PhosphoSIGNOR Website Tutorial

Overview

PhosphoSIGNOR is a specialized resource within the SIGNOR platform, focusing on phosphorylation-mediated signaling events. It provides curated information on phosphorylation sites, including kinases, phosphatases, substrates, and their functional consequences.

Navigating the Homepage

• Search by Protein – Look up curated data for kinases, phosphatases, or substrates.
• Search by Modified Residue – Search based on specific phosphorylated amino acid residues or sequences.
• Advanced Search(beta) – Search paths that link phenotypes to specific phosphorylation/dephosphorylation sites.
• Multi-protein Search – Search a list of proteins to generate their phospho-interaction networks.

How to Use PhosphoSIGNOR

1. Search by Protein

1. Select the protein type: Kinase, Phosphatase, or Substrate.
2. Enter the protein gene name (autocomplete function can assist with the selection within curated biological entities) or UniProt identifier.
3. Click Submit to view associated phosphorylation/dephosphorylation data.

2. Search by Modified Residue

• Residue Search: type protein ID or gene name, select specific curated residue from the dropdown menu.
• Sequence Search:
• Search by alignment: type protein sequence and search within curated data by alignment with sequences annotated in the SIGNOR dataset.
• Quick search: type protein ID or gene name, select specific sequence from the dropdown menu.
• Advanced Search: type protein gene name or UniProt ID, select specific curated residue. Click on Find Path to Phenotype to access results.

3. Multi-protein Search

Type a list of proteins to generate a network among them.

• select Connect to view a network of only interactions the searched proteins have with each other.
• select All to view a network of all the interactions the searched proteins are in.
• select Include Bridge Proteins to view a network of interactions the searched proteins have with each other, including bridge proteins (first neighbors).

Additional Features

• Statistics – Summary of data entries and curated events.
• APIs – Programmatic access to integrate with your tools.
• Downloads – Download datasets in bulk for offline use.
• About – Learn more about the project and team.

Tips for Effective Use

• Use precise protein identifiers (e.g., UniProt IDs) for better results.
• Explore the API and Download section for large-scale or automated analysis.