Contents IFN_24h_RNA_vs_RVFV_24h_RNA



S5 H.1: Statistical overview

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SUMMARY


MA plots with GeneOntology extension:


Heat map based on fold change selection

S5 H.2: Differential expressed genes

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S5 H.3: Piano GO enrichment

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UP/DOWNIDNameDescriptionP-value
DOWNGO:0000139Golgi membrane"The lipid bilayer surrounding any of the compartments of the Golgi apparatus." [GOC:mah]9.999e-05
DOWNGO:0048471perinuclear region of cytoplasm"Cytoplasm situated near, or occurring around, the nucleus." [GOC:jid]9.999e-05
DOWNGO:0005764lysosome"A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." [GOC:mah, ISBN:0198506732]9.999e-05
DOWNGO:0005874microtubule"Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle." [ISBN:0879693568]9.999e-05
DOWNGO:0005743mitochondrial inner membrane"The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae." [GOC:ai]9.999e-05
DOWNGO:0005975carbohydrate metabolic process"The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule." [GOC:mah, ISBN:0198506732]9.999e-05
DOWNGO:0005747mitochondrial respiratory chain complex I"A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. It contains about 25 different polypeptide subunits, including NADH dehydrogenase (ubiquinone), flavin mononucleotide and several different iron-sulfur clusters containing non-heme iron. The iron undergoes oxidation-reduction between Fe(II) and Fe(III), and catalyzes proton translocation linked to the oxidation of NADH by ubiquinone." [GOC:mtg_sensu, ISBN:0198547684]9.999e-05
DOWNGO:0005777peroxisome"A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism." [GOC:pm, PMID:9302272, UniProtKB-KW:KW-0576]0.000149985
DOWNGO:0045296cadherin binding"Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion." [GOC:bf]9.999e-05
DOWNGO:0000502proteasome complex"A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core." [GOC:rb, http://en.wikipedia.org/wiki/Proteasome]9.999e-05
DOWNGO:0006979response to oxidative stress"Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC:jl, PMID:12115731]0.00589945
DOWNGO:0015031protein transport"The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]9.999e-05
DOWNGO:0005765lysosomal membrane"The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm." [GOC:ai]9.999e-05
DOWNGO:0043209myelin sheath"An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system." [GOC:cjm, GOC:jl, NIF_Subcellular:sao-593830697, Wikipedia:Myelin]9.999e-05
DOWNGO:0003735structural constituent of ribosome"The action of a molecule that contributes to the structural integrity of the ribosome." [GOC:mah]9.999e-05
DOWNGO:0000786nucleosome"A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures." [GOC:elh]9.999e-05
UPGO:0006366transcription from RNA polymerase II promoter"The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs)." [GOC:jl, GOC:txnOH, ISBN:0321000382]9.999e-05
UPGO:0000978RNA polymerase II core promoter proximal region sequence-specific DNA binding"Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II." [GOC:txnOH]9.999e-05
UPGO:0001077transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding"Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:txnOH]9.999e-05
UPGO:0044212transcription regulatory region DNA binding"Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:jl, GOC:txnOH, SO:0005836]9.999e-05
UPGO:0006357regulation of transcription from RNA polymerase II promoter"Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH]9.999e-05
UPGO:0043123positive regulation of I-kappaB kinase/NF-kappaB signaling"Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling." [GOC:jl]0.0024498
UPGO:0051092positive regulation of NF-kappaB transcription factor activity"Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB." [GOC:dph, GOC:tb, PMID:15087454, PMID:15170030]0.0010999
UPGO:0043565sequence-specific DNA binding"Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding." [GOC:jl]9.999e-05
UPGO:0006955immune response"Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]9.999e-05
UPGO:0004842ubiquitin-protein transferase activity"Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages." [GOC:BioGRID, GOC:jh2, PMID:9635407]9.999e-05
UPGO:0001078transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding"Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:txnOH]9.999e-05
UPGO:0006974cellular response to DNA damage stimulus"Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC:go_curators]9.999e-05
UPGO:0061630ubiquitin protein ligase activity"Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues." [GOC:BioGRID, GOC:dph, GOC:mah, GOC:tb, PMID:22863777]9.999e-05
UPGO:0006281DNA repair"The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID:11563486]9.999e-05
UPGO:0010628positive regulation of gene expression"Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb]0.0122989
UPGO:0032088negative regulation of NF-kappaB transcription factor activity"Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB." [GOC:dph, GOC:rl, GOC:tb]0.000849915
UPGO:0006954inflammatory response"The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages." [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732]0.0246476
UPGO:0001047core promoter binding"Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH]9.999e-05
UPGO:0000977RNA polymerase II regulatory region sequence-specific DNA binding"Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II." [GOC:txnOH]0.00019998
UPGO:0071222cellular response to lipopolysaccharide"Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria." [GOC:mah]9.999e-05
UPGO:0003682chromatin binding"Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC:jl, ISBN:0198506732, PMID:20404130]0.0142985
UPGO:0090090negative regulation of canonical Wnt signaling pathway"Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes." [GOC:dph, GOC:tb]0.015548