©2018 Larance Laboratory.

Resources

Web-based resources

General

  • http://www.uniprot.org/ Uniprot provides a good summary of each protein’s available data. It also provides direct links to many other resource pages for that protein

  • https://www.ncbi.nlm.nih.gov/pubmed Pubmed allows for searches of abstracts and keywords across ALL journal articles. Using the Gene Name (or a synonym) to search pubmed could provide articles mentioning the protein of interest.

  • https://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (PMC) allows for searches of the full-text across FREE-ACCESS journal articles only. Using the Gene Name (or a synonym) to search PMC could provide articles mentioning the protein of interest anywhere in the manuscript including tables and figure legends. Check the tables in the paper for the Gene Name (or a synonym).

  • https://amp.pharm.mssm.edu/Harmonizome/ Search for proteins and their functional terms extracted and organized from over a hundred publicly available resources.

  • https://pharos.nih.gov/idg/index Pharos is the user interface to the Knowledge Management Center (KMC) for Illuminating the Druggable Genome.

Protein-Protein Interactions

  • http://string-db.org/ STRING is an awesome resource that brings together many types of data to provide connections between proteins. It may provide links between proteins of known function and your protein. It will look for associations in other species.

  • https://honiglab.c2b2.columbia.edu/PrePPI/ Aggregates different data sources with protein-protein interaction data/publications/predictions.

  • http://elm.eu.org/ Provides predictions for functional sites (protein binding or post-translational modification) within proteins

  • https://scansite4.mit.edu/ Provides predictions for functional sites (protein binding or post-translational modification) within proteins.

Protein Structure

Localisation (Subcellular & Tissue Distribution)

  • http://www.proteinatlas.org A large group dedicated to making multiple antibodies against every human protein. These antibodies are used to stain human tissues for that protein to measure it’s abundance/localisation/tissue specificity.

  • http://compartments.jensenlab.org/Search Aggregates different data sources with subcellular localisation data/predictions.

  • https://www.proteomicsdb.org/ Aggregates different data sources with protein abundance data across different human tissues and human cell lines.

  • https://www.peptracker.com/epd Provides a graphically rich interface to a variety of proteome-wide experiments in human cells, mouse cells/tissues and C. elegans nematodes. Various protein characteristics are measured including localisation, turnover rate etc..

  • http://prolocate.cabm.rutgers.edu/index.cgi Provides a graphically rich interface for protein localisation data in rat liver tissue.

Protein Post-translational Modifications

  • http://www.phosphosite.org Aggregates different data sources with protein post-translational modification data and publications.

  • https://scansite4.mit.edu/ Provides predictions for functional sites (protein binding or post-translational modification) within proteins.

Protein Sequence or DNA Sequence Conservation

Human and Model Animal Phenotypes

scRNA-Seq

Genomic Promoter Analysis