{"text_format":"3","workbook":"xls","n_sheets":1,"sheets":["Additional File 7"],"read":"whole","date_system":"1900","formulas":"cached_only"}

{"sheet":"Additional File 7","index":0,"n_rows":31,"n_cols":4,"rows_kept":31,"merged":[[1,0,1,2],[2,0,16,2],[28,3,30,3]],"flags":["formulas_cached_only"]}
[]
["Methods:"]
["A comparison of annotations included in the 4-fold filtered gene list (refered to as 'poly(I:C) response' in this workbook) to that of the 166 common response genes reported by Huang et al (refered to as 'Influenza reponse' in this workbook) was made using DAVID.  Huang et al had assigned each of the 166 genes an early, middle or late phase of response for each of the three pathogens studied (e.coli, c. albicans and influenza).  The phase assigments of the influenza pathogen were used to compare with our data as it is known to induce a similar response as poly(I:C).  Each of the poly(I:C) response gene lists were individually assigned to an early middle or late phase of response.  A gene was assigned to the Early phase if there was a 4-fold change in expression for either the 3 hour or 6 hour time point.  Likewise, a gene was assigned to the middle phase if a 4-fold response was observed at the 12 hour time point, and the Late phase if at the 24 hour time point.  These phase assignments correspond most closely with those of Huang et al.  In contrast to Huang et al, our data has 3 phases of down regulation where Huang only reports 1 phase of down regulation.  \n\nThe list of gene IDs associated with each Influenza phase and poly(I:C) phase were input into DAVID for analysis.  Background for the Influenza genes was the entire human genome, and background for poly(I:C) was the entire mouse genome.  The Functional Annotation Chart for each phase was copied and compared between Influenza and poly(I:C) responses.  Significant (p-value <= 0.05) common and unique Gene Ontology (GO) terms are summarized below where Blue is Biological Process, Red is Molecular Function and Green is Cellular Component.  \n\nQ Huang, D Liu, P Majewski, LC Schulte, JM Korn, RA Young, ES Lander, N Hacohen: The plasticity of dendritic cell responses to pathogens and their components. Science 2001, 294:870-5."]
{"$rows_empty":15}
[null,"Temporal Classifications","Color Scheme:"]
[null,"Early = 0 to 6 hours","Biological Process"]
[null,"Middle = 8 to 12 hours","Molecular Function"]
[null,"Late = 18 to 24 hours","Cellular Component"]
[null,null,"Bold terms are more general terms.  Terms after the colon are more specific terms.  Not all terms are included in the table."]
[]
[null,"Common Annotations","Poly (I:C) Only","Influenza Only"]
["Early Up","cell death: apoptosis\nmacromolecule metabolic/catabolic process: modification-dependent protein catabolic process\nmulticellular orgamismal process: cytokine production\nimmune system process: antigen processing and presentation, immune response\nresponse to stimulus: defense response, response to virus\ncatalytic activity: hydrolase activity\nbinding: protein binding\ncell part: cytoplasm","response to stimulus: innate immune response\nregulation of biological process: positive regulation of apoptosis, negative regulation of cell proliferation, negative regulation of viral reproduction\nmetabolic process: proteolysis involved in cellular protein catabolic process, post-translational protein modification, ISG15-protein conjugation\ncatalytic activity/transferase activity: 2'-5'-oligoadenylate synthetase activity\ncatalytic activity/hydrolase activity: GTPase activity, helicase activity, double-stranded RNA adenosine deaminase activity\nbinding: nucleotide/nucleoside binding, ATP binding, GTP binding, nucleic acid binding, double-stranded RNA binding, left-handed Z-DNA binding\ncell part: intracellular, external side of plasma membrane\nmacromolecular complex: MHC class I protein complex","immune system process: antigen processing and presentation of peptide antigen, antigen processing and presentation following phagocytosis\nresponse to stimulus: inflamatory response, chemotaxis, response to lipopolysaccharide\nsignaling: lipopolysaccaride-mediated siganling pathway, I-kappaB kinase/NF-kappaB cascade, JAK-STAT cascade\nregulation of biological process: regulation of metabolic process, regulation of cytokine/chemokine production, regulation of cellular biosynthetic process, regulation of signaling process, positive regulation of signal transduction, positive regulation of JNK cascade, positive regulation of translation\nestablishment of localization: oligopeptide transport\ncatalytic activity: hydrolase activity, threonine-type endopeptidase activity, MAP kinase tyrosine/serine/threonine phosphatase activity\ntransporter activity: oligopeptide transporter activity\nbinding: chemokine receptor binding, MHC class I protein binding, TAP1/2 binding\ncell part: cell fraction, intracellular part\nextracellular region part: extracellular space\nmacomolecular complex: MHC class I peptide loading complex, TAP complex"]
["Middle Up","cell death: positive regulation of programmed cell death, induction of apoptosis\ndevelopmental process: cell differentiation, cell development\nbiological regulation: regulation of biological quality\nsignaling process: intra cellular signaling cascade\nimmune system process: immune response\nresponse to stimulus: response to stress/biotic stimulus","immune system process: adaptive immune response, T-helper I type immune response, lymphocyte proliferation, T cell proliferation\nmetabolic process: aromatic compound biosynthetic process\nsignaling: enoplasmic reticulum protein signaling\ncellular process: vesicle docking during exocytosis\nbiological regulation: negative regulation of cell cycle, regulation of immune system process, regulation of T cell activation, regulation of activated T cell proliferation \ncatalytic activity: protein kinase activity\nmacromolecular complex: MHC class I protein complex","response to stimulus: inflamatory response, locomotory behanior\nlocalization: localization of cell\ncellular process: cellular component movement\nmulti-organism process: response to virus\nbiological regulation: negative regulation of cellular metabolic process, negative regulation of transcription DNA -dependant, positive reguation of signal transduction, positive regulation of I-kappaB kinase/NF-kappaB cascade\nbinding: cytokine activity, tumor necrosis factor receptor binding\ncell part: cell fraction\nextracellular region part: extracellular space"]
["Late Up","biological regulation: regulation of biological quality/process\nresponse to stimulus: response to external stimulus, response to wounding, response to stress","biological regulation: regulation of developmental process, regulation of biological quality, regulation of cell shape\norganelle part: nuclear chromosome part","developmental process: cell differentiation\nsignaling: protein kinase cascade\nbiological regulation: regulation of biological quality, homeostatic process, chemical/cellular homeostasis, cation/ion homeostasis, cellular calcium ion homeostasis, regulation of apoptosis, negative regulation of cell proliferation, regulation of viral genome replication\ncellular process: chemotaxis, lymphocyte activation\nimmune system process: humoral immune response\nlocalization: localization of cell\nresponse to stimulus: inflamatory response, response to oxidative stress, response to virus\nbinding: cytokine/chemokine binding, C-C chemokine receptor activity, chemokine activity\nchemoattractant activity\nmolecular transducer activity: thyroid horomone receptor activity\nextracellular region part: extracellular space\norganelle part: nuclear body, PML body"]
["Early Down","None","ribosome biogenesis and assembly","cellular process: cellular membrane organization, vesicle-mediated transport, endocytosis\nresponse to stimulus: response to wounding, defense response, infamatory response\nsignaling process: signal transmission/transduction, intracellular signaling cascade, second messenger mediated siganling\nmolecular tranducer activity: receptor activity\ncell part: membrane part, integral to plasma membrane"]
["Middle Down","None","cellular component organization: organelle organization, cellular component assembly\ncellular process: ribosome biogenesis\nmetabolic process: nitrogen compound metabolic process, catabolic process, primary metabolic process, cellular metabolic process, small molecule metabolic process, macromolecule metabolic process, organic acid metabolic process, cellular biosynthetic process, heterocycle metabolic process, gene expression, cellular nitrogen compound catabolic process, DNA/RNA metabolic process, protein modification process, tRNA metabolic process, cellular amino acid metabolic process, glutamine metabolic process, peptidyl-arginine methylation, tRNA-aminoacylation for protein translation, IMP biosythetic process\nbinding: adenyl nucleotide binding, ribonucleotide binding, ATP binding, nucleic acid binding, DNA replication origin binding, RNA binding, snoRNA binding\ncatalytic activity: ligase activity, aminoacyle-tRNA ligase activity, transferase activity, methyltransferase activity, histone-arginine N-methyltransferase activity, hydrolase activity, exonuclease activity\ncell part: intracellular part, membrane part, nuclear membrane part, \nmembrane-bounded organelle: mitochondrion, nucleus\nnon-membrane-bounded organelle: nuclear chromosome\norganelle part: chromosomal part, replication fork, chromosome centromeric region, Cajal body, organelle envelope, organelle lumen, nuclear part, nucleolar part, nuclear lumen\nmacromolecular complex: protein-DNA complex, replisome, alpha DNA polymerase primase complex, nuclear origin of replication recognition complex\n"]
["Late Down","response to stimulus: response to stress","cellular component organization: mitochondrion organization, release of cytochrome c from mitochondria\ncellular process: cell division, cell cycle phase\nmetabolic process: promary metobolic process, DNA repair, cellular carbohydrate metabolic process, RNA metabolic process, cellular catabolic process, gene expression, macromolecule catabolic process\nbinding: receptor binding, growth factor activity, nucleotide binding, purine ribonucleotide binding\nenzyme regulator activity: cyclin-dependent protein kinase regulator activity\ncell part: intracellular membrane-bounded organelle, nucleus "]