Netpath
Encyclopedia
NetPath is a manually curated resource of human signal transduction
pathways. It is a joint effort between Pandey Lab at the Johns Hopkins University
and the Institute of Bioinformatics (IOB), Bangalore, India, and is also worked on by other parties.
NetPath hosts 20 signaling pathways including 10 pathways with a major role in the regulation of immune system
and 10 pathways with relevance to regulation of cancer
.
s, enzyme-protein substrate reactions which bring about post translational modifications (PTMs) and also a catalogue of genes which are differentially regulated upon activation of specific ligand
mediated receptor
pathways. The molecules which localises to different cellular organelle
s due to their PTMs or specific protein-protein interactions which occur downstream of ligand-receptor mediated pathway are available under translocation events. Recently, NetPath has also curated the molecules involved in the transcriptional regulation
of genes in the context of immune signaling pathways. The reactions in NetPath are curated by PhD level scientists from experimental evidence available in published research articles. NetPath also contains textual description of its reactions with information on PTMs, dependence of PTMs on various signaling reactions, subcellular location, protein interaction domains
or motifs and the cell type or cell line in which reactions are proved. The information in NetPath is linked to their corresponding research articles and are frequently updated. Each pathway is subjected to different level of internal quality checks and peer-review by the pathway experts and authorities.
, PSI-MI and SBML
formats. BioPAX is an emerging standard for pathway data exchange. The pathways are made available under an adaptive Creative Commons License 2.5
which stipulates that the pathways may be used if adequate credit is given to the authors.
for the "Cancer Cell Map". The following cancer signaling pathways are hosted by Netpath:
(USA) and Gary Bader's lab at the University of Toronto
, Canada. Currently, students from 3 major Indian Universities namely Pondicherry University
, University of Pune
and University of Mysore
are participants of this community effort.
Signal transduction
Signal transduction occurs when an extracellular signaling molecule activates a cell surface receptor. In turn, this receptor alters intracellular molecules creating a response...
pathways. It is a joint effort between Pandey Lab at the Johns Hopkins University
Johns Hopkins University
The Johns Hopkins University, commonly referred to as Johns Hopkins, JHU, or simply Hopkins, is a private research university based in Baltimore, Maryland, United States...
and the Institute of Bioinformatics (IOB), Bangalore, India, and is also worked on by other parties.
NetPath hosts 20 signaling pathways including 10 pathways with a major role in the regulation of immune system
Immune system
An immune system is a system of biological structures and processes within an organism that protects against disease by identifying and killing pathogens and tumor cells. It detects a wide variety of agents, from viruses to parasitic worms, and needs to distinguish them from the organism's own...
and 10 pathways with relevance to regulation of cancer
Cancer
Cancer , known medically as a malignant neoplasm, is a large group of different diseases, all involving unregulated cell growth. In cancer, cells divide and grow uncontrollably, forming malignant tumors, and invade nearby parts of the body. The cancer may also spread to more distant parts of the...
.
Overview
The 20 pathways contain information pertaining to protein-protein interactionProtein-protein interaction
Protein–protein interactions occur when two or more proteins bind together, often to carry out their biological function. Many of the most important molecular processes in the cell such as DNA replication are carried out by large molecular machines that are built from a large number of protein...
s, enzyme-protein substrate reactions which bring about post translational modifications (PTMs) and also a catalogue of genes which are differentially regulated upon activation of specific ligand
Ligand (biochemistry)
In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In a narrower sense, it is a signal triggering molecule, binding to a site on a target protein.The binding occurs by intermolecular forces, such as ionic bonds, hydrogen...
mediated receptor
Receptor (biochemistry)
In biochemistry, a receptor is a molecule found on the surface of a cell, which receives specific chemical signals from neighbouring cells or the wider environment within an organism...
pathways. The molecules which localises to different cellular organelle
Organelle
In cell biology, an organelle is a specialized subunit within a cell that has a specific function, and is usually separately enclosed within its own lipid bilayer....
s due to their PTMs or specific protein-protein interactions which occur downstream of ligand-receptor mediated pathway are available under translocation events. Recently, NetPath has also curated the molecules involved in the transcriptional regulation
Transcriptional regulation
Transcriptional regulation is the change in gene expression levels by altering transcription rates. -Regulation of transcription:Regulation of transcription controls when transcription occurs and how much RNA is created...
of genes in the context of immune signaling pathways. The reactions in NetPath are curated by PhD level scientists from experimental evidence available in published research articles. NetPath also contains textual description of its reactions with information on PTMs, dependence of PTMs on various signaling reactions, subcellular location, protein interaction domains
Protein domain
A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural...
or motifs and the cell type or cell line in which reactions are proved. The information in NetPath is linked to their corresponding research articles and are frequently updated. Each pathway is subjected to different level of internal quality checks and peer-review by the pathway experts and authorities.
Development
NetPath was developed using PathBuilder, an open source software application for annotating and developing pathway resources. PathBuilder enables annotation of molecular events including protein-protein interactions, enzyme-substrate relationships and protein translocation events via manual or automatic methods. The features of PathBuilder include automatic validation of data formats, built-in modules for visualizing pathways, automated import of data from other pathway resources, export of data in several standard data exchange formats and an application programming interface for retrieving pathway datasets.Data availability
All the 20 pathways are freely downloadable in BioPAXBioPAX
BioPAX is a RDF/OWL-basedstandard language to represent biological pathwaysat the molecular and cellular level. Its major use is to facilitate the exchange of pathway data....
, PSI-MI and SBML
SBML
The Systems Biology Markup Language is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers...
formats. BioPAX is an emerging standard for pathway data exchange. The pathways are made available under an adaptive Creative Commons License 2.5
Creative Commons licenses
Creative Commons licenses are several copyright licenses that allow the distribution of copyrighted works. The licenses differ by several combinations that condition the terms of distribution. They were initially released on December 16, 2002 by Creative Commons, a U.S...
which stipulates that the pathways may be used if adequate credit is given to the authors.
Immune signaling pathways
The following immune signaling pathways are hosted by Netpath:- B cell receptor pathway
- T cell receptor pathway
- Interleukin-1 pathway
- Interleukin-2 pathway
- Interleukin-3 pathway
- Interleukin-4 pathway
- Interleukin-5 pathway
- Interleukin-6 pathway
- Interleukin-7 pathway
- Interleukin-9 pathway
Cancer signaling pathways
The cancer signaling pathways were developed in collaboration with the Computational Biology Center at Memorial Sloan–Kettering Cancer Center and with Bader Lab at the University of TorontoUniversity of Toronto
The University of Toronto is a public research university in Toronto, Ontario, Canada, situated on the grounds that surround Queen's Park. It was founded by royal charter in 1827 as King's College, the first institution of higher learning in Upper Canada...
for the "Cancer Cell Map". The following cancer signaling pathways are hosted by Netpath:
- Epidermal growth factor receptor Pathway
- Transforming growth factor beta receptor pathway
- Tumor necrosis factor alpha pathway
- Alpha6 Beta4 Integrin pathway
- Inhibitor of DNA binding pathway
- Hedgehog pathway
- Notch pathway
- Wnt pathway
- Androgen receptor pathway
- Kit receptor pathway
Current statistics
| Curated pathways | 20 |
| Molecules involved | 1,682 |
| Physical interactions | 1,800 |
| Genes transcriptionally regulated | 6,582 |
| Transport | 201 |
| Enzyme catalysis | 1,218 |
| PubMed citations | 11,739 |
Community participation programme
The community participation programme is aimed at training the students in various universities from India on curation of pathway reactions. This is a joint programme led by the Institute of Bioinformatics, Bangalore, India with active participation from Dr. Akhilesh Pandey's laboratory at the Johns Hopkins UniversityJohns Hopkins University
The Johns Hopkins University, commonly referred to as Johns Hopkins, JHU, or simply Hopkins, is a private research university based in Baltimore, Maryland, United States...
(USA) and Gary Bader's lab at the University of Toronto
University of Toronto
The University of Toronto is a public research university in Toronto, Ontario, Canada, situated on the grounds that surround Queen's Park. It was founded by royal charter in 1827 as King's College, the first institution of higher learning in Upper Canada...
, Canada. Currently, students from 3 major Indian Universities namely Pondicherry University
Pondicherry University
Pondicherry University is a Central University in Pondicherry, India. Founded in 1985 by the Government of India,has emerged as India's fastest growing Central University and it is an affiliating University with a jurisdiction spread over the Union Territories of Pondicherry, Lakshadweep and...
, University of Pune
University of Pune
The University of Pune , is a university located in northwestern Pune, India. It was founded in 1949. Spread over a campus, the university is home to 46 academic departments...
and University of Mysore
University of Mysore
The University of Mysore , is a public university in India. The University founded during the reign of Krishnaraja Wodeyar IV, the Maharaja of Mysore, and was conceptualized on the basis of a report on educational progress in the United States and Australia, submitted by Messrs Thomas Denham and...
are participants of this community effort.