(Alliance for Cell Signalling)-developed RNAi vectors
- Antibodypedia, wiki-based web portal that allows
users to share information about antibodies
public repository for microarray data
cultures and bioproducts
Home Page at NCBI
a compendium of searchable protocols.
Structure and Function Webpage
- DNA Data Bank of Japan DDJB
- EMBL-EBI, European
a joint project between EMBL - EBI and the Sanger Institute to develop
a software system which produces and maintains automatic annotation
on metazoan genomes.
- ExPASy proteomics
server of the Swiss Institute for Bioinformatics; access to SWISS-PROT,
TrEmBL, other databases and proteomics tools
full length expression cDNAs
Genecards is a searchable, integrated database of human genes that
provides concise genomic related information on all known and predicted
- GenomeNet, Japanese
network of database and computational services
- National Center
for Biotechnology Information (NCBI), gateway to GenBank; Entrez;
Pubmed; OMIM; data-mining tools
Protocols Exchange, an open resource where the community of scientists pool their experimental know-how to help accelerate research.
Cancer Microarray Project, Stanford; a gene expression database
for the molecular pharmacology of cancers
Acids Research Methods Online
Protein Database, searchable database of information on proteins
that are localised to the nucleus of vertebrate cells.
- Oncomine, web application that integrates and unifies high-throughput cancer profiling data
Structural Genomics Knowledgebase, free
site with which to explore advances in structural biology and structural
BioKnowledge Library, access via subscription only
- UCSC Genome Browser
- EcoCyc, database
of E. coli genes and metabolism
European Saccharomyces cerevisiae Archive for Functional Analysis
database of the Drosophila genome
Database, integrated database of the human transcriptome
(Munich Information Center for Protein Sequences), includes comprehensive
yeast genome database
Genome Informatics, integrated access to data on the genetics,
genomics, and biology of the laboratory mouse, the Jackson laboratory.
pombe GeneDB, This database contains all S. pombe (fission yeast)
known and predicted protein coding genes, pseudogenes, transposons,
tRNAs, rRNAs, snRNAs, snoRNAs and other known and predicted non-coding
the biology and genome of C. elegans
A curated set of physical and genetic interactions.
a web-based application that warehouses genome-wide microarray data
mapping patterns of histone modifications and other chromatin features
for the model organism Saccharomyces cerevisiae.
Structure and Function Page. Information on chromatin biology, histones
and epigenetics -- their impact on biological processes and the researchers
that study them.
Epistatic-Mini Array Profiles (E-MAP) database.
information hyperlinked over proteins
Research Education Centre, offers research synopses on an assortment
of miRNA applications coupled with a comprehensive database of peer-reviewed
an integrated research project to study the regulation of mitosis in
human cells. The project aims to test all human genes for involvement
in mitosis by RNAi, then identify a subset which will be studied intensively
for changes in phosphorylation, subcellular localization and involvement
in protein complexes.
- Pathway Interaction
Database, an authoritative database for exploring signaling pathways.
- Yeast interactome.
A Physical Interactome Map of Saccharomyces Cerevisiae.
- CBC Prediction
Servers Protein Function Analysis
Database - Harper Lab Proteomic Database.
This site contains all of the IP-MS/MS data from the following papers:
- The Human DUB Interactome (Sowa et al., Cell, 2009)
- The Human Autophagy Pathway (Behrends et al., Nature, 2010)
- The Human ERAD Pathway (Christianson et al., Nature Cell Biology,
- ELM The Eukaryotic
Linear Motif resource for Functional Sites in Proteins
- ExPASy Proteomic
a fold recognition method using structural environment-specific substitution
tables and structure-dependent gap penalties
- Integrated Protein Domains InterProScan
predicts serine and threonine phosphorylation sites in yeast proteins.
(Nuclear Protein database) Protein domains. Search the database
for proteins containing a given motif or domain.
PARP link. A web resource on the PARP protein family and poly(ADP-ribosyl)ation.
- PBIL Sequence
Analysis (Pôle Bioinformatique Lyonnais)
- Phosida, phosphorylation
site database. Phosida allows retrieval of phosphorylation data of
any protein of interest. It lists phosphorylation sites associated
with particular projects and proteomes or, alternatively, displays
phosphorylation sites found for any protein or protein group of interest.
A database of S/T/Y phosphorylation sites
an expert curated knowledgebase of protein phosphorylation
Protein Homology/analogY Recognition Engine
Functional Analysis resource at EBI
Families database of alignments and HMMs Pfam
- Proteopedia - wiki-based interactive 3D encyclopaedia
of proteins and molecules
- PSIPRED - protein structure prediction server
cerevisiae Phosphorylome database.
- Secondary Structure Prediction Methods Wellcome
Modular Architecture Research Tool (SMART), protein domain finder
sumoylation site prediction
- Clustal Omega Clustal Omega is a new multiple alignment sequence program that uses seeded guide trees and HMM profile-profile techniques to generate alignments.
constructs multiple protein sequence alignments using information from
database searches and secondary structure prediction.
of mouse strains carrying targeted mutations in genes affecting biological
responses to DNA damage Version 7.
Ageing Genomic Resources, a web resource that brings together
databases and computational tools to help understand the biology
of DNA Damage Response and Repair Genes in the Mouse and Correlation
with Cancer Risk Modifiers. Electronically accessible database that
compares the locations of mouse genes involved in DNA repair, apoptosis,
cell cycle and signal transduction with those of known cancer risk modifier
- Methods in Enzymology, Volume 408, Page 1-582 (2006)
Repair, Part A.
- Methods in Enzymology, Volume 409, Page 1-575 (2006)
Repair, Part B.
Database of DNA repair genes.
the first comprehensive database resource for systems biology of DNA
damage and repair, Nucleic Acids Research article.
- Review article: Database and Bioinformatics Tools
for the Study of DNA Repair