BP

GO:0000122

negative regulation of transcription from RNA polymerase II promoter

Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.

ISS

BP

GO:0001080

nitrogen catabolite activation of transcription from RNA polymerase II promoter

A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.

IC

BP

GO:0006367

transcription initiation from RNA polymerase II promoter

Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.

TAS

BP

GO:0006954

inflammatory 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.

IEA

BP

GO:0007043

cell-cell junction assembly

The aggregation, arrangement and bonding together of a set of components to form a junction between cells.

IEA

BP

GO:0007165

signal transduction

The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.

TAS

BP

GO:0007219

Notch signaling pathway

A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.

IEA

BP

GO:0008206

bile acid metabolic process

The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.

IEA

BP

GO:0010804

negative regulation of tumor necrosis factor-mediated signaling pathway

Any process that decreases the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor.

IEA

BP

GO:0010988

regulation of low-density lipoprotein particle clearance

Any process that modulates the rate, frequency or extent of low-density lipoprotein particle clearance. Low-density lipoprotein particle clearance is the process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.

IDA

BP

GO:0015721

bile acid and bile salt transport

The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

TAS

BP

GO:0030522

intracellular receptor signaling pathway

Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.

ISS

BP

GO:0032088

negative 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.

IEA

BP

GO:0032692

negative regulation of interleukin-1 production

Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 production.

IEA

BP

GO:0032703

negative regulation of interleukin-2 production

Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production.

IEA

BP

GO:0032715

negative regulation of interleukin-6 production

Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production.

IEA

BP

GO:0034142

toll-like receptor 4 signaling pathway

Any series of molecular signals generated as a consequence of binding to toll-like receptor 4.

IDA

BP

GO:0034162

toll-like receptor 9 signaling pathway

Any series of molecular signals generated as a consequence of binding to toll-like receptor 9.

IEA

BP

GO:0034255

regulation of urea metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving urea.

ISS

BP

GO:0034971

histone H3-R17 methylation

The modification of histone H3 by addition of a methyl group to arginine at position 17 of the histone.

IDA

BP

GO:0035356

cellular triglyceride homeostasis

Any process involved in the maintenance of an internal steady state of triglyceride within a cell or between a cell and its external environment.

IDA

BP

GO:0035774

positive regulation of insulin secretion involved in cellular response to glucose stimulus

Any process that increases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.

IEA

BP

GO:0038183

bile acid signaling pathway

A series of molecular signals initiated by the binding of a bile acid to a receptor, and ending with regulation of a downstream cellular process, e.g. transcription.

ISS

BP

GO:0038185

intracellular bile acid receptor signaling pathway

A series of molecular signals initiated by a bile acid binding to an receptor located within a cell, and ending with regulation of a downstream cellular process, e.g. transcription.

IDA

BP

GO:0042593

glucose homeostasis

Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.

IEA

BP

GO:0042742

defense response to bacterium

Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.

IEA

BP

GO:0043066

negative regulation of apoptotic process

Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.

IDA

BP

GO:0043124

negative regulation of I-kappaB kinase/NF-kappaB signaling

Any process that stops, prevents, or reduces the frequency, rate or extent of -kappaB kinase/NF-kappaB signaling.

IDA

BP

GO:0043401

steroid hormone mediated signaling pathway

A series of molecular signals mediated by a steroid hormone binding to a receptor.

IEA

BP

GO:0045087

innate immune response

Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.

IEA

BP

GO:0045944

positive regulation of transcription from RNA polymerase II promoter

Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.

IMP

BP

GO:0046628

positive regulation of insulin receptor signaling pathway

Any process that increases the frequency, rate or extent of insulin receptor signaling.

IEA

BP

GO:0050728

negative regulation of inflammatory response

Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.

IEA

BP

GO:0055089

fatty acid homeostasis

Any process involved in the maintenance of an internal steady state of fatty acid within an organism or cell.

IEA

BP

GO:0061178

regulation of insulin secretion involved in cellular response to glucose stimulus

Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.

IDA

BP

GO:0070857

regulation of bile acid biosynthetic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids.

TAS

BP

GO:0070858

negative regulation of bile acid biosynthetic process

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids.

IDA

BP

GO:0071222

cellular 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.

IEA

BP

GO:0071398

cellular response to fatty acid

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 fatty acid stimulus.

IDA

BP

GO:0071417

cellular response to organonitrogen compound

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 an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.

ISS

BP

GO:0071638

negative regulation of monocyte chemotactic protein-1 production

Any process that stops, prevents, or reduces the frequency, rate, or extent of production of monocyte chemotactic protein-1.

IEA

BP

GO:0072615

interleukin-17 secretion

The regulated release of any member of the interleukin-17 family of cytokines from a cell.

IDA

BP

GO:0090181

regulation of cholesterol metabolic process

Any process that modulates the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.

TAS

BP

GO:1902714

negative regulation of interferon-gamma secretion

Any process that stops, prevents or reduces the frequency, rate or extent of interferon-gamma secretion.

IDA

BP

GO:1904179

positive regulation of adipose tissue development

Any process that activates or increases the frequency, rate or extent of adipose tissue development.

IEA

BP

GO:1904468

negative regulation of tumor necrosis factor secretion

Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor secretion.

IDA

BP

GO:2000188

regulation of cholesterol homeostasis

Any process that modulates the frequency, rate or extent of cholesterol homeostasis.

IEA

BP

GO:2000213

positive regulation of glutamate metabolic process

Any process that activates or increases the frequency, rate or extent of glutamate metabolic process.

ISS

BP

GO:2001250

positive regulation of ammonia assimilation cycle

Any process that activates or increases the frequency, rate or extent of ammonia assimilation cycle.

IEA

BP

GO:2001275

positive regulation of glucose import in response to insulin stimulus

Any process that activates or increases the frequency, rate or extent of glucose import in response to insulin stimulus.

IEA

CC

GO:0005654

nucleoplasm

That part of the nuclear content other than the chromosomes or the nucleolus.

TAS

CC

GO:0005719

nuclear euchromatin

The dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin.

IDA

MF

GO:0000980

RNA polymerase II distal enhancer sequence-specific DNA binding

Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.

IDA

MF

GO:0001077

transcriptional 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.

IDA

MF

GO:0001190

transcriptional activator activity, RNA polymerase II transcription factor binding

Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.

IDA

MF

GO:0003700

transcription factor activity, sequence-specific DNA binding

Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.

TAS

MF

GO:0003705

transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding

Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.

IDA

MF

GO:0003707

steroid hormone receptor activity

Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function.

IEA

MF

GO:0003713

transcription coactivator activity

Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.

TAS

MF

GO:0003714

transcription 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.

TAS

MF

GO:0004879

RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding

Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.

ISS

MF

GO:0004887

thyroid hormone receptor activity

Combining with thyroid hormone and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.

IEA

MF

GO:0005515

protein binding

Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

IPI

MF

GO:0008270

zinc ion binding

Interacting selectively and non-covalently with zinc (Zn) ions.

IEA

MF

GO:0016922

ligand-dependent nuclear receptor binding

Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein.

TAS

MF

GO:0032052

bile acid binding

Interacting selectively and non-covalently with bile acids, any of a group of steroid carboxylic acids occurring in bile.

ISS|TAS

MF

GO:0038181

bile acid receptor activity

Combining with a bile acid and transmitting the signal to initiate a change in cell activity. A bile acid is any member of a group of steroid carboxylic acids occurring in bile.

IDA

MF

GO:0043565

sequence-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.

IDA

MF

GO:0046965

retinoid X receptor binding

Interacting selectively and non-covalently with a retinoid X receptor.

IEA

MF

GO:1902122

chenodeoxycholic acid binding

Interacting selectively and non-covalently with chenodeoxycholic acid.

IDA