Contents Mock_6h_RNA_vs_RVFV_6h_RNA



S5 C.1: Statistical overview

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SUMMARY


MA plots with GeneOntology extension:


Heat map based on fold change selection

S5 C.2: Differential expressed genes

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S5 C.3: Piano GO enrichment

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No heat map of the GSEA available, because to few significant entries found to use the plot function of the Piano package.

UP/DOWNIDNameDescriptionP-value
DOWNGO:0005198structural molecule activity"The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell." [GOC:mah, GOC:vw]0.009901
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]0.009901
DOWNGO:0031012extracellular matrix"A structure lying external to one or more cells, which provides structural support for cells or tissues." [GOC:mah, NIF_Subcellular:nlx_subcell_20090513]0.009901
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]0.009901
DOWNGO:0055037recycling endosome"An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane." [GOC:dph, GOC:jid, GOC:kmv, GOC:rph, PMID:10930469, PMID:15601896, PMID:16246101, PMID:21556374, PMID:21562044]0.009901
DOWNGO:0010951negative regulation of endopeptidase activity"Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins." [GOC:dph, GOC:tb]0.009901
DOWNGO:0005694chromosome"A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684]0.009901
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]0.009901
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]0.009901
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]0.009901
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]0.009901
DOWNGO:0031982vesicle"Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles]0.009901
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]0.009901
DOWNGO:0043005neuron projection"A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:jl, http://www.cogsci.princeton.edu/~wn/]0.009901
DOWNGO:0006631fatty acid metabolic process"The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [ISBN:0198547684]0.009901
DOWNGO:0060271cilium assembly"The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:BHF, GOC:cilia, GOC:dph, GOC:kmv, GOC:pr, GOC:vw, ISBN:0198506732, PMID:13978319, PMID:27350441, Reactome:R-HSA-5617833.2]0.009901
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]0.009901
DOWNGO:0050660flavin adenine dinucleotide binding"Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2." [CHEBI:24040, GOC:ai, GOC:imk, ISBN:0198506732]0.009901
DOWNGO:0008289lipid binding"Interacting selectively and non-covalently with a lipid." [GOC:ai]0.0247525
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]0.009901
DOWNGO:0000139Golgi membrane"The lipid bilayer surrounding any of the compartments of the Golgi apparatus." [GOC:mah]0.009901
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]0.009901
DOWNGO:0005929cilium"A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body." [GOC:cilia, GOC:curators, GOC:kmv, GOC:vw, ISBN:0198547684, PMID:16824949, PMID:17009929, PMID:20144998]0.009901
DOWNGO:0003735structural constituent of ribosome"The action of a molecule that contributes to the structural integrity of the ribosome." [GOC:mah]0.009901
DOWNGO:0005840ribosome"An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732]0.009901
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]0.009901
UPGO:0016604nuclear body"Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins." [GOC:ma, PMID:10330182]0.009901
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]0.009901
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]0.009901
UPGO:0045087innate immune response"Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens." [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu]0.009901
UPGO:0019882antigen processing and presentation"The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149, PMID:15771591, PMID:15928678]0.009901
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]0.009901
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]0.009901
UPGO:0009615response to virus"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 a stimulus from a virus." [GOC:hb]0.009901
UPGO:0002376immune system process"Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]0.009901
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]0.009901
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]0.009901
UPGO:0003714transcription corepressor activity"Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867]0.009901
UPGO:0000209protein polyubiquitination"Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain." [ISBN:0815316194]0.009901
UPGO:0001650fibrillar center"A structure found most metazoan nucleoli, but not usually found in lower eukaryotes; surrounded by the dense fibrillar component; the zone of transcription from multiple copies of the pre-rRNA genes is in the border region between these two structures." [PMID:10754561]0.009901
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]0.009901
UPGO:0031965nuclear membrane"Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space." [GOC:mah, GOC:pz]0.009901
UPGO:0005125cytokine activity"Functions to control the survival, growth, differentiation and effector function of tissues and cells." [ISBN:0198599471]0.009901
UPGO:0000932P-body"A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing." [GOC:clt, PMID:12730603]0.009901
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]0.009901
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]0.009901
UPGO:0042981regulation of apoptotic process"Any process that modulates the occurrence or rate of cell death by apoptotic process." [GOC:jl, GOC:mtg_apoptosis]0.009901
UPGO:0003725double-stranded RNA binding"Interacting selectively and non-covalently with double-stranded RNA." [GOC:jl]0.009901
UPGO:0051607defense response to virus"Reactions triggered in response to the presence of a virus that act to protect the cell or organism." [GOC:ai]0.009901
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]0.009901
UPGO:0008033tRNA processing"The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group." [GOC:jl, PMID:12533506]0.009901
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]0.009901
UPGO:0016607nuclear speck"A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy." [http://www.cellnucleus.com/]0.009901
UPGO:0042612MHC class I protein complex"A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules." [GOC:add, GOC:jl, ISBN:0120781859, ISBN:0781735149]0.009901
UPGO:0002474antigen processing and presentation of peptide antigen via MHC class I"The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules." [GOC:add, ISBN:0781735149, PMID:15224092, PMID:15771591]0.009901
UPGO:0007623circadian rhythm"Any biological process in an organism that recurs with a regularity of approximately 24 hours." [GOC:bf, GOC:go_curators]0.009901
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]0.009901
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]0.009901