1 KO mice (Walzer et al. 9) SUPPLEMENTAL TABLE 1. Continued Affy ID Entrez Gene ID Gene SAM ranka Gene ontology and other literature 214290_s_at 8337 Histone 2, H2aa 21 Function: DNA binding 218280_x_at(HIST2H2AA) 26 Process: chromosome organization and biogenesis (sensu Eukaryota); nucleosome assembly Component: chromosome; nucleosome; nucleus 210164_at 3002 Granzyme B (granzyme 2, 22 Function: granzyme B activity; peptidase activity; serine-type cytotoxic T-lymphocyte- endopeptidase activity associated serine esterase 1) Process: apoptosis; cleavage of lamin; cytolysis; proteolysis (GZMB) Component: cytoplasm; immunological synapse; nucleus 202746_at 9452 Integral membrane protein 23 Component: integral to membrane; membrane 2A (ITM2A) 203828_s_at 9235 Interleukin 32 (IL-32) 25 Function: cytokine activity Process: cell adhesion; immune response Component: extracellular space 202859_x_at 3576 Interleukin 8 (IL-8) 28 Function: chemokine activity; interleukin-8 receptor binding; protein binding Process: G-protein coupled receptor protein signaling pathway; angiogenesis; calcium-mediated signaling; cell cycle arrest; cell motility; cell-cell signaling; chemotaxis; induction of positive chemotaxis; intracellular signaling cascade; negative regulation of cell proliferation; neutrophil activation; neutrophil chemotaxis; regulation of cell adhesion; regulation of retroviral genome replication; response to stimulus Component: extracellular space 204103_at 6351 Chemokine (C-C motif) 30 Function: chemokine activity; receptor signaling protein ligand 4 (CCL4) tyrosine kinase activity Process: cell adhesion; cell motility; cell-cell signaling; chemotaxis; establishment and/or maintenance of cell polarity; inflammatory response; response to stimulus; response to virus; signal transduction; viral genome replication Component: extracellular space 211796_s_at 28566 T-cell receptor beta variable 31 21-1 (TRBV21-1) a SAM rank: The ranking by P value in the SAM analysis performed on all transcripts on the chip. REFERENCE LIST 1. Houtman R, Krijgsveld J, Kool M, et al. Lung proteome alterations in a mouse model for nonallergic asthma. Proteomics. 2003; 3: 2008. 2. Hawkins TE, Roes J, Rees D, Monkhouse J, Moss SE. Immunological development and cardiovascular function are normal in annexin VI null mutant mice. Mol. Cell. Biol. 1999; 19: 8028. 3. Mayran N, Traverso V, Maroux S, Massey-Harroche D. Cellular and subcellular localizations of annexins I, IV, and VI in lung epithelia. Am J Physiol Lung Cell Mol Physiol 1996; 270: L863. 4. Dubois T, Soula M, Moss SE, Russo-Marie F, Rothhut B. Potential interaction between annexin VI and a 56-kDa protein kinase in T cells. Biochem. Biophys. Res Commun. 1995; 212: 270. 5. Lin HC, Sudhof TC, Anderson RG. Annexin VI is required for budding of clathrin-coated pits. Cell 1992; 70: 283. 6. Takashi S, Park J, Fang S, Koyama S, Parikh I, Adler KB. A peptide against the N-terminus of myristoylated alanine-rich C kinase substrate inhibits degranulation of human leukocytes in vitro. Am. J. Respir. Cell Mol. Biol. 2006; 34: 647. 7. Rogers DF, Barnes PJ. 2006. Treatment of airway mucus hypersecretion. Ann. Med. 2006; 38: 116. 8. Li Y, Martin LD, Spizz G, Adler KB. MARCKS protein is a key molecule regulating mucin secretion by human airway epithelial cells in vitro. J. Biol. Chem. 2001; 276: 40982. 9. Walzer T, Galibert L, De Smedt T. 2005. Dendritic cell function in mice lacking Plexin C1. Int. Immunol. 2005; 17: 943..
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