What is NetPro™?
NetPro™ is a comprehensive Knowledgebase of Protein-Protein, Protein-Small molecule and Small molecule-Small molecule interactions, consisting of > 3,00,000 interactions captured from ~ 55,000 references.
What is the source of NetPro™ interactions?
Interactions are completely manually curated from Pubmed literature.
Who can use NetPro™?
NetPro™ can be used by different groups in pharmaceutical companies for drug discovery - for target identification, to explore SAR data, high throughput data analysis,etc.. Systems biologists and other researchers working in the area of molecular mechanism and signaling pathways can also derive benefits from NetPro™.
What types of interactions are covered?
NetPro™ covers non-directional 'bind' or 'associate' & directional interactions of 9 different classes - activate, bind, decrease, increase, inhibit, modification, regulates activity, regulates expression, transport regulation, are covered. More specific interaction terms under each of the major classes are used, as cited by the authors in literature. E.g., class 'increase' defines quantitative changes in the target molecule, for which specific interaction terms like increases expression, decreases degradation, decreases cleavage, increase stability are present.
Both direct (physical associations) and indirect (effector having an influence on the target even in absence of a physical association) interactions.
Does NetPro™ provide customized updates?
Yes.
How frequent are NetPro™ updations?
Routine updations are done quarterly. Customized updates based on requirement.
What standards does NetPro™ follow?
Proteins are mapped to Entrez gene IDs, Small molecule to CAS IDs or Molecular Connections Internal Ids (in absence of a public identifier), Pathway terms and biological processes are GO compliant, Diseases are Mesh/OMIM compliant, Cell lines are taken from ATCC etc. Domains mapped to pfam Ids.
What are the facts covered in an interaction?
Experimental evidences like method and location of the interaction; attributes of the interacting molecules like PTM, mutation etc; disease, pathway and process relevance of the interaction; regulators; domain and residue information; kinetics data.
What are the major organisms covered in NetPro™?
Human, Mouse, Rat are amongst the major classes of the 37 organisms covered in NetPro™.
What is Homo sapiens-e?
If the source of a protein/gene is not known, then the symbol for Homo sapiens is taken and the species is captured as Homo sapiens-e (Homo sapiens-extrapolated).
Are clinically relevant drugs covered in NetPro™?
Yes.
What are the molecule types present in NetPro™?
Small molecule, Protein, RNA, DNA, complex, fusion proteins, synergistically acting molecules.
What are the disease information available?
a) Increase or decrease of an interaction in a particular disease condition
b) Therapeutic value of an interacting molecule in a disease
c) Altered expression or mutation of a protein in a disease
What is 'indirect assay'?
Generally activity of a molecule is deciphered using certain functional assays or measurement of a third molecule. We take indirect assay to bring out such scenarios.
What types of kinetics data are covered?
Dose and time dependent parameters, pharmacokinetics/ pharmacodynamics parameters etc. are covered.
What is a regulator?
A third molecule (protein or small molecule) or a factor (eg. Hypoxia) having an influence on the core interaction either by enhancing, reducing or triggering is captured as positive, negative or stimulate respectively.
How are the terms 'induce' and 'stimulate' used for a regulator in NetPro™?
'Stimulate' is used as a regulation type to describe the trigger which initiates an interaction, while 'Induce' is used as a regulation type which does not have a role on the effector molecule (Molecule A) but has an inducing role on the target (Molecule B).
What is 'Molecule attribute'?
It's the property of the molecule involved in an interaction (e.g. Tyr phosphorylated MAPK1).
What kind of 'pathway' information is available?
Pathways involved or not involved in an interaction are captured.
What is 'interaction result'?
The outcome of an interaction is captured, which may be an effected process or product formation.
Does NetPro™ cover domain, residue etc for PTM and physical associations?
Yes. Domain, residue, motif, and other interacting regions are present in a standard format. PFAM identifiers are present for domain information.
Is it possible to draw a pathway from the dataset?
Yes, using Cytoscape.
How could I visualize and analyze the data?
The data format is compatible to be visualized & analyzed using Cytoscape.
How do I know if my area of interest is covered in the sample set?
Search box enabled with autosuggest feature would show the words as you type in.
How could I limit search to a desired field?
Search terms can be limited to a specific field using the following prefixes to the queried term:
d: for disease
m: for molecule
p: for pathway
c: for cell/cell line
v: for verb/verb category (find below the verb/verb categories in ''What types of interactions are captured?'')
Example: Upon typing m:a, all molecule entries starting with the letter 'a' will appear
Yes. AND, OR and NOT can be effectively used in your queries.
Example:
INS AND Alzheimer Disease will fetch only those interactions where both terms are present
PSEN2 OR Alzheimer Disease will fetch those interactions where at least one of the terms is present
INS NOT immune response will fetch interactions where INS is present but not immune response
How can I subscribe to NetPro™?
You can subscribe to NetPro™ on an annual basis or perpetual basis. It can be single seat or multiple user or company wide. For more information. For more information
click here.
NetPro™ data offers Flexibility to Customize, Extend and Integrate in-house data, tools and federated data sources, as we use Standards like MeSH, UniProt, GO and PubChem ontologies for mapping.
What are the data formats in NetPro™?
NetPro™ data is provided in XML format, PSIMI format. Other formats can be custom developed as per client needs.
