Pathway Studio ResNet Database Description and Workflow Examples
Jun 10, 2015
Entity Type | Definition |
Cell Process | Basic processes occurring within and carried out by the cell. Cell processes may contain proteins as property = child concepts. |
Clinical Parameter | Parameters measured in clinical |
Complex | Several polypeptides that form a complex via physical interactions. |
Disease | Health conditions and diseases |
Functional Class | Classes of proteins, such as enzyme families. Functional classes contain proteins as property = child concepts. |
Protein | Genes and gene products defined by Entrez Gene, including proteins, miRNAs, pseudogenes and non-coding RNAs |
Small Molecule | ResNet Mammal: Naturally occurring metabolites and small molecules found in cells; ResNet Mammal + ChemEffect® adds drugs (including biologically active peptides and antibody drugs), environmental chemicals and non-naturally occurring small molecules. |
Treatment | Non-chemical treatments and environmental conditions |
Complex
Property Name | Property Type | Source | Description |
Name | short string | GO Cellular Component with manual curation | The display name for a complex. |
Alias | short string | manual curation from multiple sources | Other identifiers assigned to the complex. |
MedScanID | short string | MedScan | Internal Elsevier’s identifier |
GO ID | short string | http://geneontology.org/ | The Gene Ontology project provides a controlled vocabulary of terms for describing gene product characteristics. |
KEGG ID | short string | http://www.genome.jp/kegg/ | KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. |
Functional Class
Property Name | Property Type | Source | Description |
Name | short string | http://www.expasy.org/ | The display name for the functional class |
Alias | short string | Manual curation from multiple sources | Other identifiers assigned to the functional class |
MedScanID | short string | MedScan | Internal Elsevier’s identifier |
GO ID | short string | http://geneontology.org/ | The Gene Ontology project provides a controlled vocabulary of terms for describing gene product characteristics. |
Cell | dictionary | http://geneontology.org/ | Gene Ontology – Cellular Component. Not all cellular |
Localization | processes have localization assignment. | ||
Mol Function | dictionary | http://geneontology.org/ | Functional classes with associated activities: ligand, phosphatases, protein kinases, receptor and transcription factor are annotated as such in the Mol Function property. |
Description | short string | manually curated from multiple sources | Full names of the functional class. |
EC Number | short string | Enzyme Commission Number | The Enzyme Commission number (EC number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze. |
Protein
Property Name | Property Type | Source | Description |
Name | short string | Entrez official gene symbol http://www.ncbi.nlm.nih.gov/gquery/ | Display symbol for a gene |
Alias | short string | Entrez with manual curation | Other identifiers assigned to the protein. |
MedScanID | short string | MedScan dictionary – Elsevier | Internal Elsevier’s identifier |
GO ID | short string | http://geneontology.org/ | The Gene Ontology project provides a controlled vocabulary of terms for describing gene product characteristics. |
Cell Localization | dictionary | http://geneontology.org/ | Gene Ontology – Cellular Component. The Gene Ontology project provides a controlled vocabulary of terms for describing gene product characteristics. Cellular Process entities are derived from Gene |
Organism | dictionary | http://www.ncbi.nlm.nih.gov/taxonomy | The Entrez Taxonomy database displays the species names (and higher-level classification) of all of the organisms that are represented in the Entrez sequence databases (or any of the other Entrez databases that are indexed by taxonomy). |
Primary Cell Localization | dictionary | http://geneontology.org | Gene Ontology – Cellular Component. The Gene Ontology project provides a controlled vocabulary of terms for describing gene product characteristics. Cellular Process entities are derived from Gene |
Notes | long Text |
| Summary of gene/gene product function provided by RefSeq |
Description | short string | Official full name from Entrez | Full name for the gene |
EC Number | short string |
| The Enzyme Commission number (EC number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze. |
Ensembl ID | short string | http://www.ensembl.org/ |
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GenBank ID | short string | http://www.ncbi.nlm.nih.gov/ |
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Homologene ID | short string | http://www.ncbi.nlm.nih.gov/homologene | An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species. |
Hugo ID | short string | http://www.genenames.org/ | HUGO Gene Nomenclature Committee is a curated online repository of HGNC-approved gene nomenclature, gene families and associated resources including links to genomic, proteomic and phenotypic information. |
Human chromosome position | short string | http://www.ncbi.nlm.nih.gov/gene | Gene cytoband location |
KEGG ID | short string | http://www.genome.jp/kegg/ | KEGG is a database resource for understanding high-level functions and utilities of the biological system, |
such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. | |||
LocusLink ID | short string | http://www.ncbi.nlm.nih.gov/LocusLink | Old NCBI identifier that has transitioned to Entrez IDs. |
MGI ID | short string | http://www.informatics.jax.org/ | Mouse Genome Informatics identifier for genes. |
Mouse chromosome position | short string | http://www.ncbi.nlm.nih.gov/gene | Gene cytoband location |
OMIM ID | short string | http://omim.org/ | Online Mendelian Inheritance in Man® is an Online Catalog of Human Genes and Genetic Disorders. OMIM focuses on the relationship between phenotype and genotype. |
PIR ID | short string | http://pir.georgetown.edu/pirwww/index.shtml | Integrated Protein Informatics Resources for Genomic, Proteomic and Systems Biology Research |
RGD ID | short string | http://rgd.mcw.edu/wg/home | Rat Genome Database gene identifiers. |
Rat chromosome position | short string | http://www.ncbi.nlm.nih.gov/gene | Gene cytoband location |
Swiss-Prot Accession | short string | http://www.uniprot.org/ | The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. |
Swiss-Prot ID | short string |
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Unigene ID | short string | http://www.ncbi.nlm.nih.gov/unigene | UniGene computationally identifies transcripts from the same locus; analyzes expression by tissue, age, and health status; and reports related proteins (protEST).and clone resources. |
miRBase ID | short string | http://www.mirbase.org/ | miRBase is a database of published miRNA sequences and annotation. |
Small Molecule
Property Name | Property Type | Source | Description |
Name | short string | PubChem compounds and manual curation from multiple sources | Display name for the small molecule |
Alias | short string | PubChem compounds and manual curation from multiple sources | Other identifiers assigned to the small molecule. |
MedScanID | short string | MedScan dictionary – Elsevier | Internal Elsevier’s identifier |
Molecular Weight | Numerical | https://pubchem.ncbi.nlm.nih.gov/ | Molecular weight of a small molecule |
Rotatable Bond Count | Numerical | https://pubchem.ncbi.nlm.nih.gov/ | Number of rotatable bonds in the molecule. Rotatable bonds are defined as single bonds between heavy atoms. It doesn't include ring bonds, those connected to a heavy atom that is attached to only hydrogens or amide bonds. |
CAS ID | short string | https://www.cas.org/content/chemical-substances/faqs | A CAS Registry Number, is a unique numerical identifier assigned by Chemical Abstracts Service (CAS) to every chemical substance described in the open scientific literature. |
ChEBI ID | short string | http://www.ebi.ac.uk/chebi/init.do | ChEBI stands for 'Chemical Entities of Biological Interest'. It is a freely available database of 'small molecular entities', developed at the EBI. The term 'molecular entity' encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, |
radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. | |||
HMDB ID | short string | http://www.hmdb.ca/ | The Human Metabolome Database (HMDB) is an electronic database containing detailed information about small molecule metabolites found in the human body. |
IUPAC Name | short string | http://www.iupac.org/ | Name assigned according to the IUPAC nomenclature of organic chemistry, |
InChIKey | short string | http://www.iupac.org/ | The IUPAC International Chemical Identifier (InChITM) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations. |
KEGG ID | short string | http://www.genome.jp/kegg/ | KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. |
Molecular Formula | short string | https://pubchem.ncbi.nlm.nih.gov/ | Molecular formula of a small molecule |
PharmaPendium Name | short string | https://www.pharmapendium.com /#/home | The name of the drug as it appears in Pharmapendium. Elsevier’s PharmaPendium offers dedicated data modules that provide insights and information on the critical focused areas of drug development, drug safety, ADME and drug-drug interactions. |
PubChem CID | short string | https://pubchem.ncbi.nlm.nih.gov/ | The PubChem Compound Database contains validated chemical depiction information provided to describe substances in PubChem Substance. Structures stored within PubChem Compounds are pre-clustered and cross-referenced by identity and similarity groups. A compound identifier (CID) is the permanent identifer for a unique chemical structure. Each stereoisomer of a compound has its own CID. It is also possible for different tautomeric forms of the same compound to have different CID's. |
PubChem SID | short string | http://pubchem.ncbi.nlm.nih.gov/ | The PubChem Compound Database contains validated chemical depiction information provided to describe substances in PubChem Substance. Structures stored within PubChem Compounds are pre-clustered and cross-referenced by identity and similarity groups. A substance identifier (SID) is the permanent identifier for a depositor-supplied molecule. Each SID corresponds to a unique external registry ID provided by a PubChem data source. |
Reaxys ID | short string | https://www.reaxys.com | Elsevier’s Reaxys and Reaxys Medicinal Chemistry combine comprehensive databases of chemistry data and literature with powerful search interfaces. They return relevant extracted data and citations in optimal formats for chemistry research. Both can seamlessly integrate into an existing environment of tools and systems, saving time and reducing the risk of inconsistencies. |
XLogP | Numerical | https://pubchem.ncbi.nlm.nih.gov/ | A partition coefficient or distribution coefficient that is a measure of differential solubility of a compound in two solvents. |
XLogP-AA | short string | https://pubchem.ncbi.nlm.nih.gov/ | A partition coefficient or distribution coefficient that is a measure of differential solubility of a compound in two solvents. |
Cell Process
Property Name | Property Type | Source | Description |
Name | short string |
Manual curation from GO http://geneontology.org/ | Display name for the cell process |
Alias | short string | Manual curation from multiple sources | Other identifiers assigned to the cell process. |
MedScanID | short string | MedScan dictionary – Elsevier | Internal Elsevier’s identifier |
GO ID | short string | http://geneontology.org/ | The Gene Ontology project provides a controlled vocabulary of terms for describing gene product characteristics. Cellular Process entities are derived from Gene Ontology with additional manual curation. |
Cell localization | dictionary | http://geneontology.org/ | Gene Ontology – Cellular Component. The Gene Ontology project provides a controlled vocabulary of terms for describing gene product characteristics. Cellular Process entities are derived from Gene Ontology with additional manual curation. |
Description | short string | manually curated | Full name for the cell process |
Treatment
Property Name | Property Type | Source | Description |
Name | short string | Manually curated from multiple sources | Display name for the treatment |
Alias | short string | Manually curated from multiple sources | Other identifiers assigned to the treatment. |
MedScanID | short string | MedScan dictionary – Elsevier | Internal Elsevier’s identifier |
Clinical Parameters
Property Name | Property Type | Source | Description |
Name | short string | Manually curated from multiple sources | Display name for the clinical parameter |
Alias | short string | Manually curated from multiple sources | Other identifiers assigned to the clinical parameter |
MedScan | short string | MedScan dictionary – Elsevier | ID assigned in the MedScan dictionary (text mining tool) |
Disease
Property Name | Property Type | Source | Description |
Name | short string | MeSH with manual curation, OphaNet with manual curation http://www.ncbi.nlm.nih.gov/mesh http://www.orpha.net/consor/cgi-bin/index.php | Display name for the disease |
Alias | short string | MeSH with manual curation, OphaNet with manual curation http://www.ncbi.nlm.nih.gov/mesh http://www.orpha.net/conso | Other identifiers assigned to the disease. |
r/cgi-bin/index.php | |||
MedScanID | short string | MedScan dictionary – Elsevier | Internal Elsevier’s identifier |
MeSH heading | short string | https://www.nlm.nih.gov/mesh/ | MeSH (Medical Subject Headings) is the National Library of Medicine controlled vocabulary thesaurus used for indexing articles for PubMed. |
Additional Annotation for Entities
Property Name | Description |
ObjectType | For entities, the object types are each entity type (protein, small molecule, etc.) For relations, the object types are each relation type (expression, binding, etc.) |
ChildConcepts | Concepts (proteins) mapped to a concept. For example, functional classes include all the proteins associated with the functional class as “child concepts.” |
ParentConcepts | The ontological parent of a protein, which can be a functional class, or cellular process |
URN | Elsevier internal identifier |
The following relation types are included in the Mammal+ChemEffect+DiseaseFx Database.
Type | Filtering Field Name | Sub-Categories | Definition |
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Binding | - | - | Direct physical interaction between two molecules. This relation type has no Direction and no Effect |
Biomarker | BiomarkerType | diagnostic, prognostic | Molecule was reported as a biomarker for a disease (Disease Protein/ Complex/Functional class/small molecule). This relation type has no Effect. |
ChemicalReaction | - | - | Enzyme catalyzes reaction involving small molecule |
ClinicalTrial | Phase | N/A, Phase 0, Phase 1, Phase1/Phase2, Phase2, Phase2/Phase3, Phase 3, Phase4 | Disease/cell process relation representing clinical trials conducted for a drug against a disease (from clinicaltrials.gov) (Small molecule Disease, CellProcess). This relation type has no Effect Food and Drug Administration (FDA) categories for describing the clinical trial of a drug based on the study's characteristics. There are five phases:
Phase 0: Exploratory study involving very limited human exposure to the drug, with no therapeutic or diagnostic goals.
Phase 1: Studies that are usually conducted with healthy volunteers and that emphasize safety.
Phase 2: Studies that gather preliminary data on effectiveness (whether the drug works in people who have a certain disease or condition. Safety continues to be evaluated, and short-term adverse events are studied.
Phase 3: Studies that gather more information about safety and effectiveness by studying different populations and different dosages and by using the drug in combination with other drugs.
Phase 4: Studies occurring after FDA has approved a drug for marketing. These studies gather additional information about a drug's safety, efficacy, or optimal use.
|
DirectRegulation | - | - | Regulator influences target activity by direct physical interaction (excluding promoter binding interactions) |
Expression | - | - | Regulator changes protein abundance by affecting levels of transcript or protein stability |
FunctionalAssociation | - | - | Disease is associated to cell process, clinical parameter or another disease. This relation type has no Direction and no Effect. |
GeneticChange | ChangeType | gene deletion, mutation, gene amplification, epigenic methylation | Genetic changes associated with a disease (Disease Protein/ Complex/Functional class) |
miRNAEffect | - | - | The inhibitory effect of a miRNA on its mRNA target. These relations have two sources: 1) literature, 2) Public databases: miRanda (human, mouse, rat), PicTar(human) and TargetScan (human, mouse, rat). |
This information is provided in the field “source.” | |||
MolSynthesis | - | - | Regulator changes the concentrations of the target (usually a small molecule target) |
MolTransport | - | - | Regulator changes the localization of the target (molecular translocation, export, import etc.) |
PromoterBinding | - | - | Regulator binds to the promoter of a gene |
ProtModification | Mechanism | acetylation, cleavage, deacetylation, demethylation, dephosphorylation, direct interaction, methylation, phosphorylation, posttrascriptional inhibition, proteolysis, ubiquitination | Regulator changes the modification of the target molecule, usually by a direct interaction |
QuantitativeChange | QuantitativeType | expression, abundance, activity | Changes in abundance/activity/expression of a gene/protein/small molecule associated with a disease (Disease Protein/ Complex/Functional class) |
Regulation | - | - | Regulator changes the activity of the target by an unknown mechanism (direct or indirect). This is a less specific relation type than others provided |
StateChange | Change Type | alternative splicing, phosphorylation | Changes in a protein’s posttranslational modification status or alternative splicing events associated with a disease (Disease Protein/ Complex/Functional class) |
Most of the annotations for relations share common annotations fields. Below is a list of shared annotations for all relation types except Clinical Trials. Relations are assigned effect (positive, negative, or unknown) and directionality except Binding and Functional Association. Biomarker is assigned directionality but has no assigned effect.
Property Name | Property Type | Source | Description |
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CellType | dictionary | Elsevier’s Natural Language Processing (NLP) tool | Contains cell name recognized by Elsevier NLP in the supporting sentence or in the text upstream from the sentence |
Organ | dictionary | Elsevier’s Natural Language Processing (NLP) tool | Contains organ name recognized by Elsevier NLP in the supporting sentence or in the text upstream from the sentence |
Organism | dictionary | Elsevier’s Natural Language Processing (NLP) tool | Contains organism name recognized by Elsevier NLP in the supporting sentence or in the text upstream from the sentence |
Tissue | dictionary | Elsevier’s Natural Language Processing (NLP) tool | Contains tissue recognized by Elsevier NLP in the supporting sentence or in the text upstream from the sentence |
CellLineName | short string | Elsevier’s Natural | Contains cell line name recognized by Elsevier NLP in the |
Language Processing (NLP) tool | supporting sentence or in the text upstream from the sentence | ||
Effect | dictionary | Elsevier’s Natural Language Processing (NLP) tool | Relations are assigned effect (positive, negative, or unknown) except binding, functional association and biomarker. |
TextMods | long text | Elsevier’s Natural Language Processing (NLP) tool | The “TextMods” property for a reference indicates a substitution has been made in the original text resulting in the display of the full entity name in place of the abbreviation appearing in the original text. |
Title | long text | Elsevier’s Natural Language Processing (NLP) tool | Article title |
msrc | long text | Elsevier’s Natural Language Processing (NLP) tool | Display name in UI: Sentence. Contains sentence recognized by Elsevier NLP supporting the relation |
PubYear | numerical | Elsevier’s Natural Language Processing (NLP) tool | Publication year of the article with the sentence |
Authors | short string | Elsevier’s Natural Language Processing (NLP) tool | Article author |
DOI | short string | Elsevier’s Natural Language Processing (NLP) tool | Document Object Identifier |
EMBASE | short string | Elsevier’s Natural Language Processing (NLP) tool | Embase article identifier |
ESSN | short string | Elsevier’s Natural Language Processing (NLP) tool | Electronic ISSN number |
ISSN | short string | Elsevier’s Natural Language Processing (NLP) tool | International Standard Serial Number |
Journal | short string | Elsevier’s Natural Language Processing (NLP) tool | Journal name for a journal not included in PubMed |
MedlineTA | short string | Elsevier’s Natural Language Processing (NLP) tool | Journal name for journals from Pubmed |
PII | short string | Elsevier’s Natural Language Processing (NLP) tool | Publisher Item Identifier |
PMID | short string | Elsevier’s Natural Language Processing (NLP) tool | Pubmed abstract identifier |
PUI | short string | Elsevier’s Natural Language | Publisher Item Identifier from Embase |
Processing (NLP) tool | |||
PubVersion | short string | Elsevier’s Natural Language Processing (NLP) tool | Version number of article |
TextRef | short string | Elsevier’s Natural Language Processing (NLP) tool | Information in the TextRef field indicates if the relation was identified in an abstract, title, body of a paper or when no location can be identified. For example: #title:1 means the “first sentence of the article’s title’ #abs:9 meand the ‘9th sentence of the article’s abstract’ #body:21 means the ‘21st sentence of the article’s body’ #cont:21 means the ‘21st sentence of the article’s extracted text with no identifiable parts |
mref | short string | Elsevier’s Natural Language Processing (NLP) tool | Display name in UI: MedLine reference. Contains Pubmed abstract identifier (PMID) |
Clinical Trials
Clinical Trials data is obtained directly from ClinicalTrials.gov (it is not literature extracted using MedScan).
Property Name | Property Type | Source | Description |
Phase | dictionary | clinicaltrials.gov | Food and Drug Administration (FDA) categories for describing the clinical trial of a drug based on the study's characteristics, such as the objective and number of participants. There are five phases:
Phase 0: Exploratory study involving very limited human exposure to the drug, with no therapeutic or diagnostic goals (for example, screening studies, microdose studies)
Phase 1: Studies that are usually conducted with healthy volunteers and that emphasize safety. The goal is to find out what the drug's most frequent and serious adverse events are and, often, how the drug is metabolized and excreted.
Phase 2: Studies that gather preliminary data on effectiveness (whether the drug works in people who have a certain disease or condition). For example, participants receiving the drug may be compared with similar participants receiving a different treatment, usually an inactive substance (called a placebo) or a different drug. Safety continues to be evaluated, and short-term adverse events are studied.
Phase 3: Studies that gather more information about safety and effectiveness by studying different populations and different dosages and by using the drug in combination with other drugs.
Phase 4: Studies occurring after FDA has approved a drug for marketing. These including postmarket requirement and commitment studies that are required of or agreed to by the sponsor. These studies gather additional information about a drug's safety, efficacy, or |
optimal use. | |||
msrc | long text | text extraction | Display name in UI: Sentence. Contains sentence recognized by Elsevier NLP supporting the relation |
TrialStatus | dictionary | clinicaltrials.gov | The status of the trial: Active not recruiting, approved for marketing, available, completed, enrolling by invitation, no longer available, not yet recruiting, recruiting, suspended temporarily not available, terminated, withdrawn, withheld |
Condition | long text | clinicaltrials.gov | A disease, disorder, syndrome, illness, or injury that is being studied. On ClinicalTrials.gov, conditions may also include other health-related issues such as lifespan, quality of life, and health risks. |
Intervention | long text | clinicaltrials.gov | A process or action that is the focus of a clinical study. This can include giving participants drugs, medical devices, procedures, vaccines, and other products that are either investigational or already available. Interventions can also include noninvasive approaches such as surveys, education, and interviews. |
Title | long text | clinicaltrials.gov | The title given to the specific study. |
Collaborator | short string | clinicaltrials.gov | A collaborator is an organization other than the sponsor that provides support for a clinical study. This may include funding, design, implementation, data analysis, or reporting. |
Company | short string | clinicaltrials.gov | The company sponsoring the trial. |
NCT ID | short string | clinicaltrials.gov | ClinicalTrials.gov identifier |
Start | short string | clinicaltrials.gov | The start date of the study. |
TextRef | short string | MedScan Reader | TextRef for clinical trials includes the NCT identifier |
mref | short string | Elsevier’s Natural Language Processing (NLP) tool | Display name in UI: MedLine reference. Contains Pubmed abstract identifier (PMID) |
Additional Annotation for Relations
Property Name | Description |
Effect | The described effect of a relation (positive, negative, unknown) on a target. |
In/Out | Indicator of the directionality of the relation (in or out from the entity). In the |
RelationNumberOfReferences | The number of sentences from which the relation has been extracted. |
URN | Elsevier internal identifier |
Groups in ResNet consist simply of a list of entities. Ontologies are presented as groups.
Pathways in ResNet include both entities and relations. The Elsevier curated pathway collection includes over 1300 pathways. A complete list of the pathways included in the ResNet database is provided at the end of this document (see Appendix).
Two ontologies are included in ResNet: Gene Ontology (cellular component, molecular function, and biological process) and Pathway Studio Ontology.
Gene Ontology:
The Gene Ontology IDs, from the Gene Ontology Consortium, for each protein and cellular process are listed in their annotation fields. Please visit http://geneontology.org/ for more information.
Pathway Studio Ontology:
Pathway Studio Ontology was designed from a different prospective than 'the Gene Ontology' (GO) provided by the Gene Ontology Consortium. Whereas GO is a multi-level hierarchy with multiple, often overlapping, functional descriptions of genes, Pathway Studio Ontology consists of a non-overlapping core set of cell-level molecular function groups. To complement the molecular function groups, Elsevier has defined the cellular process groups that represent the most basic and well-established cellular processes. Elsevier experts have manually assigned proteins to these groups based on protein primary function. The result is a well-designed organization of proteins that reflect the current knowledge of their primary function(s) in the cell. Organism-level biological processes can be represented by combination of basic cellular processes and molecular function groups. ResNet Mammal, Pathway Studio Ontology includes 8,666 genes and 1006 miRNAs, organized in 519 groups, with 11,788 'assignments'. Cellular Processes:
Biochemical Pathways: | 41 groups | 1573 proteins |
Metabolite/Ion Transport: | 42 groups | 1053 proteins |
Structural Processes: (DNA replication, translation, actin polymerization, endocytosis) | 63 groups | 3814 proteins |
Molecular Functions:
Ligands: | 42 groups | 448 proteins |
Receptors: | 68 groups | 930 proteins |
Signaling Proteins: | 155 groups | 766proteins |
miRNAs: | 10 groups | 2154 miRNAs |
Transcription Factors: | 94 groups | 1,822 proteins |
Disease Regulation:
Oncogenes: | 1 group | 271 proteins |
Tumor Suppressors: | 1 group | 92 proteins |
APPENDIX: WORKFLOW EXAMPLES
The examples below include the biological question, the relation types and the entity types selected, and considerations for each workflow.
| Question | Wizard Selections | Considerations |
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Gene/Protein Expression | |||
1 | What proteins (transcription factors) bind to the promoter of a gene(s)? | initial selection: protein directionality: upstream entity type: protein relation type: promoterbinding | Finds transcription factors for genes (directly binding to promoters) |
2 | What known miRNAs regulate expression of a gene(s)? | initial selection: protein directionality: upstream entity type: protein relation type: miRNAEffect
| Finds miRNA targets. |
3 | What proteins are involved in the expression of a gene(s), either directly or indirectly? | initial selection: protein directionality: upstream entity type: protein relation type: promoterbinding or expression | Finds both direct expression regulators (promoterbinding) and proteins with possibly an indirect effect on expression (expression) |
Physical Interaction with Proteins | |||
4 | What proteins bind to a protein? | initial selection: protein directionality: (all) entity type: protein relation type: binding or directregulation | Identifies protein binding partners (no additional regulatory event known) Binding relations have no directionality (DirectRegulation is regulation through a direct physical interaction and can also be considered here.) |
5 | What small molecules bind to a protein? | initial selection: protein directionality: (all) entity type: small molecules relation type: binding or directregulation | Identifies small molecules that bind to a protein (no additional regulatory event known) (DirectRegulation is regulation through a direct physical interaction and can also be considered here.) |
| Question | Wizard Selections | Considerations |
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6 | What proteins regulate a protein through a direct physical interaction? | initial selection: protein directionality: upstream entity type: protein relation type: directregulation | Finds proteins that regulate the activity of a target protein through a direct physical interaction Can also consider "protmodification" relations |
7 | What small molecules regulate a protein through direct physical interactions? | initial selection: protein directionality: upstream entity type: small molecule relation type: directregulation | Finds small molecules that regulate the activity of a protein through a direct physical interaction (Drugs/non-naturally occurring small molecules included in ChemEffect data) |
Protein Modification(s) | |||
8 | What protein(s) acetylate/deacetylate a protein? | initial selection: protein directionality: upstream entity type: protein relation type: protmodification mechanism: acetylation or deacetylation | Identifies proteins involved in acetylation/deacetylation of target protein(s). |
9 | What protein(s) cleave a protein? | initial selection: protein directionality: upstream entity type: protein relation type: protmodification mechanism: cleavage | Identifies proteins involved in the proteolytic cleavage of target protein(s). |
10 | What proteins(s) methylate/demethylate a protein? | initial selection: protein directionality: upstream entity type: protein relation type: protmodification mechanism: methylation or demethylation | Identifies proteins involved in the methylation/demethylation of target protein(s). |
11 | What protein(s) phosphorylate/dephosphorylate a protein? | initial selection: protein directionality: upstream entity type: protein relation type: protmodification mechanism: phosphorylation or dephosphorylation | Identifies protein(s) involved in the phosphorylation/ dephosphorylation of target protein(s). |
| Question | Wizard Selections | Considerations |
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12 | What protein(s) ubiquitinate a protein? | initial selection: protein directionality: upstream entity type: protein relation type: protmodification mechanism: ubiquitination | Identifies proteins involved in the ubiquitination of target protein(s). |
Protein /Small Molecule Transport | |||
13 | What protein mediates the translocation of a protein or small molecule? | initial selection: protein or small molecule directionality: upstream entity type: protein relation type: moltransport | Identifies proteins involved in the translocation of a protein or small molecule target. |
14 | What small molecule mediates the translocation of a protein | initial selection: protein directionality: upstream entity type: small molecule relation type: moltransport | Identifies small molecules involved in the translocation of a protein target. |
| Question | Wizard Selections | Considerations |
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Proteins/Small molecules involved in chemical interactions | |||
15 | What enzymes are involved in a chemical reaction with a small molecule? | initial selection: small molecule directionality: all entity type(s): proteins, functional classes relation type: chemical reaction | Identifies functional classes and proteins that catalyze chemical reactions of small molecules. Most metabolism enzymes in the metabolism pathways are represented by functional classes. |
Protein/Small Molecule associations and changes in Diseases and Cell Processes | |||
16 | What proteins are known to be associated with a disease or cellular process? | initial selection: disease or cell process directionality: upstream entity type: protein relation type: regulation | Identifies proteins known to be associated with a specific disease or cellular process. (More specific data relating proteins to diseases is available in DiseaseFx data including statechange, genetic change and quantitativechange.) |
17 | What small molecules are associated with a disease or cellular process? | initial selection: disease or cell process directionality: upstream entity type: small molecules relation type: regulation | Identifies small molecules that are associated with diseases or cellular processes. Small molecule association with diseases and cell processes through regulation relations are found in the ChemEffect® Database. In addition, more information about small molecules associated with diseases can be found in the DiseaseFx database through quantitivechange and biomarker relations. |
18 | What proteins are known to change in expression, activity or abundance in a disease? | initial selection: disease directionality: downstream entity type: protein relation type: quantitativechange quantitativeType: expression or abundance or activity | Identifies proteins that are changed in activity abundance or expression in a disease. Quantitativechange relations are found only in DiseaseFx data |
19 | What small molecules are known to change in abundance in a disease? | initial selection: disease directionality: downstream entity type: small molecules relation type: quantitativechange quantitativetype: abundance | Identifies small molecules that are changed in abundance in a disease. Quantitativechange relations are found in DiseaseFx data |
| Question | Wizard Selections | Considerations |
---|---|---|---|
20 | What proteins with genetic mutations are associated with a disease? | initial selection: disease directionality: downstream entity type: protein relation type: geneticchange | Identifies proteins with genetic changes (gene deletions, amplifications, mutations, epigenic changes, or methylation) associated with a disease. Geneticchange relations are found in DiseaseFx data. |
21 | What proteins or small molecules are diagnostic for a disease? | initial selection: disease directionality: downstream entity type: protein relation type: biomarker biomarkertype: diagnostic | Identifies proteins/small molecules know to be diagnostic for a disease. Biomarker relations are found in DiseaseFx data. |
22 | What proteins or small molecules are prognostic for a disease? | initial selection: disease directionality: downstream entity type: protein relation type: biomarker biomarkertype: prognostic | Identifies proteins/small molecules known to be prognostic for a disease. Biomarker relations are found in DiseaseFx data. |
23 | What protein phosphorylation/dephosphorylation events are associated with a disease? | initial selection: disease directionality: downstream entity type: protein relation type: statechange changetype: phosphorylation or dephosphorylation | Identifies post translational protein phosphorylation/dephosphorylation events associated with a disease. Statechange relations are found in DiseaseFx data. |
24 | What protein/gene splice variants are associated with a disease? | initial selection: disease directionality: downstream entity type: protein relation type: statechange changetype: alternative splicing | Identifies alternate gene splicing events/splice variants associated with a disease. Statechange relations are found only in DiseaseFx data. |
| Question | Wizard Selections | Considerations |
---|---|---|---|
Small Molecule concentrations | |||
25 | What proteins regulate the synthesis or catabolism of a small molecule? | initial selection: small molecule directionality: upstream entity type(s): protein relation type(s): molsynthesis
| Identifies proteins that regulat the concentrations of small molecules through metabolic events |
Clinical Trials | |||
26 | What small molecules/drugs have been tested in clinical trials for a disease? | initial selection: small molecules directionality: downstream entity type(s): disease or cell process relation type: clinicaltrials | Identifies small molecules/drugs that have been involved in clinical trials. Drugs are included in ChemEffect Data. Clinicaltrials relations are included in DiseaseFx data. Monoclonal antibodies are represented as small molecules on the ChemEffect database. |
Functional Associations between Diseases and Cell Processes | |||
27 | What cellular processes are associated with a disease? | initial selection: disease directionality: (all) entity type: cellular process relation type: functional class | Identifies associations between cellular processes and diseases (no directionality in the relations). Functionalassociation relations are found in DiseaseFx data. |
APPENDIX: LIST OF CURATED PATHWAYS IN RESNET MAMMAL+CHEMEFFCT+DISEASEFX
Cell Process Pathways |
Apoptosis |
Apoptosis |
Cleavage of Lamina in Apoptosis |
Cell Division |
Centriole Duplication and Separation |
Chromosome Condensation |
Kinetochore Assembly |
Nuclear Envelope |
Sister Chromatid Cohesion |
Spindle Assembly |
Cellular Contacts |
Adherens Junction Assembly (Cadherins) |
Adherens Junction Assembly (Nectin) |
Desmosome Assembly |
Extracellular Matrix Turnover |
Focal Junction Assembly |
Gap Junction Assembly |
Hemidesmosome Assembly |
Tight Junction Assembly (Claudins) |
Tight Junction Assembly (JAMs) |
Tight Junction Assembly (Occludin) |
Chromatin Remodeling |
CHRAC Chromatin Remodeling |
INO80 Chromatin Remodeling |
NURD Chromatin Remodeling |
NURF Chromatin Remodeling |
SRCAP Chromatin Remodeling |
SWI/SNF BRG1/BAF Chromatin Remodeling |
SWI/SNF BRG1/PBAF Chromatin Remodeling |
SWI/SNF BRM/BAF Chromatin Remodeling |
TRRAP/TIP60 Chromatin Remodeling |
Complement Activation |
Alternative Complement Pathway |
Classical Complement Pathway |
Lectin-Induced Complement Pathway |
Cytoskeleton Assembly |
Actin Cytoskeleton Assembly |
Actomyosin-Based Movement |
Intermediate Filament Polymerization |
Microtubule Cytoskeleton Assembly |
DNA Repair |
Direct DNA Repair |
Double Strand DNA Homologous Repair |
Double Strand DNA Non-Homologous Repair |
Single-Strand Base Excision DNA Repair |
Single-Strand Mismatch DNA Repair |
Single-Strand Nucleotide Excision DNA Repair |
Histone Modification |
Histone Acetylation |
Histone and DNA Methylation |
Histone Phosphorylation |
Histone Sumoylation |
Histone Ubiquitylation |
Mitochondrial |
Mitochondrial DNA Replication and Transcription |
Mitochondrial Fusion and Fission |
Mitochondrial Protein Transport |
Transcription |
mRNA Transcription and Processing |
rRNA Transcription and Processing |
tRNA Transcription and Processing |
Vesicular Transport |
Co-Translational ER Protein Import |
Endosomal Recycling |
ER-Associated Degradation |
Exocytosis |
Golgi to Endosome Transport |
Peroxisome Protein Import and Peroxisome Division |
Secretory Pathway: Golgi Transport |
Transcytosis |
Cell Cycle |
Circadian Clock |
Coagulation Cascade |
DNA Replication |
mRNA Degradation |
Presentation of Endogenous Peptide Antigen |
Protein Folding |
Protein Nuclear Import and Export |
RNA Gene Silencing |
Telomere Maintenance |
Translation |
Ubiquitin-Dependent Protein Degradation | |||||||||||||||||||
Cell Signaling | |||||||||||||||||||
Actin Cytoskeleton Regulation | |||||||||||||||||||
Adherens Junction Regulation | |||||||||||||||||||
Adipocytokine Signaling | |||||||||||||||||||
Apoptosis Regulation | |||||||||||||||||||
Axon Guidance | |||||||||||||||||||
B Cell Activation | |||||||||||||||||||
Cell Cycle Regulation | |||||||||||||||||||
Focal Adhesion Regulation | |||||||||||||||||||
Gap Junction Regulation | |||||||||||||||||||
Gonadotrope Cell Activation | |||||||||||||||||||
Guanylate Cyclase Pathway | |||||||||||||||||||
Hedgehog Pathway | |||||||||||||||||||
Insulin Action | |||||||||||||||||||
Mast Cell Activation | |||||||||||||||||||
Melanogenesis | |||||||||||||||||||
NK Cell Activation | |||||||||||||||||||
Notch Pathway | |||||||||||||||||||
Skeletal Myogenesis Control | |||||||||||||||||||
T Cell Activation | |||||||||||||||||||
Tight Junction Regulation | |||||||||||||||||||
Translation Control | |||||||||||||||||||
Disease Collections | |||||||||||||||||||
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Expression Targets Pathways | |||||||||||||||||
B-cell Receptors Expression Targets | |||||||||||||||||
CD19 Expression Targets | |||||||||||||||||
CD21 Expression Targets | |||||||||||||||||
CD81 Expression Targets | |||||||||||||||||
Gamma Globulins Expression Targets | |||||||||||||||||
Cell Adhesion Molecules Expression Targets | |||||||||||||||||
CTGF/AP-1/CREB/MYC Expression Targets | |||||||||||||||||
CTGF/FOXO3A Expression Target | |||||||||||||||||
CTGF/NCOR2 Expression Target | |||||||||||||||||
Fibrinogen Expression Targets | |||||||||||||||||
Fibronectin Expression Targets | |||||||||||||||||
ICAM1 Expression Targets | |||||||||||||||||
NCAM1 Expression Targets | |||||||||||||||||
PECAM1 Expression Targets | |||||||||||||||||
Cytokines Expression Targets | |||||||||||||||||
Chemokines Expression Targets | |||||||||||||||||
CCL11 Expression Targets | |||||||||||||||||
CCL15 Expression Targets | |||||||||||||||||
CCL16 Expression Targets | |||||||||||||||||
CCL2 Expression Targets | |||||||||||||||||
CCL3 Expression Targets | |||||||||||||||||
CCL3L1 Expression Target | |||||||||||||||||
CCL4 Expression Targets | |||||||||||||||||
CCL5 Expression Targets | |||||||||||||||||
CCL7 Expression Target |
CCL8 Expression Targets |
CXCL12 Expression Targets |
IL8 Expression Targets |
Colony Stimulating Factors Expression Targets |
CSF2/NF-kB Expression Targets |
CSF2/STAT Expression Targets |
CSF3 Expression Targets |
Erythropoietin Expression Targets |
Erythropoietin/AP-1/MYC/CREB Expression Targets |
Erythropoietin/ELK-SRF Expression Targets |
Erythropoietin/FOXO3A Expression Targets |
Erythropoietin/NF-kB Expression Targets |
Erythropoietin/STAT Expression Targets |
Growth Hormones Expression Targets |
CSH1-GHR Expression Targets |
CSH1-PRLR Expression Targets |
FLT3LG/AP-1/CREB/CREBBP Expression Targets |
GAS6/AP-1/CREB Expression Targets |
GH1-GHR/NF-kB/ELK-SRF/MYC Expression Targets |
GH1-GHR/STAT Expression Targets |
GH1-PRLR Expression Targets |
GH2-GHR Expression Target |
PGF/AP-1/CREB/CREBBP/MYC Expression Targets |
Interferons Expression Targets |
IFNA1-IFNR Expression Targets |
IFNB1-IFNR Expression Targets |
IFNG-IFNR Expression Targets |
IFNW1-IFNR Expression Target |
Interleukins Expression Targets |
IL10 Expression Targets |
IL11 Expression Targets |
IL12B Expression Targets |
IL13 Expression Targets |
IL15 Expression Targets |
IL2 Expression Targets |
IL21 Expression Targets |
IL22 Expression Targets |
IL3 Expression Targets |
IL31 Expression Targets |
IL4 Expression Targets |
IL5 Expression Targets |
IL6 Expression Targets |
IL7 Expression Targets |
IL9 Expression Targets |
Leptin Expression Targets |
Leptin/ELK-SRF Expression Targets |
Leptin/STAT Expression Targets |
Oncostatin M Expression Targets |
OSM-IL6ST/LIFR Expression Targets |
OSM-OSMR Expression Targets |
Prolactin Expression Targets |
PRL-GHR/NF-kB/ELK-SRF/MYC Expression Targets |
PRL-GHR/STAT Expression Targets |
PRL-PRLR Expression Targets |
Thrombopoietin Expression Targets |
Thrombopoietin/AP-1/CREB/CREBBP/MYC Expression Targets |
Thrombopoietin/FOXO3A Expression Target |
Thrombopoietin/SP1 Expression Targets |
Thrombopoietin/SPI1 Expression Targets |
Thrombopoietin/STAT Expression Targets |
CLCF1 Expression Targets |
CNTF Expression Targets |
CTF1 Expression Targets |
LIF Expression Targets |
Delta/Notch Expression Targets |
ADAM17 Expression Targets |
DLL1 Expression Targets |
DLL3 Expression Targets |
DLL4 Expression Targets |
JAG1 Expression Targets |
NOTCH Expression Targets |
GPCR Ligands Expression Targets |
Signaling via Gi |
Acetylcholine Expression Targets |
Dopamine/Gi Expression Targets |
Dronabinol/Anandamide Expression Targets |
LPA Expression Targets |
NPY Expression Targets |
SST Expression Targets |
Signaling via Gq |
Adenosine Expression Targets |
AVP/Gq -> CREB/ELK-SRF/AP-1/EGR Expression Targets |
AVP/Gq -> MEF/MYOD/NFATC/MYOG Expression Targets |
AVP/Gq -> STAT Expression Targets |
CCK Expression Targets |
EDN1 Expression Targets |
EDN3 Expression Targets |
Epinephrine/Gq Expression Targets |
F2 -> AP-1/CREB/ELK-SRF/SP1 Expression Targets |
F2 -> STAT1/NF-kB Expression Targets |
GAST Expression Targets |
Glutamate/Gq Expression Targets |
GNRH1 Expression Targets |
GNRH2 Expression Targets |
IFNA1/Gq Expression Targets |
Morphine Expression Targets |
Noreadrenaline/Gq Expression Targets |
NTS Expression Targets |
OXT Expression Targets |
PAF/Gq -> AP-1/ATF1/CREB/ERK-SRF Expression Targets |
PAF/Gq -> NF-kB Expression Targets |
PLG -> AP-1/CREB/ELK-SRF/SP1 Expression Targets |
PLG -> STAT1/NF-kB Expression Targets |
POMC Expression Targets |
Prostaglandin F Expression Targets |
Serotonin/Gq Expression Targets |
Thromboxane A2 Expression Targets |
Signaling via Gq/i |
CXCL1 Expression Targets |
CXCL2 Expression Targets |
CXCL3 Expression Targets |
CXCL5 Expression Targets |
CXCL6 Expression Targets |
S1P Expression Targets |
Signaling via Gq/s |
ADCYAP1 Expression Targets |
AGT/CREB Expression Targets |
AGT/ELK-SRF Expression Targets |
AGT/STAT Expression Targets |
AGT/TP53 Expression Targets |
Epinephrine/Gs Expression Targets |
Noradrenaline/Gs Expression Targets |
PGE1 Expression Targets |
TAC1 Expression Targets |
VIP Expression Targets |
Signaling via Gs |
AVP/Gs -> CREB/ELK-SRF/AP-1/EGR Expression Targets |
AVP/Gs -> MEF/MYOD/NFATC/MYOG Expression Targets |
AVP/Gs -> STAT Expression Targets |
Dopamine/Gs Expression Targets |
FSHR Expression Targets |
GCG Expression Targets |
Serotonin/Gs Expression Targets |
Neurotrophins Expression Targets |
BDNF Expression Targets |
NGF/AP-1/TP53/MYC Expression Targets |
NGF/CREB/CEBPB/MEF2A Expression Targets |
NGF/FOXO/MYCN/ELK-SRF Expression Targets |
NGF/SMAD3/NF-kB Expression Targets |
NTF3 Expression Targets |
NTF4 Expression Targets |
NK-cell Receptors Expression Targets |
CD247 Expression Targets |
FCGR3A Expression Targets |
RAGE Ligands Expression Targets |
HMGB1 Expression Targets |
S100A Expression Targets |
S100B Expression Targets |
S100P Expression Target |
TTR Expression Targets |
Receptor Tyrosine Kinases Expression Targets |
Growth Factors Expression Targets |
EGFR Ligands Expression Targets |
AREG Expression Targets |
AREG/AP-1 Expression Targets |
AREG/CREB/CREBBP Expression Targets |
AREG/CTNN Expression Targets |
AREG/FOXO3A Expression Target |
AREG/HIF1A Expression Targets |
AREG/NCOR2 Expression Targets |
AREG/NFATC Expression Target |
AREG/SMAD1 Expression Target |
AREG/STAT Expression Targets |
BTC Expression Targets |
BTC/AP-1/ATF/CREB Expression Targets |
BTC/CTNN Expression Targets |
BTC/EP300/ETS/ETV/SP1 Expression Targets |
BTC/NFATC Expression Targets |
BTC/STAT Expression Targets |
EGF Expression Targets |
EGF/AP-1/ATF Expression Targets |
EGF/CREB/CREBBP/ELK-SRF/MYC Expression Targets |
EGF/CTNN Expression Targets |
EGF/FOXO3A Expression Targets |
EGF/HIF1A Expression Targets |
EGF/MEF/MYOD/NFATC Expression Targets |
EGF/NCOR2 Expression Target |
EGF/STAT Expression Targets |
EGF/TP53 Expression Targets |
EREG Expression Targets |
EREG/AP-1/ATF Expression Targets |
EREG/CREB Expression Target |
EREG/CTNNB/CTNND Expression Target |
EREG/EP300/SP1 Expression Targets |
EREG/FOXO3A Expression Target |
EREG/HIF1A Expression Target |
EREG/STAT Expression Targets |
HBEGF Expression Targets |
HBEGF/AP-1/ATF Expression Targets |
HBEGF/CREB/MYC Expression Targets |
HBEGF/EP300/ETS/ETV/SP1 Expression Targets |
HBEGF/FOXO3A Expression Target |
HBEGF/HIF1A Expression Targets |
HBEGF/MEF/MYOD Expression Target |
HBEGF/STAT Expression Targets |
HBEGF/TP53 Expression Targets |
TGFA Expression Targets |
TGFA/AP-1/ATF Expression Targets |
TGFA/CREB/CREBBP/ELK-SRF/MYC Expression Targets |
TGFA/CTNNB/CTNND Expression Targets |
TGFA/FOXO3A Expression Targets |
TGFA/HIF1A Expression Targets |
TGFA/MEF/MYOD/NFATC Expression Targets |
TGFA/STAT Expression Targets |
TGFA/TP53 Expression Targets |
FGF Expression Targets |
FGF1 Expression Targets |
FGF1/AP-1/CREB/ELK-SRF/MYC Expression Targets |
FGF1/NCOR2 Expression Target |
FGF1/RUNX Expression Targets |
FGF1/STAT Expression Targets |
FGF10 Expression Targets |
FGF10/AP-1/CREB/CREBBP/MYC Expression Targets |
FGF10/FOXO3A Expression Target |
FGF10/STAT Expression Targets |
FGF18 Expression Targets |
FGF18/AP-1/CREB Expression Targets |
FGF18/STAT Expression Targets |
FGF2 Expression Targets |
FGF2/AP-1/CREB/CREBBP/ELK-SRF/MYC Expression Targets |
FGF2/FOXO3A Expression Targets |
FGF2/NCOR2 Expression Targets |
FGF2/RUNX Expression Targets |
FGF2/STAT Expression Targets |
FGF23 Expression Targets |
FGF23/NCOR2 Expression Targets |
FGF4 Expression Targets |
FGF4/AP-1/MYC Expression Targets |
FGF7 Expression Targets |
FGF7/AP-1/CREB/CREBBP/MYC Expression Targets |
FGF7/FOXO3A Expression Target |
FGF7/RUNX Expression Targets |
FGF8 Expression Targets |
FGF8/AP-1/CREB/MYC Expression Targets |
FGF8/RUNX Expression Targets |
FGF8/STAT Expression Targets |
FGF9 Expression Targets |
FGF9/AP-1/CREB/MYC Expression Targets |
FGF9/RUNX Expression Targets |
FGF9/STAT Expression Targets |
HGF Expression Targets |
HGF/AP-1/CREB/ELK-SRF/MYC Expression Targets |
HGF/FOXO3A Expression Targets |
HGF/STAT Expression Targets |
Insulin/IGF Expression Targets |
IGF1 Expression Targets |
IGF1/CEBPA/FOXO1A Expression Targets |
IGF1/ELK-SRF/HIF1A/MYC/SREBF Expression Targets |
IGF1/MEF/MYOD/MYOG Expression Targets |
IGF1/STAT Expression Targets |
IGF2 Expression Targets |
IGF2/CEBPA/FOXO1A Expression Targets |
IGF2/HIF1A/MYC Expression Targets |
IGF2/MEF/MYOD Expression Targets |
IGF2/STAT Expression Targets |
Insulin Expression Targets |
Insulin/CEBPA/CTNNB/FOXA/FOXO Expression Targets |
Insulin/ELK-SRF/HIF1A/MYC/SREBF Expression Targets |
Insulin/MEF/MYOD Expression Targets |
Insulin/STAT Expression Targets |
PDGFR Ligands Expression Targets |
CSF1 Expression Targets |
CSF1/AP-1/CREB/CREBBP/MYC Expression Targets |
CSF1/FOXO3A Expression Targets |
CSF1/STAT Expression Targets |
KITLG Expression Targets |
KITLG/AP-1/CREB/CREBBP/MYC Expression Targets |
KITLG/STAT Expression Targets |
PDGFB Expression Targets |
PDGFB/AP-1/CREB/MYC Expression Target |
PDGFB/FOXO3A Expression Target |
PDGFB/STAT Expression Target |
PDGFC Expression Targets |
PDGFC/CREB Expression Target |
PDGFC/STAT Expression Target |
PDGFD Expression Targets |
PDGFD/AP-1 Expression Targets |
PDGFD/STAT Expression Targets |
PDGF/AP-1/CREB/CREBBP/MYC Expression Targets |
PDGF/FOXO3A Expression Targets |
PDGF/STAT Expression Targets |
VEGF Expression Targets |
FIGF Expression Targets |
FIGF/AP-1 Expression Target |
FIGF/NCOR2 Expression Target |
VEGFA Expression Targets |
VEGFA/AP-1/CREBBP/MYC Expression Targets |
VEGFA/ATF/CREB/ELK-SRF Expression Targets |
VEGFA/CTNNB/CTNND Expression Targets |
VEGFA/FOXO3A Expression Targets |
VEGFA/NCOR2 Expression Target |
VEGFA/NFATC Expression Targets |
VEGFA/STAT Expression Targets |
VEGFC Expression Targets |
VEGFC/ATF Expression Target |
VEGFC/CTNNB Expression Target |
EGFR Ligands Expression Targets |
Growth Factors Expression Targets |
NRG1/AP-1/ATF Expression Targets |
NRG1/Catenin Expression Targets |
NRG1/CREB/CREBBP/ELK-SRF/MYC Expression Targets |
NRG1/EP300/ETS/ETV/SP1 Expression Targets |
NRG1/FOXO3A Expression Targets |
NRG1/HIF1A Expression Target |
NRG1/MEF/MYOD Expression Targets |
NRG1/STAT Expression Targets |
NRG1/TP53 Expression Target |
ANGPT1/CREB/CREBBP Expression Targets |
ANGPT1/STAT Expression Targets |
ANGPT2/AP-1/CREBBP/MYC Expression Targets |
ANGPT2/STAT Expression Targets |
Collagen/NF-kB Expression Targets |
EFNA1/STAT Expression Target |
EphrinR Expression Targets |
GDNF/HSF1 Expression Targets |
MDK/PTN Expression Targets |
PAF Expression Targets |
RPTP Expression Targets |
PTPRC/BCL6 Expression Targets |
PTPRC/STAT6 Expression Targets |
PTPRJ Expression Targets |
T-cell Receptors Expression Targets |
CD22/72/279 Expression Targets |
CD22/NF-kB Expression Targets |
CD22/STAT Expression Targets |
CD72/AP-1 Expression Targets |
CD72/CREB/CREBBP Expression Targets |
CD72/NFATC Expression Targets |
CD72/NF-kB Expression Targets |
CD72/STAT Expression Target |
PDCD1/AP-1 Expression Targets |
PDCD1/ATF/CREB/CREBBP Expression Targets |
PDCD1/NFATC Expression Targets |
PDCD1/NF-kB Expression Targets |
PDCD1/STAT Expression Targets |
CD8 Expression Targets |
CD8/AP-1 Expression Targets |
CD8/ATF/CREB/CREBBP Expression Targets |
CD8/NFATC Expression Targets |
CD8/NF-kB Expression Targets |
CD8/STAT Expression Targets |
CD80 Expression Targets |
CD80/AP-1 Expression Targets |
CD80/ATF/CREB/CREBBP Expression Targets |
CD80/NFATC Expression Targets |
CD80/NF-kB Expression Targets |
CD80/STAT Expression Targets |
CD86 Expression Targets |
CD86/AP-1 Expression Targets |
CD86/ATF/CREB/CREBBP Expression Targets |
CD86/NFATC Expression Targets |
CD86/NF-kB Expression Targets |
CD86/STAT Expression Targets |
IL16 Expression Targets |
IL16/AP-1 Expression Targets |
IL16/ATF/CREB/CREBBP Expression Target |
IL16/NF-kB Expression Targets |
IL16/STAT Expression Targets |
CD2 Expression Targets |
TCR/AP-1 Expression Targets |
TCR/CREB/CREBBP/ATF Expression Targets |
TCR/NFAT Expression Targets |
TCR/NF-kB Expression Targets |
TCR/STAT Expression Targets |
TGFB Superfamily Expression Targets |
BMP Expression Targets |
BMP15-BMPR2 Expression Targets |
BMP2-BMPR2 Expression Targets |
BMP4-BMPR2 Expression Targets |
BMP6-ACVR2A Expression Targets |
BMP7-ACVR2 Expression Targets |
BMP7-BMPR2/ACVR2 Expression Targets |
INHB Expression Targets |
INHBA-ACVR2/ACVR1 Expression Targets |
INHBA-ACVR2/BMPR Expression Targets |
INHBB-ACVR2 Expression Target |
Other ACVR/BMPR Ligands Expression Targets |
AMH-AMHR2 Expression Targets |
GDF5-BMPR2/ACVR2 Expression Targets |
MSTN-ACVR2/ACVR1 Expression Targets |
MSTN-ACVR2/BMPR Expression Targets |
NODAL-ACVR2B Expression Targets |
TDGF1-ACVR2B Expression Targets |
TGFB Expression Targets |
TGFB1-ACVRL1 Expression Targets |
TGFB1-TGFBR1 Expression Targets |
TGFB1-TGFBR1/AP-1 Expression Targets |
TGFB1-TGFBR2 Expression Targets |
TGFB2-TGFBR1 Expression Targets |
TGFB2-TGFBR2 Expression Targets |
TGFB3-TGFBR1 Expression Targets |
TGFB3-TGFBR2 Expression Targets |
TNF Family Expression Targets |
CD40LG/ATF2/AP-1/TP53/E2F Expression Targets |
CD40LG/NF-kB/ELK-SRF/CREB/NFATC Expression Targets |
CD40LG/STAT Expression Targets |
EDA Expression Targets |
FASLG Expression Targets |
LTA Expression Targets |
TNF/AP-1 Expression Targets |
TNF/CREB Expression Targets |
TNF/ELK-SRF Expression Targets |
TNF/NF-kB Expression Targets |
TNF/STAT Expression Targets |
TNF/TP53/ATF Expression Targets |
TNFSF10 Expression Targets |
TNFSF13 Expression Targets |
TNFSF13B Expression Targets |
TNFSF14 Expression Targets |
Toll-like Receptors Expression Targets |
IL1A Expression Targets |
IL1B Expression Targets |
IL1B/NO Expression Targets |
IL1B/PGE2 Expression Targets |
TLR1/2/6 Expression Targets |
TLR3 Expression Targets |
TLR4/AP-1 Expression Targets |
TLR4/AP-1/EGR1/HIF1A Expression Targets |
TLR4/NF-kB/IRF Expression Targets |
TLR5 Expression Targets |
TLR7 Expression Targets |
TLR9 Expression Targets |
Urokinase Expression Targets |
PLAU/ELK-SRF/AP-1 Expression Targets |
PLAU/STAT1 Expression Targets |
WNT Expression Targets |
Canonical WNT Signaling Expression Targets |
WNT1 Expression Targets |
WNT2 Expression Targets |
WNT3A Expression Targets |
WNT4 Expression Targets |
WNT5A Expression Targets |
WNT7A Expression Targets |
WNT7B Expression Targets |
WNT9A Expression Targets |
WNT9B Expression Targets |
Immunological Pathways |
Antigen Processing |
MHC1-Mediated Antigen Presentation |
MHC2-Mediated Antigen Presentation |
B-cell Activation |
T-cell-Dependent B-cell Activation |
T-cell-Independent B-cell Activation |
Natural Killer Cell Receptors Signaling |
Leukocyte Adhesion to Endothelial Cell |
Natural Killer Cell Activation through C-type Lectin-like Receptors |
Natural Killer Cell Activation through ITAM-Containing Receptors |
Natural Killer Cell Activation through ITSM-Containing Receptors |
Natural Killer Cell Inhibitory Receptor Signaling |
Production of Immunoglobulins |
Activation of Immunoglobulin Class-Switch Recombination |
Immunoglobulin Class-Switch Recombination via Alternative End-Joining |
Immunoglobulin Class-Switch Recombination via Classical Non-Homologous End-Joining |
Natural Killer Cell Activation through Integrins and non-ITAM-Containing Receptors |
V(D)J Recombination |
V(D)J Recombination Activation |
Receptors of Antigen Recognition in Innate Immune System |
Antiviral Signaling through Pattern Recognition Receptors |
DCIR1 (CLEC4A) Signaling |
Dectin-1 (CLEC7A) Signaling |
Dectin-2 (CLEC6A), Mincle (CLEC4E), and BDCA2 (CLEC4C) Signaling |
Mannose Receptor Signaling |
NOD-like Receptors in Pathogen Recognition |
TLR4 Signaling in Leukocytes |
Toll-like Receptors Act through MYD88 Signaling |
Toll-like Receptors Act through MYD88-TIRAP Signaling |
Transcriptional Activation of Immunoglobulin Genes |
Self Tolerance |
CD8+ T-cell Activation |
Central T-cell Tolerance |
DC-SIGN (CD209) Signaling |
Model of T-cell Maturation |
Natural Killer Cell Activation |
Peripheral T-cell Tolerance Overview |
T-cell Positive Selection and Neglect-Induced Death |
T-cell Activation and Differentiation |
Cell Death Mediated by Cytotoxic Cells |
Regulatory T-cell Differentiation |
T-cell Receptor Signaling |
Th1 Cell Differentiation |
Th17 Cell Differentiation |
Th2 Cell Differentiation |
Metabolic Pathways |
Alanine metabolism |
Alpha oxidation of phytanic acid |
Amino sugars synthesis |
Arachidonic acid metabolism |
Ascorbate biosyntesis |
Aspartate metabolism |
Bile acid metabolism (alternative pathway) |
Bile acids metabolism |
Biosynthesis of cholesterol |
Biotin metabolism |
Branched chain amino acids metabolism |
Caffeine metabolism |
Capecitabine and Fluorafur metabolism |
Cholesterol catabolism |
D-amino acid metabolism |
Ethanol metabolism |
Fatty acid biosynthesis |
Fatty acid oxidation |
Folate biosynthesis |
Galactose metabolism |
Ganglioside-type glycosphingolipid biosynthesis |
Globoside-type glycosphingolipid biosynthesis |
Glu/Gln/Pro metabolsm |
Glucose metabolism |
Glutathione metabolism |
Glycogen metabolism |
Glycosylphosphatidylinositol(GPI)-anchor biosynthesis |
Glyoxylate and glycerate metabolism |
Heme biosynthesis |
Heme oxidation |
Histidine metabolism |
Inositol phosphate metabolism |
Irinotecan metabolism |
Ketonogenesis |
Lacto- and neolacto-type glycosphingolipid biosynthesis |
Lipoyl-protein complex biosynthesis I |
Lipoyl-protein complex biosynthesis II |
L-sugars oxidation |
Lysine metabolsm |
Malonate, propanoate and beta-alanine metabolism |
Mannose metabolism |
Metabolism of estrogens and androgens |
Metabolism of glucocorticoids and mineralcorticoids |
Metabolism of glycerophospholipids and ether lipids |
Metabolism of triacylglycerols |
Methionine metabolism |
Mevalonate pathway |
N-Glycan biosynthesis |
Nicotinate and nicotinamide metabolism |
Omega-3-fatty acid metabolism |
Omega-6-fatty acid metabolism |
Organophosphorus compounds degradation |
Pentose-phosphate shunt |
Phenylalanine and Tyrosine metabolism |
Polysaccharide degradation |
Pterine biosynthesis |
Purine metabolism |
Pyrimidine metabolism |
Pyruvate metabolism |
Respiratory chain and oxidative phosphorylation |
Riboflavin metabolism |
ROS metabolism |
Selencompound biosynthesis |
Ser/Gly/Thr/Cys metabolism |
Serine and Glycine metabolism |
Sphingolipid metabolism |
Sulfur metabolism |
Tricarboxylic acid cycle |
Tryptophan metabolism |
Ubiquinoine biosynthesis |
Ubiquinoine biosynthesis in humans |
Ubiquinoine biosynthesis in rats |
Urea cycle and arginine metabolism |
Vitamin A (retinol) metabolism and visual cycle |
Vitamin B1(thiamine) metabolism |
Vitamin B5 (pantothenate) metabolism and biosynthesis of CoA and holo-ACP |
Vitamin B6 (pyridoxine) metabolism |
Vitamin K metabolism |
Nociception Pathways |
Neuronal Signaling |
Adrenergic receptors |
ADRA1 -> ion channels |
ADRA2A -> hyperpolarization |
ADRA2A -> neurotransmitter release |
ADRA2C/ADRB2 -> synaptic endocytosis |
ADRB1 -> ion channels |
ATP receptors |
P2RXs -> synaptic transmission |
P2RY1/2/4/6 -> potassium channels |
P2RY11/13/14 -> IL8/10 production |
P2RY2/12/13/14 -> N-type calcium channel |
Bradykinin receptors |
BDKRB1/2 -> ion channels |
Cannabinoid receptors |
CNR1/2 -> membrane transport |
Cholecystokinin B receptor |
CCKBR -> neurotransmitter uptake |
Dopamine receptors |
DRD1/3 -> potassium uptake |
DRD2 -> TRPC1 transcription |
DRD2/4 -> membrane transport |
DRD3 -> dopamine uptake |
Ephrin receptors |
EPHB -> NMDA receptor activation |
GABA receptors |
GABA(A)R -> membrane hyperpolarization |
GABA(B)R -> postsynaptic inhibition |
Galanin receptors |
GALR1/2/3 -> neurotransmitter metabolism |
GFs signaling |
GFs/TNF -> ion channels |
Glutamate receptors |
AMPA receptors -> calcium influx |
GRM1/5 (postsynaptic) -> ion channels |
GRM2-4/6-8 (presynaptic) -> glutamate release attenuation |
NMDA receptor -> synaptic excitation |
NMDA receptors -> Ca2+/CREB activation/PGE2 synthesis |
Glycine receptor |
GlyR -> synaptic inhibition |
Histamine receptor |
HRH1/2 -> membrane polarization |
HRH1/3 -> synaptic transmission |
Muscarinic receptors |
CHRM1/2/3/5 -> ion channels |
Neuropeptide Y receptor |
NPY1R -> CRH/POMC production |
Neurotrophin receptors |
NTRK1/2/3 -> acetylcholine production |
Nicotinic receptors |
CHRNA3-B4/A4-B2/A7 -> ion transport |
CHRNA7 -> NOS1 production |
Opioid receptors |
OPRD/OPRM -> ion channels |
OPRK -> pain perception |
OPRL1 -> ion channels |
Serotonin receptors |
HTR1 -> membrane transport |
HTR2 -> membrane transport |
HTR3A -> cation transport |
HTR4/6/7 -> cation channels |
Substance P receptor |
TACR1 -> membrane transport |
Trace amine receptor |
TAAR1 -> neurotransmitter uptake |
Neurotransmitter Release Cycles |
Acetylcholine release cycle |
Dopamine release cycle |
Epinephrine/Norepinephrine release cycle |
GABA release cycle |
Glutamate release cycle |
Serotonin release cycle |
Reference Nociception Pathways |
Regulation of calcium flux |
Regulation of potassium flux |
Regulation of sodium flux |
Summarized nociception-related expression targets |
Summarized vascular motility pathway |
Tissue Signaling |
Non-transcriptionally Regulated Processes |
Adenosine receptors |
ADORA1/2A -> exocytosis |
ADORA2A/B -> vasodilation |
ADORA3 -> mast cell degranulation |
Adrenergic receptors |
ADRA1 -> prostaglandin generation |
ADRA1 -> vasoconstriction |
ADRA2C/ADRB2 -> vasoconstriction |
ADRB1 -> prostaglandin generation |
ADRB1/3 -> vasodilation |
Bradykinin receptors |
BDKRB1/2 -> prostaglandin generation |
BDKRB1/2 -> vasodilation |
Calcitonin receptor-like receptor |
CGRP -> calcium influx |
Cannabinoid receptors |
CNR1/2 -> vascular motility |
Endothelin receptors |
EDNRA/B -> vascular motility |
Histamine receptors |
HRH1/2 -> vascular motility |
Leptin signaling |
Leptin -> NO production/vasodilation |
Muscarinic receptors |
CHRM1/2/3 -> vascular motility |
Prostaglandin receptors |
PTGER2/3 -> inflammation-related expression targets |
PTGIR -> IL6 production |
Serotonin receptors |
HTR1 -> vascular motility |
HTR4/6/7 -> vasodilation |
Transcriptionally Regulated Processes |
Adrenergic receptors |
ADRA1A -> IL6 production |
Bradykinin receptors |
BDKRB1/2 -> interleukins production |
Cannabinoid receptors |
CNR1/2 -> IL1B/2/4/6/10 production |
Chemokine receptor 1 |
Nociception-related CCR1 expression targets |
Corticotropin releasing hormone receptor |
CRH -> synthesis of corticosteroids |
Dopamine receptors |
Nociception-related DRD1/5 expression targets |
Nociception-related DRD2 expression targets |
Galanin receptors |
GALR1/2/3 -> POMC/NPY production |
Histamine receptor |
HRH2/4 -> IL6/10 production |
Interleukin signaling |
Nociception-related IL1B expression targets |
Nociception-related IL6 expression targets |
Leptin signaling |
Leptin -> CD25/IL6/IL10 production |
Muscarinic receptors |
CHRM1 -> IL2 production |
Neurotensin receptor |
Nociception-related NTSR1 expression targets |
Nicotinic receptors |
CHRNA7 -> IL8 production |
Prostaglandin receptors |
PTGDR -> vasodilation |
PTGER1/4 -> vascular motility |
PTGER2/3 -> vascular motility |
PTGFR -> vasoconstriction |
PTGIR -> vasodilation |
Serotonin receptors |
HTR1 -> IL6 production |
HTR5 -> TNF production |
HTR7 -> IL6 production |
Substance P receptor |
TACR1 -> TNF/IL6/IL8 production |
Signaling Pathways |
Receptor Signaling |
Advanced Glycosylation End Product-specific Receptor |
AGER -> CREB/SP1 signaling |
AGER -> NF-kB signaling |
B-cell Receptors |
B-cell receptor -> AP-1 signaling |
B-cell receptor -> NFATC signaling |
B-cell receptor -> NF-kB signaling |
CD19 -> AP-1/ELK-SRF signaling |
CD19 -> NF-kB signaling |
Cytokine Receptors |
CNTFR -> STAT3 signaling |
CSF2R -> NF-kB signaling |
CSF2R -> STAT signaling |
CSF3R -> STAT signaling |
ErythropoietinR -> AP-1/CREB/MYC signaling |
ErythropoietinR -> ELK-SRF/FOS signaling |
ErythropoietinR -> FOXO3A signaling |
ErythropoietinR -> NF-kB signaling |
ErythropoietinR -> STAT signaling |
GHR -> ELK-SRF/MYC signaling |
GHR -> NF-kB signaling |
GHR -> STAT signaling |
IFNAR -> STAT signaling |
IFNGR -> STAT signaling |
LeptinR -> ELK-SRF signaling |
LeptinR -> STAT signaling |
LIFR -> STAT5A signaling |
OncostatinR -> STAT3 signaling |
ProlactinR -> STAT signaling |
ThrombopoietinR -> AP-1/CREB/ELK-SRF/MYC signaling |
ThrombopoietinR -> SP1 signaling |
ThrombopoietinR -> SPI1 signaling |
ThrombopoietinR -> STAT signaling |
Frizzled Receptor family |
FrizzledR -> CTNNB signaling |
FrizzledR -> JUN/PAX2 signaling |
G-protein-coupled Receptors |
Gi-coupled Receptors |
CannabinoidR -> AP-1/EGR signaling |
CCR1 -> STAT signaling |
CCR2/5 -> STAT signaling |
CCR5 -> TP53 signaling |
CholinergicRm -> CREB/ELK-SRF signaling |
CXCR4 -> STAT signaling |
DopamineR2 -> AP-1/CREB/ELK-SRF signaling |
DopamineR2 -> NF-kB signaling |
EDG2 -> ELK-SRF signaling |
NeuropeptideYR -> ATF/CREB signaling |
SerotoninR1 -> FOS signaling |
SomatostatinR -> ATF1/TP53 signaling |
G-protein-coupled Receptors |
ThrombinR -> AP-1/CREB/ELK-SRF/SP1 signaling |
ThrombinR -> NF-kB signaling |
ThrombinR -> STAT1 signaling |
ThromboxaneR -> CREB signaling |
Gq/i-coupled Receptors |
EDG3/5 -> AP-1/ELK-SRF signaling |
EndothelinRb -> AP-1/CREB/ELK-SRF signaling |
IL8R -> CREB/EGR signaling |
Gq/s-coupled Receptors |
AdrenergicRb -> CREB signaling |
AdrenergicRb -> STAT3 signaling |
AngiotensinR -> CREB/ELK-SRF/TP53 signaling |
AngiotensinR -> STAT signaling |
EndothelinRa -> AP-1/CREB signaling |
ProstaglandinIR -> ATF1/ELK-SRF/CREB signaling |
TachykininR -> ELK-SRF signaling |
VIPR -> CREB/CEBP signaling |
Gq-coupled Receptors |
AdenosineR -> AP-1 signaling |
AdenosineR -> NF-kB signaling |
AdrenergicRa -> ELK-SRF signaling |
AdrenergicRa -> STAT1 signaling |
AdrenergicRa -> STAT3 signaling |
BradykininR -> STAT3 signaling |
CholecystokininR -> ELK-SRF signaling |
CholecystokininR -> STAT signaling |
GNRHR -> ELK-SRF signaling |
GRM1/5 -> CREB signaling |
NeurotensinR -> ELK-SRF/AP-1/EGR signaling |
OpioidR -> CREB/ELK-SRF/STAT3 signaling |
OxytocinR -> ELK-SRF/GATA/AP-1 signaling |
ProstaglandinFR -> ATF1/ELK-SRF/CREB signaling |
PTAFR -> AP-1/ATF1/CREB/ERK-SRF signaling |
PTAFR -> NF-kB signaling |
PTAFR -> STAT3 signaling |
SerotoninR2 -> ELK-SRF/GATA4 signaling |
SerotoninR2 -> STAT3 signaling |
VasopressinR1 -> CREB/ELK-SRF/AP-1/EGR signaling |
VasopressinR1 -> MEF/MYOD/NFATC/MYOG signaling |
VasopressinR1 -> STAT signaling |
Gs-coupled Receptors |
DopamineR1 -> CREB/ELK-SRF signaling |
FSHR -> CREB/ELK-SRF/GATA4 signaling |
FSHR -> FOXO1A signaling |
GlucagonR -> CREB/ELK-SRF/SP1 signaling |
SerotoninR4/6/7 -> NR3C signaling |
VasopressinR2 -> CREB/ELK-SRF/AP-1/EGR signaling |
VasopressinR2 -> MEF/MYOD/NFATC/MYOG signaling |
VasopressinR2 -> STAT signaling |
Integrins and Cell Adhesion Receptors |
FibronectinR -> AP-1/ELK-SRF/SREBF signaling |
FibronectinR -> CTNNB signaling |
FibronectinR -> ICAP-1A/MYC signaling |
FibronectinR -> NF-kB signaling |
ICAM1 -> AP-1/CREB/ELK-SRF signaling |
ICAM2 -> CTNNB/FOXO/STAT3 signaling |
MacrophageR -> CEBPB/NF-kB signaling |
NCAM1 -> CREB/ELK-SRF/MYC signaling |
PECAM -> CTNNB1 signaling |
PECAM -> SP1 signaling |
PECAM -> STAT signaling |
SELE -> ELK-SRF signaling |
Sialophorin -> CTNNB/MYC/TP53 signaling |
Interleukin Receptors |
IL10R -> STAT signaling |
IL11R -> STAT3 signaling |
IL12R -> NF-kB/NFATC signaling |
IL12R -> STAT signaling |
IL13R -> STAT signaling |
IL13R -> STAT6 signaling |
IL15R -> NF-kB/NFATC signaling |
IL15R -> STAT signaling |
IL21R -> STAT signaling |
IL22R -> STAT3 signaling |
IL2R -> ELK-SRF/MYC signaling |
IL2R -> STAT signaling |
IL31R -> STAT signaling |
IL3R -> STAT signaling |
IL4R -> ELK-SRF/HMGY signaling |
IL4R -> STAT signaling |
IL5R -> SOX4 signaling |
IL5R -> STAT signaling |
IL6R -> CEBP/ELK-SRF signaling |
IL6R -> STAT signaling |
IL6ST -> STAT5B signaling |
IL7R -> FOXO/NF-kB signaling |
IL7R -> STAT signaling |
IL9R -> STAT signaling |
NK-cell Receptors |
FcIgER -> ELK-SRF signaling |
FcIgER -> NFATC1 signaling |
Notch Receptors |
Notch -> EP300/ASCL signaling |
Notch -> LEF1 signaling |
Notch -> MEF/MYOD signaling |
Notch -> NF-kB signaling |
Notch -> RBPJ/HES/HEY signaling |
Notch -> SMAD3 signaling |
Notch -> TCF3 signaling |
Protein Tyrosine Phosphatase Receptors |
PTPRC -> BCL6 signaling |
PTPRC -> STAT6 signaling |
PTPRF -> CTNNB signaling |
PTPRJ -> CTNND signaling |
PTPRU -> CTNNB signaling |
Receptor Tyrosine Kinases |
Growth Factor Receptors |
HGFR |
HGFR -> AP-1/CREB/MYC signaling |
HGFR -> FOXO3A signaling |
HGFR -> STAT signaling |
EGFR family |
EGFR -> AP-1/ATF2 signaling |
EGFR -> AP-1/CREB/ELK-SRF/MYC signaling |
EGFR -> CTNND signaling |
EGFR -> NCOR2 signaling |
EGFR -> SMAD1 signaling |
EGFR -> ZNF259 signaling |
EGFR/ERBB -> STAT signaling |
EGFR/ERBB2 -> CTNNB signaling |
EGFR/ERBB2 -> HIF1A signaling |
EGFR/ERBB2 -> TP53 signaling |
EGFR/ERBB3 -> MEF/MYOD/NFATC/MYOG signaling |
ERBB2/3 -> EP300/ETS/ETV/SP1 signaling |
FGFR family |
FGFR -> AP-1/CREB/CREBBP/ELK-SRF/MYC signaling |
FGFR -> RUNX2 signaling |
FGFR1 -> STAT signaling |
FGFR3 -> STAT signaling |
PDGFR family |
CSF1R -> STAT signaling |
KIT -> MITF signaling |
KIT -> STAT signaling |
PDGFR -> AP-1/MYC signaling |
PDGFR -> FOXO3A signaling |
PDGFR -> STAT signaling |
VEGFR family |
VEGFR -> AP-1/CREB/MYC signaling |
VEGFR -> ATF/CREB/ELK-SRF signaling |
VEGFR -> CTNNB signaling |
VEGFR -> CTNND signaling |
VEGFR -> FOXO3A signaling |
VEGFR -> NFATC signaling |
VEGFR -> STAT signaling |
Insulin Receptors |
IGF1R -> CEBPA/FOXO1A signaling |
IGF1R -> ELK-SRF/HIF1A/MYC/SREBF signaling |
IGF1R -> MEF/MYOD/MYOG signaling |
IGF1R -> STAT signaling |
InsulinR -> CTNNB/FOXA/FOXO signaling |
InsulinR -> ELK-SRF/SREBF signaling |
InsulinR -> STAT signaling |
ALK -> STAT signaling |
AngiopoietinR -> AP-1 signaling |
AngiopoietinR -> FOXO signaling |
AngiopoietinR -> STAT signaling |
DDR1 -> NF-kB signaling |
EphrinR -> actin signaling |
EphrinR -> STAT signaling |
GDNF -> HSF1 signaling |
NTRK -> AP-1/CREB/ELK-SRF/MYC/SMAD3/TP53 signaling |
NTRK -> FOXO/MYCN signaling |
T-cell Receptors |
CD2 -> NFATC1 signaling |
CD2 -> STAT signaling |
T-cell receptor -> AP-1 signaling |
T-cell receptor -> ATF/CREB signaling |
T-cell receptor -> CREBBP signaling |
T-cell receptor -> NFATC signaling |
T-cell receptor -> NF-kB signaling |
T-cell receptor -> STAT signaling |
TGFBR family |
ActivinR -> SMAD2/3 signaling |
ActivinR/BMPR -> SMAD1/5/9 signaling |
TGFBR -> AP-1 signaling |
TGFBR -> ATF/GADD/MAX/TP53 signaling |
TGFBR -> CREB/ELK-SRF signaling |
TGFBR -> MEF/MYOD/MYOG signaling |
TGFBR -> SMAD1/5/9 signaling |
TGFBR/BMPR -> SMAD2/3 signaling |
TNFR family |
EctodysplasinR -> AP-1 signaling |
EctodysplasinR -> LEF1 signaling |
EctodysplasinR -> NF-kB signaling |
NGFR -> AP-1/CEBPB/CREB/ELK-SRF/TP53 signaling |
NGFR -> MEF signaling |
NGFR -> NF-kB signaling |
TNFR -> AP-1/ATF/TP53 signaling |
TNFR -> CREB/ELK-SRF signaling |
TNFR -> NF-kB signaling |
TNFRSF1A -> AP-1/ATF/TP53 signaling |
TNFRSF1A -> CREB/ELK-SRF signaling |
TNFRSF1A -> STAT signaling |
TNFRSF5 -> STAT signaling |
TNFRSF5/13B -> NFATC1 signaling |
TNFRSF5/6 -> RB1/E2F signaling |
TNFRSF6 -> DDIT3 signaling |
TNFRSF6 -> FOXO3A signaling |
TNFRSF6 -> HSF1 signaling |
Toll-like Receptors |
IL1R -> NF-kB signaling |
IL1R -> STAT3 signaling |
TLR -> AP-1 signaling |
TLR1/2/6 -> NF-kB signaling |
TLR3 -> IRF signaling |
TLR3 -> NF-kB signaling |
TLR4 -> IRF signaling |
TLR4/5/7/9 -> NF-kB signaling |
Urokinase Receptor |
UrokinaseR -> ELK-SRF signaling |
UrokinaseR -> STAT signaling |
CD38 -> NF-kB signaling |
CholinergicRn -> CREB signaling |
EphrinB -> JUN signaling |
Atlas of Signaling |
Toxicity Pathways |
Drug Toxicity Pathways |
Acetaminophen-Induced Hepatotoxicity |
Clozapine-Induced Granulocytopenia |
Cocaine-Induced Hepatotoxicity |
Cyclosporine-Induced Nephrotoxicity |
Dexamethasone-Induced Diabetes |
Dexamethasone-Induced Neurotoxicity |
Dexamethasone-Induced Osteoporosis |
Doxorubicin-Induced Cardiotoxicity |
Ethanol-Induced Hepatotoxicity |
Ritonavir-Induced Cardiovascular Dysfunction |
Ritonavir-Induced Diabetes |
Tamoxifen-Induced Endometrial Cancer |
Valdecoxib-Induced Ischemic Disease |
General Mechanisms of Toxicity |
Cytosolic Calcium Overload |
ER Stress (Unfolded Protein Response) |
Glutamate-Mediated Excitotoxicity |
Hypoxia-Induced Mitochondrial Damage |
Protein Oxidation and Nitration Products as Disease Biomarkers |
ROS and RNS in the Regulation of Vasoconstriction and Vasodilation |
ROS in Angiotensin-Mediated Cardiovascular Remodeling and Hypertrophy |
ROS in Neutrophil-Mediated Cell Damage |
ROS in Triggering Vascular Inflammation |