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education.
REACTOME | BIOLOGICAL OXIDATIONS Biological oxidations. All organisms are constantly exposed to foreign chemicals every day. These can be man-made (drugs, industrial chemicals) or natural (alkaloids, toxins from plants and animals). Uptake is usually via ingestion but inhalation and transdermal routes are also common.The very nature of many chemicals that make themsuitable
REACTOME | REGULATION OF GENE EXPRESSION IN ENDOCRINE Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells. Studies in mouse model systems indicate that the transcription factor neurogenin 3 plays a central role in the induction of endocrine differentiation in the developing pancreas(Servitja
REACTOME | CYCLIN A/B1/B2 ASSOCIATED EVENTS DURING G2/M Cyclin A/B1/B2 associated events during G2/M transition. Cell cycle progression is regulated by cyclin-dependent protein kinases at both the G1/S and the G2/M transitions. The G2/M transition is regulated through the phosphorylation of nuclear lamins and histones (reviewed in Sefton, 2001). The two B-type cyclins localize to different regions REACTOME | IRS ACTIVATION Stable Identifier. IRS is one of the mediators of insulin signalling events. It is activated by phosphorylation and triggers a cascade of events involving PI3K, SOS, RAF and the MAP kinases. The proteins mentioned under IRS are examples of IRS family members acting as indicated. More family members are to be confirmed and added in thefuture.
REACTOME | CD22 MEDIATED BCR REGULATION BCR activation is highly regulated and coreceptors like CD22 (SIGLEC2) set a signalling threshold to prevent aberrant immune response and autoimmune disease (Cyster et al. 1997, Han et al. 2005). CD22 is a glycoprotein found on the surface of B cells during restricted stages of development. CD22 is a member of the receptors of the sialic acid REACTOME | METAL SEQUESTRATION BY ANTIMICROBIAL PROTEINS Type. Metals are necessary for all forms of life including microorganisms, evidenced by the fact that metal cations are constituents of approximately 40% of all proteins crystallized to date (Waldron KJ et al. 2009; Foster AW et al. 2014; Guengerich FP 2014, 2015). The ability of microorganisms to maintain the intracellularmetal quota is
REACTOME | NEGATIVE REGULATORS OF DDX58/IFIH1 SIGNALING RIG-I-mediated production of IFN can, in turn, increase the transcription of RIG-I itself, thus setting into motion an IFN amplification loop, which if left unchecked, could become deleterious to the host. This module mainly focuses on the endogenous negative regulation of the RIG-I-like receptor (RLR) family proteins RIG-I andMDA5.
REACTOME | PURINERGIC SIGNALING IN LEISHMANIASIS INFECTION Purinergic signaling in leishmaniasis infection. The purinoreceptors are divided into inotropic (P2XR) and metabotropic (P2YR) subtypes whose ligands are the nucleotides ATP and UDP respectively (Cekic et al. 2016). The binding of these nucleotides to their receptors on macrophages have been associated with the activation of theinflammasome
REACTOME | ACTIVATION OF GENE EXPRESSION BY SREBF (SREBP) Activation of gene expression by SREBF (SREBP) After transiting to the nucleus SREBPs (SREBP1A/1C/2, SREBFs) bind short sequences, sterol regulatory elements (SREs), in the promoters of target genes (reviewed in Eberle et al. 2004, Weber et al. 2004). SREBPs alone are relatively weak activators of transcription, with SREBP1C being significantly HOME - REACTOME PATHWAY DATABASEDOCSDOWNLOADTABLE OF CONTENTSDOISDATA SCHEMAORCID INTEGRATION PROJECT Reactome is a free, open-source, curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology andeducation.
REACTOME | BIOLOGICAL OXIDATIONS Biological oxidations. All organisms are constantly exposed to foreign chemicals every day. These can be man-made (drugs, industrial chemicals) or natural (alkaloids, toxins from plants and animals). Uptake is usually via ingestion but inhalation and transdermal routes are also common.The very nature of many chemicals that make themsuitable
REACTOME | REGULATION OF GENE EXPRESSION IN ENDOCRINE Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells. Studies in mouse model systems indicate that the transcription factor neurogenin 3 plays a central role in the induction of endocrine differentiation in the developing pancreas(Servitja
REACTOME | CYCLIN A/B1/B2 ASSOCIATED EVENTS DURING G2/M Cyclin A/B1/B2 associated events during G2/M transition. Cell cycle progression is regulated by cyclin-dependent protein kinases at both the G1/S and the G2/M transitions. The G2/M transition is regulated through the phosphorylation of nuclear lamins and histones (reviewed in Sefton, 2001). The two B-type cyclins localize to different regions REACTOME | IRS ACTIVATION Stable Identifier. IRS is one of the mediators of insulin signalling events. It is activated by phosphorylation and triggers a cascade of events involving PI3K, SOS, RAF and the MAP kinases. The proteins mentioned under IRS are examples of IRS family members acting as indicated. More family members are to be confirmed and added in thefuture.
REACTOME | CD22 MEDIATED BCR REGULATION BCR activation is highly regulated and coreceptors like CD22 (SIGLEC2) set a signalling threshold to prevent aberrant immune response and autoimmune disease (Cyster et al. 1997, Han et al. 2005). CD22 is a glycoprotein found on the surface of B cells during restricted stages of development. CD22 is a member of the receptors of the sialic acid REACTOME | METAL SEQUESTRATION BY ANTIMICROBIAL PROTEINS Type. Metals are necessary for all forms of life including microorganisms, evidenced by the fact that metal cations are constituents of approximately 40% of all proteins crystallized to date (Waldron KJ et al. 2009; Foster AW et al. 2014; Guengerich FP 2014, 2015). The ability of microorganisms to maintain the intracellularmetal quota is
REACTOME | NEGATIVE REGULATORS OF DDX58/IFIH1 SIGNALING RIG-I-mediated production of IFN can, in turn, increase the transcription of RIG-I itself, thus setting into motion an IFN amplification loop, which if left unchecked, could become deleterious to the host. This module mainly focuses on the endogenous negative regulation of the RIG-I-like receptor (RLR) family proteins RIG-I andMDA5.
REACTOME | PURINERGIC SIGNALING IN LEISHMANIASIS INFECTION Purinergic signaling in leishmaniasis infection. The purinoreceptors are divided into inotropic (P2XR) and metabotropic (P2YR) subtypes whose ligands are the nucleotides ATP and UDP respectively (Cekic et al. 2016). The binding of these nucleotides to their receptors on macrophages have been associated with the activation of theinflammasome
REACTOME | ACTIVATION OF GENE EXPRESSION BY SREBF (SREBP) Activation of gene expression by SREBF (SREBP) After transiting to the nucleus SREBPs (SREBP1A/1C/2, SREBFs) bind short sequences, sterol regulatory elements (SREs), in the promoters of target genes (reviewed in Eberle et al. 2004, Weber et al. 2004). SREBPs alone are relatively weak activators of transcription, with SREBP1C being significantlyREACTOMEFIVIZ
Overview. The ReactomeFIViz app is designed to find pathways and network patterns related to cancer and other types of diseases. This app accesses the Reactome pathways stored in the database, help you to do pathway enrichment analysis for a set of genes, visualize hit pathways using manually laid-out pathway diagrams directly in Cytoscape, and investigate functional relationships among genes REACTOME | OTHER SEMAPHORIN INTERACTIONS Other semaphorin interactions. There are eight classes of semaphorins and four types of plexins. Semaphorin (SEMA) classes 1 and 2 are found in invertebrates and classes 3-7 are vertebrate sempahorines. Sempahorin class 3 is secreted, whereas the other classes are synthesised as transmembrane proteins. Vertebrate plexins (PLXNs) areclassified
REACTOME | CYTOSOLIC SULFONATION OF SMALL MOLECULES Cytosolic sulfonation of small molecules. Two groups of sulfotransferease (SULT) enzymes catalyze the transfer of a sulfate group from 3-phosphoadenosine 5-phosphosulfate (PAPS) to a hydroxyl group on an acceptor molecule, yielding a sulfonated acceptor and 3-phosphoadenosine 5-phosphate (PAP). One is localized to the Golgiapparatus and
REACTOME | PPARA ACTIVATES GENE EXPRESSION PPARA activates gene expression. The set of genes regulated by PPAR-alpha is not fully known in humans, however many examples have been found in mice. Genes directly activated by PPAR-alpha contain peroxisome proliferator receptor elements (PPREs) in their promoters and include: 1) genes involved in fatty acid oxidation and ketogenesis(Acox1
REACTOME | CARGO TRAFFICKING TO THE PERICILIARY MEMBRANE Myristoylated cargo such as peripheral membrane protein Nephrocystin-3 (NPHP3) is targeted to the cilium in a UNC119- and ARL3-dependent manner, while ARL13B is required for the PDE6-dependent ciliary localization of INPP5E (Wright et al, 2011; Humbert et al, 2012; reviewed in Li et al, 2012). ARL6 was also identified as BBS3, a genethat when
REACTOME | MET PROMOTES CELL MOTILITY MET promotes cell motility. Direct and indirect interactions of MET with integrins, focal adhesion kinase PTK2 (FAK1), tensin-4 (TNS4) and GTPases RAP1 and RAC1, induce morphological changes that promote cell motility and play an important role in HGF-induced invasiveness of cancer cells (Weidner et al. 1993, Beviglia et al. 1999, Sakkab et al REACTOME | COLLAGEN CHAIN TRIMERIZATION Collagen chain trimerization. The C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the composition of the trimer, brings the individual chains into the correct register and initiates formation of the triple REACTOME | HEDGEHOG LIGAND BIOGENESIS Hedgehog ligand biogenesis. Mammalian genomes encode three Hedgehog ligands, Sonic Hedgehog (SHH), Indian Hedgehog (IHH) and Desert Hedgehog (DHH). These secreted morphogens can remain associated with lipid rafts on the surface of the secreting cell and affect developmental processes in adjacent cells. Alternatively, they can bereleased by
REACTOME | VITAMIN D (CALCIFEROL) METABOLISM Vitamin D (calciferol) metabolism. Vitamin D3 (VD3, cholecalciferol) is a steroid hormone that principally plays roles in regulating intestinal calcium absorption and in bone metabolism. It is obtained from the diet and produced in the skin by photolysis of 7-dehydrocholesterol and released into the bloodstream. REACTOME | ACYL CHAIN REMODELLING OF PS Acyl chain remodelling of PS. In the acyl chain remodelling pathway (Lands cycle), phosphatidylserine (PS) is hydrolysed by phopholipases and subsequently reacylated by acyltransferases. These cycles modify the fatty acid composition of glycerophospholipids to generate diverse molecules asymmetrically distributed in the cell membrane HOME - REACTOME PATHWAY DATABASEDOCSDOWNLOADTABLE OF CONTENTSDOISDATA SCHEMAORCID INTEGRATION PROJECT Reactome is a free, open-source, curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology andeducation.
REACTOME | BIOLOGICAL OXIDATIONS Biological oxidations. All organisms are constantly exposed to foreign chemicals every day. These can be man-made (drugs, industrial chemicals) or natural (alkaloids, toxins from plants and animals). Uptake is usually via ingestion but inhalation and transdermal routes are also common.The very nature of many chemicals that make themsuitable
REACTOME | REGULATION OF GENE EXPRESSION IN ENDOCRINE Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells. Studies in mouse model systems indicate that the transcription factor neurogenin 3 plays a central role in the induction of endocrine differentiation in the developing pancreas(Servitja
REACTOME | CYCLIN A/B1/B2 ASSOCIATED EVENTS DURING G2/M Cyclin A/B1/B2 associated events during G2/M transition. Cell cycle progression is regulated by cyclin-dependent protein kinases at both the G1/S and the G2/M transitions. The G2/M transition is regulated through the phosphorylation of nuclear lamins and histones (reviewed in Sefton, 2001). The two B-type cyclins localize to different regions REACTOME | IRS ACTIVATION Stable Identifier. IRS is one of the mediators of insulin signalling events. It is activated by phosphorylation and triggers a cascade of events involving PI3K, SOS, RAF and the MAP kinases. The proteins mentioned under IRS are examples of IRS family members acting as indicated. More family members are to be confirmed and added in thefuture.
REACTOME | CD22 MEDIATED BCR REGULATION BCR activation is highly regulated and coreceptors like CD22 (SIGLEC2) set a signalling threshold to prevent aberrant immune response and autoimmune disease (Cyster et al. 1997, Han et al. 2005). CD22 is a glycoprotein found on the surface of B cells during restricted stages of development. CD22 is a member of the receptors of the sialic acid REACTOME | METAL SEQUESTRATION BY ANTIMICROBIAL PROTEINS Type. Metals are necessary for all forms of life including microorganisms, evidenced by the fact that metal cations are constituents of approximately 40% of all proteins crystallized to date (Waldron KJ et al. 2009; Foster AW et al. 2014; Guengerich FP 2014, 2015). The ability of microorganisms to maintain the intracellularmetal quota is
REACTOME | NEGATIVE REGULATORS OF DDX58/IFIH1 SIGNALING RIG-I-mediated production of IFN can, in turn, increase the transcription of RIG-I itself, thus setting into motion an IFN amplification loop, which if left unchecked, could become deleterious to the host. This module mainly focuses on the endogenous negative regulation of the RIG-I-like receptor (RLR) family proteins RIG-I andMDA5.
REACTOME | PURINERGIC SIGNALING IN LEISHMANIASIS INFECTION Purinergic signaling in leishmaniasis infection. The purinoreceptors are divided into inotropic (P2XR) and metabotropic (P2YR) subtypes whose ligands are the nucleotides ATP and UDP respectively (Cekic et al. 2016). The binding of these nucleotides to their receptors on macrophages have been associated with the activation of theinflammasome
REACTOME | ACTIVATION OF GENE EXPRESSION BY SREBF (SREBP) Activation of gene expression by SREBF (SREBP) After transiting to the nucleus SREBPs (SREBP1A/1C/2, SREBFs) bind short sequences, sterol regulatory elements (SREs), in the promoters of target genes (reviewed in Eberle et al. 2004, Weber et al. 2004). SREBPs alone are relatively weak activators of transcription, with SREBP1C being significantly HOME - REACTOME PATHWAY DATABASEDOCSDOWNLOADTABLE OF CONTENTSDOISDATA SCHEMAORCID INTEGRATION PROJECT Reactome is a free, open-source, curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology andeducation.
REACTOME | BIOLOGICAL OXIDATIONS Biological oxidations. All organisms are constantly exposed to foreign chemicals every day. These can be man-made (drugs, industrial chemicals) or natural (alkaloids, toxins from plants and animals). Uptake is usually via ingestion but inhalation and transdermal routes are also common.The very nature of many chemicals that make themsuitable
REACTOME | REGULATION OF GENE EXPRESSION IN ENDOCRINE Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells. Studies in mouse model systems indicate that the transcription factor neurogenin 3 plays a central role in the induction of endocrine differentiation in the developing pancreas(Servitja
REACTOME | CYCLIN A/B1/B2 ASSOCIATED EVENTS DURING G2/M Cyclin A/B1/B2 associated events during G2/M transition. Cell cycle progression is regulated by cyclin-dependent protein kinases at both the G1/S and the G2/M transitions. The G2/M transition is regulated through the phosphorylation of nuclear lamins and histones (reviewed in Sefton, 2001). The two B-type cyclins localize to different regions REACTOME | IRS ACTIVATION Stable Identifier. IRS is one of the mediators of insulin signalling events. It is activated by phosphorylation and triggers a cascade of events involving PI3K, SOS, RAF and the MAP kinases. The proteins mentioned under IRS are examples of IRS family members acting as indicated. More family members are to be confirmed and added in thefuture.
REACTOME | CD22 MEDIATED BCR REGULATION BCR activation is highly regulated and coreceptors like CD22 (SIGLEC2) set a signalling threshold to prevent aberrant immune response and autoimmune disease (Cyster et al. 1997, Han et al. 2005). CD22 is a glycoprotein found on the surface of B cells during restricted stages of development. CD22 is a member of the receptors of the sialic acid REACTOME | METAL SEQUESTRATION BY ANTIMICROBIAL PROTEINS Type. Metals are necessary for all forms of life including microorganisms, evidenced by the fact that metal cations are constituents of approximately 40% of all proteins crystallized to date (Waldron KJ et al. 2009; Foster AW et al. 2014; Guengerich FP 2014, 2015). The ability of microorganisms to maintain the intracellularmetal quota is
REACTOME | NEGATIVE REGULATORS OF DDX58/IFIH1 SIGNALING RIG-I-mediated production of IFN can, in turn, increase the transcription of RIG-I itself, thus setting into motion an IFN amplification loop, which if left unchecked, could become deleterious to the host. This module mainly focuses on the endogenous negative regulation of the RIG-I-like receptor (RLR) family proteins RIG-I andMDA5.
REACTOME | PURINERGIC SIGNALING IN LEISHMANIASIS INFECTION Purinergic signaling in leishmaniasis infection. The purinoreceptors are divided into inotropic (P2XR) and metabotropic (P2YR) subtypes whose ligands are the nucleotides ATP and UDP respectively (Cekic et al. 2016). The binding of these nucleotides to their receptors on macrophages have been associated with the activation of theinflammasome
REACTOME | ACTIVATION OF GENE EXPRESSION BY SREBF (SREBP) Activation of gene expression by SREBF (SREBP) After transiting to the nucleus SREBPs (SREBP1A/1C/2, SREBFs) bind short sequences, sterol regulatory elements (SREs), in the promoters of target genes (reviewed in Eberle et al. 2004, Weber et al. 2004). SREBPs alone are relatively weak activators of transcription, with SREBP1C being significantlyREACTOMEFIVIZ
Overview. The ReactomeFIViz app is designed to find pathways and network patterns related to cancer and other types of diseases. This app accesses the Reactome pathways stored in the database, help you to do pathway enrichment analysis for a set of genes, visualize hit pathways using manually laid-out pathway diagrams directly in Cytoscape, and investigate functional relationships among genes REACTOME | OTHER SEMAPHORIN INTERACTIONS Other semaphorin interactions. There are eight classes of semaphorins and four types of plexins. Semaphorin (SEMA) classes 1 and 2 are found in invertebrates and classes 3-7 are vertebrate sempahorines. Sempahorin class 3 is secreted, whereas the other classes are synthesised as transmembrane proteins. Vertebrate plexins (PLXNs) areclassified
REACTOME | CYTOSOLIC SULFONATION OF SMALL MOLECULES Cytosolic sulfonation of small molecules. Two groups of sulfotransferease (SULT) enzymes catalyze the transfer of a sulfate group from 3-phosphoadenosine 5-phosphosulfate (PAPS) to a hydroxyl group on an acceptor molecule, yielding a sulfonated acceptor and 3-phosphoadenosine 5-phosphate (PAP). One is localized to the Golgiapparatus and
REACTOME | PPARA ACTIVATES GENE EXPRESSION PPARA activates gene expression. The set of genes regulated by PPAR-alpha is not fully known in humans, however many examples have been found in mice. Genes directly activated by PPAR-alpha contain peroxisome proliferator receptor elements (PPREs) in their promoters and include: 1) genes involved in fatty acid oxidation and ketogenesis(Acox1
REACTOME | CARGO TRAFFICKING TO THE PERICILIARY MEMBRANE Myristoylated cargo such as peripheral membrane protein Nephrocystin-3 (NPHP3) is targeted to the cilium in a UNC119- and ARL3-dependent manner, while ARL13B is required for the PDE6-dependent ciliary localization of INPP5E (Wright et al, 2011; Humbert et al, 2012; reviewed in Li et al, 2012). ARL6 was also identified as BBS3, a genethat when
REACTOME | MET PROMOTES CELL MOTILITY MET promotes cell motility. Direct and indirect interactions of MET with integrins, focal adhesion kinase PTK2 (FAK1), tensin-4 (TNS4) and GTPases RAP1 and RAC1, induce morphological changes that promote cell motility and play an important role in HGF-induced invasiveness of cancer cells (Weidner et al. 1993, Beviglia et al. 1999, Sakkab et al REACTOME | COLLAGEN CHAIN TRIMERIZATION Collagen chain trimerization. The C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the composition of the trimer, brings the individual chains into the correct register and initiates formation of the triple REACTOME | HEDGEHOG LIGAND BIOGENESIS Hedgehog ligand biogenesis. Mammalian genomes encode three Hedgehog ligands, Sonic Hedgehog (SHH), Indian Hedgehog (IHH) and Desert Hedgehog (DHH). These secreted morphogens can remain associated with lipid rafts on the surface of the secreting cell and affect developmental processes in adjacent cells. Alternatively, they can bereleased by
REACTOME | VITAMIN D (CALCIFEROL) METABOLISM Vitamin D (calciferol) metabolism. Vitamin D3 (VD3, cholecalciferol) is a steroid hormone that principally plays roles in regulating intestinal calcium absorption and in bone metabolism. It is obtained from the diet and produced in the skin by photolysis of 7-dehydrocholesterol and released into the bloodstream. REACTOME | ACYL CHAIN REMODELLING OF PS Acyl chain remodelling of PS. In the acyl chain remodelling pathway (Lands cycle), phosphatidylserine (PS) is hydrolysed by phopholipases and subsequently reacylated by acyltransferases. These cycles modify the fatty acid composition of glycerophospholipids to generate diverse molecules asymmetrically distributed in the cell membraneToggle navigation
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FIND REACTIONS, PROTEINS AND PATHWAYSSearch ... Go!
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PATHWAY BROWSER
Visualize and interact with Reactome biological pathways_ _
ANALYZE DATA
Merges pathway identifier mapping, over-representation, and expression analysis_ _
REACTOMEFIVIZ
Designed to find pathways and network patterns related to cancer and other types of diseases_ _
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Information to browse the database and use its principal tools fordata analysis
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Reactome is a free, open-source, curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology andeducation.
If you use Reactome in Asia, we suggest using our Chinese mirror site at reactome.ncpsb.org . The development of Reactome is supported by grants from the US National Institutes of Health (P41 HG003751) and the European Molecular Biology Laboratory.__LATEST NEWS
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