Spreadsheet: 0d58a125-545f-4996-8c37-26b7542b51b8
Sheet: Table S2

Table S2. Enrichment scores and statistics of the top 50 enriched GO gene sets from GSEA analysis of the mesenchymal versus non-mesenchymal adult and pediatric astrocytoma subtypes.
(A) [NAME] (TCGA data portal, 2010): Mesenchymal subtype (n=56) vs Classical, Proneural and Neural subtypes (n=117)
NAME | Details | SIZE | ES | NES | NOM p-val | [NAME] q-val | FWER p-val | RANK AT MAX | LEADING EDGE
PROTEOLYSIS | Genes annotated by the GO term GO:0006508. The hydrolysis of a peptide bond or bonds within a protein. | 182 | 0.58398026 | 1.8996974 | 0 | 0.14164652 | 0.084 | 1888 | tags=25%, list=10%, signal=28%
NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS | Genes annotated by the GO term GO:0051248. Any process that stops, prevents or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein. | 47 | 0.5519255 | 1.8942899 | 0.0020833334 | 0.07861595 | 0.09 | 1683 | tags=26%, list=9%, signal=28%
[NAME]* | Genes annotated by the GO term GO:0045321. A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor. | 65 | 0.7012435 | 1.888192 | 0 | 0.05559224 | 0.095 | 2303 | tags=46%, list=12%, signal=52%
NEGATIVE_REGULATION_OF_CELLULAR_PROTEIN_METABOLIC_PROCESS | Genes annotated by the GO term GO:0032269. Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. | 44 | 0.56448257 | 1.8787977 | 0.002105263 | 0.05055001 | 0.106 | 1683 | tags=27%, list=9%, signal=30%
LYMPHOCYTE_ACTIVATION* | Genes annotated by the GO term GO:0046649. A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor. | 58 | 0.7059005 | 1.8783545 | 0 | 0.040699266 | 0.107 | 2303 | tags=48%, list=12%, signal=55%
PEPTIDASE_ACTIVITY | Genes annotated by the GO term GO:0008233. Catalysis of the hydrolysis of peptide bonds. | 166 | 0.56005687 | 1.8647871 | 0 | 0.04080432 | 0.121 | 1888 | tags=26%, list=10%, signal=29%
IMMUNE_SYSTEM_PROCESS* | Genes annotated by the GO term GO:0002376. Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. | 317 | 0.704384 | 1.851205 | 0 | 0.04443936 | 0.149 | 2178 | tags=46%, list=12%, signal=51%
CELL_ACTIVATION | Genes annotated by the GO term GO:0001775. A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand. | 72 | 0.6699146 | 1.8450927 | 0 | 0.044891402 | 0.168 | 2303 | tags=42%, list=12%, signal=47%
POSITIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS | Genes annotated by the GO term GO:0051240. Any process that activates or increases the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. | 63 | 0.6814106 | 1.8424371 | 0 | 0.041433204 | 0.174 | 2915 | tags=52%, list=16%, signal=62%
MYELOID_CELL_DIFFERENTIATION* | Genes annotated by the GO term GO:0030099. The process whereby a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, [NAME], [NAME], or erythrocyte lineages. | 37 | 0.64477587 | 1.8377069 | 0.0062240665 | 0.04075537 | 0.19 | 1742 | tags=41%, list=9%, signal=45%
POSITIVE_REGULATION_OF_IMMUNE_SYSTEM_PROCESS* | Genes annotated by the GO term GO:0002684. Any process that activates or increases the frequency, rate, or extent of an immune system process. | 49 | 0.70670646 | 1.8349855 | 0 | 0.038921364 | 0.202 | 2303 | tags=49%, list=12%, signal=56%
HEMOPOIETIC_OR_LYMPHOID_ORGAN_DEVELOPMENT* | Genes annotated by the GO term GO:0048534. The process whose specific outcome is the progression of any organ involved in hemopoiesis or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation. | 75 | 0.60468143 | 1.8346964 | 0 | 0.0358256 | 0.203 | 2174 | tags=36%, list=12%, signal=41%
IMMUNE_SYSTEM_DEVELOPMENT* | Genes annotated by the GO term [NAME]. The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. | 79 | 0.59838194 | 1.828822 | 0 | 0.03542803 | 0.211 | 2174 | tags=37%, list=12%, signal=41%
HEMOPOIESIS* | Genes annotated by the GO term GO:0030097. The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. | 73 | 0.5991957 | 1.8284972 | 0 | 0.032897457 | 0.211 | 2174 | tags=36%, list=12%, signal=40%
REGULATION_OF_IMMUNE_SYSTEM_PROCESS* | Genes annotated by the GO term GO:0002682. Any process that modulates the frequency, rate, or extent of an immune system process. | 65 | 0.6733299 | 1.8283325 | 0 | 0.030704292 | 0.211 | 2915 | tags=51%, list=16%, signal=60%
LEUKOCYTE_DIFFERENTIATION* | Genes annotated by the GO term GO:0002521. The process whereby a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a plasmacytoid dendritic cell or any cell of the myeloid [NAME] or [NAME]. | 36 | 0.67451024 | 1.8281246 | 0 | 0.028785275 | 0.211 | 2174 | tags=42%, list=12%, signal=47%
RESPONSE_TO_EXTERNAL_STIMULUS | Genes annotated by the GO term GO:0009605. 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 an external stimulus. | 298 | 0.68827605 | 1.8202683 | 0 | 0.031036276 | 0.23 | 2227 | tags=42%, list=12%, signal=47%
PROTEIN_SECRETION | Genes annotated by the GO term GO:0009306. The regulated release of proteins from a cell or group of cells. | 32 | 0.6915469 | 1.8136595 | 0 | 0.032326 | 0.249 | 2941 | tags=50%, list=16%, signal=59%
CYTOKINE_PRODUCTION* | Genes annotated by the GO term GO:0001816. The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. | 71 | 0.66287917 | 1.8118788 | 0 | 0.03159998 | 0.253 | 1899 | tags=38%, list=10%, signal=42%
POSITIVE_REGULATION_OF_SIGNAL_TRANSDUCTION | Genes annotated by the GO term GO:0009967. Any process that activates or increases the frequency, rate or extent of signal transduction. | 118 | 0.58030254 | 1.8078449 | 0.002079002 | 0.03127606 | 0.259 | 2129 | tags=37%, list=11%, signal=42%
RESPONSE_TO_WOUNDING* | Genes annotated by the GO term GO:0009611. 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 indicating damage to the organism. | 181 | 0.725041 | 1.80405 | 0 | 0.031621613 | 0.271 | 2153 | tags=48%, list=12%, signal=53%
REGULATION_OF_I_KAPPAB_KINASE_NF_KAPPAB_CASCADE | Genes annotated by the GO term GO:0043122. Any process that modulates an I-kappaB kinase/NF-kappaB induced cascade. | 85 | 0.64756924 | 1.8025794 | 0 | 0.031026453 | 0.273 | 3120 | tags=49%, list=17%, signal=59%
NEGATIVE_REGULATION_OF_PROGRAMMED_CELL_DEATH | Genes annotated by the GO term GO:0043069. Any process that stops, prevents or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. | 144 | 0.53535897 | 1.7994857 | 0.0020449897 | 0.030947676 | 0.282 | 2726 | tags=30%, list=15%, signal=35%
NEGATIVE_REGULATION_OF_APOPTOSIS | Genes annotated by the GO term GO:0043066. Any process that stops, prevents or reduces the frequency, rate or extent of cell death by apoptosis. | 143 | 0.5305344 | 1.798122 | 0.0020325202 | 0.030300664 | 0.285 | 2726 | tags=29%, list=15%, signal=34%
I_KAPPAB_KINASE_NF_KAPPAB_CASCADE | Genes annotated by the GO term GO:0007249. A series of reactions initiated by the activation of the transcription factor NF-kappaB. NF-kappaB is sequestered by the inhibitor [NAME], and is released when [NAME] is phosphorylated by activated I-kappaB kinase. | 105 | 0.6074292 | 1.7936354 | 0.0020703934 | 0.031057095 | 0.298 | 3120 | tags=48%, list=17%, signal=57%
LIPID_RAFT | Genes annotated by the GO term GO:0045121. Specialized membrane domains composed mainly of cholesterol and sphingolipids, and relatively poor in polyunsaturated lipids such as glycerophospholipids. The formation of these membrane domains is promoted by the presence of cholesterol in the lipid bilayer: the rigid hexagonal rings of cholesterol can pack tightly against the saturated hydrocarbon chains of some membrane lipids, allowing these lipids to assemble into cohesive units floating in the mass of loosely packed polyunsaturated plasma membrane components. | 27 | 0.75509185 | 1.7934586 | 0 | 0.030003088 | 0.299 | 2174 | tags=56%, list=12%, signal=63%
MULTI_ORGANISM_PROCESS | Genes annotated by the GO term GO:0051704. The processes by which an organism has an effect on another organism of the same or different species. | 153 | 0.60923135 | 1.7890965 | 0.0021645022 | 0.031380057 | 0.312 | 3658 | tags=45%, list=20%, signal=56%
T_CELL_ACTIVATION* | Genes annotated by the GO term GO:0042110. The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. | 42 | 0.7394824 | 1.7880504 | 0 | 0.030621197 | 0.317 | 2303 | tags=50%, list=12%, signal=57%
INTERACTION_WITH_HOST | Genes annotated by the GO term GO:0051701. An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism. | 17 | 0.59201556 | 1.7832662 | 0.0021008404 | 0.032029167 | 0.327 | 4322 | tags=41%, list=23%, signal=54%
IMMUNE_RESPONSE* | Genes annotated by the GO term GO:0006955. Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. | 227 | 0.7230241 | 1.7815238 | 0 | 0.03150177 | 0.329 | 2227 | tags=49%, list=12%, signal=55%
RECEPTOR_COMPLEX | Genes annotated by the GO term GO:0043235. Any protein group composed of two or more subunits, which may or may not be identical, which undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. | 56 | 0.6679801 | 1.781436 | 0 | 0.030599952 | 0.329 | 3072 | tags=57%, list=17%, signal=68%
REGULATION_OF_LYMPHOCYTE_ACTIVATION* | Genes annotated by the GO term GO:0051249. Any process that modulates the frequency, rate or extent of lymphocyte activation. | 33 | 0.7232123 | 1.7797043 | 0 | 0.030783845 | 0.334 | 2303 | tags=55%, list=12%, signal=62%
RESPONSE_TO_BIOTIC_STIMULUS | Genes annotated by the GO term GO:0009607. 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 biotic stimulus, a stimulus caused or produced by a living organism. | 113 | 0.6237443 | 1.778802 | 0 | 0.030397722 | 0.34 | 3545 | tags=50%, list=19%, signal=61%
PROTEIN_AMINO_ACID_O_LINKED_GLYCOSYLATION | Genes annotated by the GO term GO:0006493. The formation of O-glycans by addition of glycosyl groups either to the hydroxyl group of peptidyl-serine, peptidyl-threonine, peptidyl-hydroxylysine, or peptidyl-hydroxyproline, or to the phenol group of peptidyl-tyrosine. | 18 | 0.68124175 | 1.7766534 | 0.008385744 | 0.030318884 | 0.347 | 2670 | tags=44%, list=14%, signal=52%
BASOLATERAL_PLASMA_MEMBRANE | Genes annotated by the GO term GO:0016323. Part of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis. | 33 | 0.6659652 | 1.7691301 | 0.005976096 | 0.032386918 | 0.37 | 1358 | tags=36%, list=7%, signal=39%
ADAPTIVE_IMMUNE_RESPONSE* | Genes annotated by the GO term GO:0002250. An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory). | 25 | 0.7852175 | 1.7680734 | 0 | 0.03200223 | 0.378 | 2381 | tags=56%, list=13%, signal=64%
BLOOD_COAGULATION* | Genes annotated by the GO term GO:0007596. The sequential process by which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. | 41 | 0.72082895 | 1.7659619 | 0.0020491802 | 0.03254753 | 0.387 | 2799 | tags=44%, list=15%, signal=52%
POSITIVE_REGULATION_OF_I_KAPPAB_KINASE_NF_KAPPAB_CASCADE | Genes annotated by the GO term GO:0043123. Any process that activates or increases the frequency, rate or extent of an I-kappaB kinase/NF-kappaB induced cascade. | 79 | 0.6320501 | 1.7658417 | 0.006198347 | 0.031691015 | 0.387 | 3120 | tags=48%, list=17%, signal=58%
POSITIVE_REGULATION_OF_IMMUNE_RESPONSE* | Genes annotated by the GO term GO:0050778. Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. | 29 | 0.68715924 | 1.7640384 | 0 | 0.031616256 | 0.393 | 2915 | tags=52%, list=16%, signal=61%
ADAPTIVE_IMMUNE_RESPONSE_GO_0002460* | Genes annotated by the GO term GO:0002460. An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains, and allowing for enhanced responses upon subsequent exposures to the same antigen (immunological memory). Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies). | 24 | 0.7935208 | 1.7633244 | 0 | 0.031047728 | 0.393 | 2178 | tags=54%, list=12%, signal=61%
REGULATION_OF_BODY_FLUID_LEVELS | Genes annotated by the GO term GO:0050878. Any process that modulates the levels of body fluids. | 55 | 0.64454323 | 1.7616718 | 0 | 0.031319126 | 0.398 | 2799 | tags=35%, list=15%, signal=41%
HEMOSTASIS | Genes annotated by the GO term GO:0007599. The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part. | 46 | 0.69397414 | 1.7610756 | 0.002057613 | 0.03064604 | 0.398 | 2799 | tags=41%, list=15%, signal=48%
INFLAMMATORY_RESPONSE* | Genes annotated by the GO term GO:0006954. 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. | 122 | 0.7493227 | 1.7606447 | 0 | 0.03018896 | 0.399 | 2147 | tags=54%, list=12%, signal=61%
NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS | Genes annotated by the GO term GO:0051093. Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). | 188 | 0.48331037 | 1.7570577 | 0.0040650405 | 0.030519893 | 0.41 | 2726 | tags=28%, list=15%, signal=32%
REGULATION_OF_IMMUNE_RESPONSE* | Genes annotated by the GO term GO:0050776. Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. | 33 | 0.65700406 | 1.7565224 | 0 | 0.030005015 | 0.41 | 2915 | tags=45%, list=16%, signal=54%
B_CELL_ACTIVATION* | Genes annotated by the GO term GO:0042113. The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. | 19 | 0.7481354 | 1.7533273 | 0 | 0.03034453 | 0.413 | 2178 | tags=53%, list=12%, signal=60%
DEFENSE_RESPONSE* | Genes annotated by the GO term GO:0006952. Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. | 257 | 0.6820253 | 1.7481945 | 0 | 0.031962637 | 0.432 | 2868 | tags=54%, list=15%, signal=63%
ENDOPEPTIDASE_ACTIVITY | Genes annotated by the GO term GO:0004175. Catalysis of the hydrolysis of nonterminal peptide linkages in oligopeptides or polypeptides, and comprising any enzyme of sub-subclasses EC:3.4.21-99. They are classfied according to the presence of essential catalytic residues or ions at their active sites. | 110 | 0.52420056 | 1.7480506 | 0.006329114 | 0.031357154 | 0.432 | 1502 | tags=24%, list=8%, signal=26%
RESPONSE_TO_OTHER_ORGANISM | Genes annotated by the GO term GO:0051707. 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 another living organism. | 78 | 0.67080843 | 1.747953 | 0 | 0.030768713 | 0.432 | 3545 | tags=56%, list=19%, signal=69%
COAGULATION* | Genes annotated by the GO term GO:0050817. The process by which a fluid solution, or part of it, changes into a solid or semisolid mass. | 42 | 0.71086454 | 1.7464352 | 0 | 0.030790797 | 0.441 | 2799 | tags=43%, list=15%, signal=50%
(B) Pediatric Astrocytoma (Paugh et al. 2010): HC3/Mesenchymal subtype (n=13) vs HC1/Proliferative and HC2/Proneural subtypes (n=40)
NAME | Details | SIZE | ES | NES | NOM p-val | [NAME] q-val | FWER p-val | RANK AT MAX | LEADING EDGE
I_KAPPAB_KINASE_NF_KAPPAB_CASCADE | Genes annotated by the GO term GO:0007249. A series of reactions initiated by the activation of the transcription factor NF-kappaB. NF-kappaB is sequestered by the inhibitor [NAME], and is released when [NAME] is phosphorylated by activated I-kappaB kinase. | 105 | 0.6595768 | 1.9057826 | 0 | 0.2634711 | 0.105 | 3393 | tags=47%, list=16%, signal=56%
REGULATION_OF_I_KAPPAB_KINASE_NF_KAPPAB_CASCADE | Genes annotated by the GO term GO:0043122. Any process that modulates an I-kappaB kinase/NF-kappaB induced cascade. | 84 | 0.66922194 | 1.8559335 | 0 | 0.28780663 | 0.221 | 3539 | tags=49%, list=17%, signal=59%
POSITIVE_REGULATION_OF_I_KAPPAB_KINASE_NF_KAPPAB_CASCADE | Genes annotated by the GO term GO:0043123. Any process that activates or increases the frequency, rate or extent of an I-kappaB kinase/NF-kappaB induced cascade. | 78 | 0.67555517 | 1.8494384 | 0 | 0.21176806 | 0.241 | 3539 | tags=49%, list=17%, signal=59%
INTRAMOLECULAR_OXIDOREDUCTASE_ACTIVITY | Genes annotated by the GO term GO:0016860. Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor are the same molecule, and no oxidized product appears. | 18 | 0.62068516 | 1.795388 | 0.001996008 | 0.2936369 | 0.387 | 2393 | tags=33%, list=12%, signal=38%
NUCLEAR_ENVELOPE_ENDOPLASMIC_RETICULUM_NETWORK | Genes annotated by the GO term GO:0042175. The continuous network of membranes encompassing the outer nuclear membrane and the endoplasmic reticulum. | 91 | 0.5171912 | 1.7933623 | 0.008130081 | 0.24285361 | 0.396 | 3765 | tags=45%, list=18%, signal=55%
PROTEIN_SECRETION | Genes annotated by the GO term GO:0009306. The regulated release of proteins from a cell or group of cells. | 32 | 0.6742901 | 1.784493 | 0 | 0.22971092 | 0.439 | 2824 | tags=38%, list=14%, signal=43%
IMMUNE_EFFECTOR_PROCESS* | Genes annotated by the GO term GO:0002252. Any process of the immune system that occurs as part of an immune response. | 36 | 0.61778104 | 1.7838286 | 0.002 | 0.19771154 | 0.439 | 3539 | tags=36%, list=17%, signal=43%
PEPTIDYL_AMINO_ACID_MODIFICATION | Genes annotated by the GO term GO:0018193. The alteration of an amino acid residue in a peptide. | 56 | 0.514182 | 1.7701207 | 0.001984127 | 0.2059169 | 0.488 | 3937 | tags=34%, list=19%, signal=42%
ESTABLISHMENT_OF_PROTEIN_LOCALIZATION | Genes annotated by the GO term GO:0045184. The directed movement of a protein to a specific location. | 182 | 0.4574978 | 1.7492359 | 0 | 0.23886599 | 0.564 | 3556 | tags=34%, list=17%, signal=41%
PROTEIN_BINDING_BRIDGING | Genes annotated by the GO term GO:0030674. Interacting selectively with two or more protein molecules, or a protein and another macromolecule or complex, simultaneously, thereby physically linking the bound proteins or complexes to each other. | 58 | 0.5392576 | 1.7489498 | 0 | 0.21597072 | 0.564 | 2223 | tags=22%, list=11%, signal=25%
ENDOPLASMIC_RETICULUM_MEMBRANE | Genes annotated by the GO term GO:0005789. The lipid bilayer surrounding the endoplasmic reticulum. | 82 | 0.5324542 | 1.747269 | 0.010162601 | 0.19961795 | 0.569 | 3756 | tags=48%, list=18%, signal=58%
POSITIVE_REGULATION_OF_SIGNAL_TRANSDUCTION | Genes annotated by the GO term GO:0009967. Any process that activates or increases the frequency, rate or extent of signal transduction. | 116 | 0.58366925 | 1.7387458 | 0 | 0.20283504 | 0.608 | 2821 | tags=37%, list=14%, signal=43%
CYSTEINE_TYPE_ENDOPEPTIDASE_ACTIVITY | Genes annotated by the GO term GO:0004197. Catalysis of the hydrolysis of nonterminal peptide linkages in oligopeptides or polypeptides; a cysteine residue is at the active center. | 39 | 0.61041176 | 1.7376728 | 0.002020202 | 0.18932988 | 0.608 | 2285 | tags=33%, list=11%, signal=37%
ENDOPLASMIC_RETICULUM_PART | Genes annotated by the GO term GO:0044432. Any constituent part of the endoplasmic reticulum, the irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. | 92 | 0.5421305 | 1.735336 | 0.012526096 | 0.18024087 | 0.614 | 4566 | tags=55%, [NAME], signal=71%
PROTEIN_TRANSPORT | Genes annotated by the GO term GO:0015031. The directed movement of proteins into, out of, within or between cells. | 150 | 0.46299627 | 1.7268208 | 0.0038834952 | 0.1846005 | 0.639 | 3556 | tags=35%, list=17%, signal=42%
RESPONSE_TO_OTHER_ORGANISM | Genes annotated by the GO term GO:0051707. 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 another living organism. | 80 | 0.62686986 | 1.7260865 | 0.003960396 | 0.17413206 | 0.641 | 1994 | tags=29%, list=10%, signal=32%
IMMUNE_RESPONSE* | Genes annotated by the GO term GO:0006955. Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. | 226 | 0.6312343 | 1.7133311 | 0 | 0.18817677 | 0.672 | 2995 | tags=38%, list=14%, signal=44%
INTRACELLULAR_PROTEIN_TRANSPORT | Genes annotated by the GO term GO:0006886. The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. | 138 | 0.45941243 | 1.7112304 | 0.003944773 | 0.18177707 | 0.679 | 4851 | tags=43%, list=23%, signal=56%
CYSTEINE_TYPE_PEPTIDASE_ACTIVITY | Genes annotated by the GO term GO:0008234. Catalysis of the hydrolysis of peptide linkages in oligopeptides or polypeptides; a cysteine residue is at the active center. | 53 | 0.56235904 | 1.703346 | 0.004056795 | 0.18886481 | 0.701 | 2879 | tags=34%, list=14%, signal=39%
PEPTIDYL_TYROSINE_PHOSPHORYLATION | Genes annotated by the GO term GO:0018108. The posttranslational phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine. | 26 | 0.59336936 | 1.7019228 | 0.009803922 | 0.18226492 | 0.705 | 3937 | tags=35%, list=19%, signal=43%
PROTEIN_LOCALIZATION | Genes annotated by the GO term GO:0008104. The processes by which a protein is transported to, or maintained in, a specific location. | 206 | 0.42913967 | 1.6972041 | 0 | 0.18461433 | 0.726 | 3556 | tags=32%, list=17%, signal=38%
JAK_STAT_CASCADE | Genes annotated by the GO term GO:0007259. The processes by which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of cytokines to their cognate receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes. | 31 | 0.6942693 | 1.6959977 | 0.006302521 | 0.17879963 | 0.732 | 2607 | tags=48%, list=13%, signal=55%
BLOOD_COAGULATION* | Genes annotated by the GO term GO:0007596. The sequential process by which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. | 42 | 0.611602 | 1.6939481 | 0.008048289 | 0.17527746 | 0.739 | 3425 | tags=40%, list=17%, signal=48%
HYDROLASE_ACTIVITY_ACTING_ON_GLYCOSYL_BONDS | Genes annotated by the GO term GO:0016798. Catalysis of the hydrolysis of any glycosyl bond. | 44 | 0.5912863 | 1.6885678 | 0.007984032 | 0.17769052 | 0.757 | 3907 | tags=45%, list=19%, signal=56%
RESPONSE_TO_WOUNDING* | Genes annotated by the GO term GO:0009611. 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 indicating damage to the organism. | 179 | 0.6116436 | 1.6853089 | 0.0021231424 | 0.17648716 | 0.768 | 3250 | tags=42%, list=16%, signal=50%
POSITIVE_REGULATION_OF_CYTOKINE_BIOSYNTHETIC_PROCESS* | Genes annotated by the GO term GO:0042108. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cytokines. | 24 | 0.69875693 | 1.6820852 | 0.0041841003 | 0.17475636 | 0.774 | 1994 | tags=29%, list=10%, signal=32%
HEMOSTASIS | Genes annotated by the GO term GO:0007599. The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part. | 47 | 0.58126116 | 1.6813279 | 0.01026694 | 0.16931255 | 0.777 | 3683 | tags=38%, list=18%, signal=46%
PEPTIDYL_TYROSINE_MODIFICATION | Genes annotated by the GO term GO:0018212. The modification of peptidyl-tyrosine. | 28 | 0.59853345 | 1.6791936 | 0.009940358 | 0.1666232 | 0.782 | 3937 | tags=36%, list=19%, signal=44%
COAGULATION* | Genes annotated by the GO term GO:0050817. The process by which a fluid solution, or part of it, changes into a solid or semisolid mass. | 43 | 0.60573906 | 1.6777278 | 0.006012024 | 0.16364588 | 0.786 | 3425 | tags=40%, list=17%, signal=47%
SKELETAL_DEVELOPMENT | Genes annotated by the GO term GO:0001501. The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton). | 101 | 0.57375866 | 1.6774597 | 0.004484305 | 0.15838933 | 0.786 | 2018 | tags=32%, list=10%, signal=35%
REGULATION_OF_SIGNAL_TRANSDUCTION | Genes annotated by the GO term GO:0009966. Any process that modulates the frequency, rate or extent of signal transduction. | 208 | 0.4822811 | 1.6745831 | 0.0020703934 | 0.15773863 | 0.792 | 2821 | tags=30%, list=14%, signal=34%
RESPONSE_TO_BIOTIC_STIMULUS | Genes annotated by the GO term GO:0009607. 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 biotic stimulus, a stimulus caused or produced by a living organism. | 115 | 0.56018484 | 1.6742839 | 0.0040983604 | 0.1535718 | 0.792 | 3439 | tags=34%, list=17%, signal=40%
PROTEASE_INHIBITOR_ACTIVITY | Genes annotated by the GO term GO:0030414. Stops, prevents or reduces the activity of a protease, any enzyme catalyzes the hydrolysis peptide bonds. | 41 | 0.6119957 | 1.674032 | 0.0058708414 | 0.14935717 | 0.793 | 2971 | tags=34%, list=14%, signal=40%
NITROGEN_COMPOUND_BIOSYNTHETIC_PROCESS | Genes annotated by the GO term GO:0044271. The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. | 25 | 0.6578273 | 1.6685168 | 0.0061728396 | 0.1535264 | 0.812 | 4235 | tags=48%, list=20%, signal=60%
POSITIVE_REGULATION_OF_IMMUNE_RESPONSE* | Genes annotated by the GO term GO:0050778. Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. | 28 | 0.635812 | 1.6648954 | 0.008695652 | 0.15559863 | 0.82 | 3539 | tags=39%, list=17%, signal=47%
SENSORY_PERCEPTION_OF_CHEMICAL_STIMULUS | Genes annotated by the GO term GO:0007606. The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. | 17 | 0.6022291 | 1.6628785 | 0.0040816325 | 0.15481713 | 0.827 | 1882 | tags=18%, list=9%, signal=19%
WOUND_HEALING* | Genes annotated by the GO term GO:0042060. The series of events that restore integrity to a damaged tissue, following an injury. | 53 | 0.5610186 | 1.658761 | 0.004149378 | 0.15763065 | 0.837 | 3425 | tags=36%, list=17%, signal=43%
CYTOKINE_PRODUCTION* | Genes annotated by the GO term GO:0001816. The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. | 71 | 0.5711609 | 1.6584932 | 0.0042283298 | 0.15390027 | 0.838 | 3106 | tags=37%, list=15%, signal=43%
PEROXISOME_ORGANIZATION_AND_BIOGENESIS | Genes annotated by the GO term GO:0007031. A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a peroxisome. | 15 | 0.5542618 | 1.6575431 | 0.027027028 | 0.15166073 | 0.841 | 4851 | tags=47%, list=23%, signal=61%
TISSUE_DEVELOPMENT | Genes annotated by the GO term GO:0009888. The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure. | 135 | 0.4718992 | 1.6555295 | 0.004158004 | 0.15150762 | 0.843 | 2945 | tags=24%, list=14%, signal=28%
IMMUNE_SYSTEM_PROCESS* | Genes annotated by the GO term GO:0002376. Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. | 319 | 0.5728425 | 1.6551651 | 0.0060975607 | 0.1483694 | 0.844 | 3439 | tags=37%, list=17%, signal=44%
RECEPTOR_COMPLEX | Genes annotated by the GO term GO:0043235. Any protein group composed of two or more subunits, which may or may not be identical, which undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. | 54 | 0.6355298 | 1.6533269 | 0.01 | 0.14763099 | 0.846 | 2469 | tags=35%, list=12%, signal=40%
CYTOKINE_SECRETION* | Genes annotated by the GO term GO:0050663. The regulated release of cytokines from a cell or group of cells. Cytokines are any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity. | 18 | 0.67240953 | 1.6500844 | 0.008639309 | 0.14918973 | 0.85 | 2433 | tags=33%, list=12%, signal=38%
POSITIVE_REGULATION_OF_TRANSLATION | Genes annotated by the GO term [NAME]. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. | 33 | 0.6265914 | 1.6486865 | 0.0020408162 | 0.14817499 | 0.855 | 2283 | tags=27%, list=11%, signal=31%
[NAME] | Genes annotated by the GO term GO:0009615. 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. | 49 | 0.66161096 | 1.6453763 | 0.01622718 | 0.15011923 | 0.861 | 1892 | tags=35%, list=9%, signal=38%
REGULATION_OF_TRANSLATION | Genes annotated by the GO term GO:0006417. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. | 89 | 0.42775258 | 1.6449201 | 0.004201681 | 0.1475714 | 0.862 | 3787 | tags=26%, list=18%, signal=31%
PROGRAMMED_CELL_DEATH | Genes annotated by the GO term GO:0012501. Cell death resulting from activation of endogenous cellular processes. | 415 | 0.43534467 | 1.6434815 | 0 | 0.1467627 | 0.867 | 3335 | tags=30%, list=16%, signal=35%
ADAPTIVE_IMMUNE_RESPONSE* | Genes annotated by the GO term GO:0002250. An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory). | 25 | 0.6952124 | 1.640711 | 0.010373444 | 0.14860992 | 0.871 | 3539 | tags=44%, list=17%, signal=53%
CYTOKINE_BIOSYNTHETIC_PROCESS* | Genes annotated by the GO term GO:0042089. The chemical reactions and pathways resulting in the formation of cytokines, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity. | 40 | 0.6468115 | 1.6368079 | 0.0061728396 | 0.1517207 | 0.873 | 3106 | tags=38%, list=15%, signal=44%
REGULATION_OF_PROTEIN_AMINO_ACID_PHOSPHORYLATION | Genes annotated by the GO term GO:0001932. Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein. | 29 | 0.54500157 | 1.6362019 | 0.009652509 | 0.14948782 | 0.874 | 5157 | tags=41%, list=25%, signal=55%
DEFENSE_RESPONSE* | Genes annotated by the GO term GO:0006952. Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. | 252 | 0.6044023 | 1.6359377 | 0.012658228 | 0.1468725 | 0.874 | 3249 | tags=39%, list=16%, signal=46%
PROTEIN_TARGETING | Genes annotated by the GO term GO:0006605. The process of targeting specific proteins to particular membrane-bound subcellular organelles. Usually requires an organelle specific protein sequence motif. | 103 | 0.4593204 | 1.6354048 | 0.004056795 | 0.14492728 | 0.874 | 3556 | tags=31%, list=17%, signal=37%
APOPTOSIS_GO | Genes annotated by the GO term [NAME]. A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle the cell and result in cell death. Apoptosis begins internally with condensation and subsequent fragmentation of the cell nucleus (blebbing) while the plasma membrane remains intact. Other characteristics of apoptosis include DNA fragmentation and the exposure of phosphatidyl serine on the cell surface. | 414 | 0.432275 | 1.6344302 | 0.0021321962 | 0.14379013 | 0.877 | 3335 | tags=30%, list=16%, signal=35%
Abbreviations: ES: enrichment score; NES: normalized enrichment score; NOM p-val: nominal p-value; [NAME] q-val = false discovery rate q-value; FWER p-val: Family-wise error rate p-value
Red text = gene sets with [NAME] of >25% and hence were excluded from analysis
* Defense/Immune Response related gene sets