Ingenuity Pathways Analysis
The Ingenuity Pathways Knowledge Base (IPKB) is the world’s largest structured database
of biological networks created from millions of individually modeled relationships between
proteins, genes, complexes, cells, tissues, drugs and diseases. This product enables
researchers to systematically analyze their experimental data in the context of biological pathways.
Biocarta pathways
Observe how genes interact in dynamic graphical models. Our online maps depict molecular
relationships from areas of active research. In an "open source" approach, this community-fed
forum constantly integrates emerging proteomic information from the scientific community.
It also catalogs and summarizes important resources providing information for over 120,000 genes
from multiple species. Find both classical pathways as well as current suggestions for new pathways.
Kyoto Encyclopedia of Genes and Genomes
KEGG is an effort to computerize current knowledge of molecular and cellular biology
in terms of the information pathways that consist of interacting molecules or genes
and to provide links from the gene catalogs produced by genome sequencing projects.
GenMapp
GenMAPP is a free computer application designed to visualize gene expression and other
genomic data on maps representing biological pathways and groupings of genes.
Integrated with GenMAPP are programs to perform a global analysis of gene expression
or genomic data in the context of hundreds of pathway MAPPs and thousands of
Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder),
and export archives of MAPPs and expression/genomic data to the web.
Identify biological interactions among genes of interest
Digest and summarize current published literature
Overlay quantitative data on biological interaction networks
Explore manually curated disease and signaling pathways
Genes and transcripts
CancerGene
The database provides a catalog of cellular genes involved in different
cancers, including genes associated with the hereditary
predisposition to cancer, viral oncogenes, and viral cancer-related genes. Note:
2 clic-search to access
the "CancerGene Card"; first clic gives a table listing all CancerGene Cards retrieved,
second clic on the one you wish to see.
Alternatively, you can type in Google: "cancergene" + "GeneID" and go directly to
the CancerGene Card
GeneCards
A database of human genes, their products and their involvement in diseases.
It offers concise information about the functions of all human genes
that have an approved symbol, as well as selected others
Gene
Gene provides a unified query environment for genes defined by sequence and/or
in NCBI's Map Viewer. You can query on names, symbols, accessions, publications,
GO terms, chromosome numbers, E.C. numbers, and many other attributes associated
with genes and the products they encode. Gene is an Entrez database.
LocusLink
Links to a lot of data mining URLs.
LocusLink provides a single query interface to curated sequence
and descriptive information about genetic loci. It presents
information on official nomenclature, aliases, sequence
accessions, phenotypes, EC numbers, MIM numbers, UniGene
clusters, homology, map locations, and related web sites.
RefSeq
RefSeq provides reference
sequence standards for the naturally occurring molecules of the central dogma, from
chromosomes to mRNAs to proteins. This identifies the contig (NT_ accessions), mRNA (XM_),
non-coding transcript (XR_), and protein (XP_) RefSeq records
provided by the NCBI Genome Annotation process. These
records are provided via automated processing.
Unigene
Each UniGene cluster contains
sequences and ESTs that represent a unique gene, as well as related
information such as the tissue types in which the gene has
been expressed and map location.
Homologene
HomoloGene is resource of curated and calculated homologs
for genes as represented by UniGene, LocusLink, and more
recently, by genomic sequences, and assembled contigs
using whole genome shotgun (WGS) reads.
GO
organizes proteins in 3 principles: molecular function, biological process and cellular component.
Onto-Express
software that rapidly correlates identified genes with
their functional and biological characteristics. You
submit a set of genes to Onto-Express, identified by
accession number or cluster ID. Then, within a
proprietary database that includes relevant information
from public sources such as UniGene, GenBank and
Ensembl, Onto-Express performs data mining to
assemble a clear overview of the genes' functions and
relationships.
Hyperlinks to general microarray gene expression tools and URLs
BRB-ArrayTools (Richard Simon & Amy Peng)
BRB ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data. .The array tools package utilizes an Excel front end.
mAdb System Home page
manage, access and analyze cDNA µArray data
generated by the NCI/CCR µArray Center.
Functional genomics List of microarray analysis softwares with hyperlinks to get them or their documentation
NETAFFX Analysis Center
correlate Affymetrix GeneChip® array results with array design and annotation information.
Cancer
Oncomine
Curated publicly available cancer microarray studies and provide data mining tools to efficiently
query genes and datasets of interest as well as meta-analyze groups of studies.
Links to various bioinformatics resources have been implemented including Unigene, Swissprot,
Biocarta, HPRD, and KEGG, among others.
CGAP
The Cancer Genome Anatomy Project aims to decipher the molecular anatomy
of cancer cells. CGAP develops profiles of cancer cells by comparing gene
expression in normal, precancerous, and malignant cells from a wide variety of tissues.
PEDB
The Prostate Expression Database started as an
effort to construct a molecular fingerprint of the normal,
preneoplastic, and neoplastic human prostate.
NCI Director's Challenge
The NCI Director's Challenge: Toward a Molecular Classification of Cancer, challenges
the scientific community to harness the power of comprehensive molecular analysis technologies
to redefine tumor classification, moving from morphological to molecular classification.
Santa Cruz
This site contains working drafts for the human genome and the mouse genome.
Ensembl
Ensembl presents up-to-date sequence data and the best possible automatic annotation
for eukaryotic genomes. Available now are human, mouse and Drosophila.
Map Viewer
The NCBI Map Viewer presents a graphical view of several types of genome maps for the mouse.
MGD
includes data on gene characterization, nomenclature, mapping, gene homologies
among mammals, sequence links, phenotypes, allelic variants and mutants,
and strain data.
GXD
integrates different types of gene expression information from the mouse and
provides a searchable index of published experiments on endogenous gene expression
during development.(
MGS
The goal of the MGS project is to integrate emerging mouse genomic sequence data
with the genetic and biological data available in MGD and GXD. MGS supports
the MouseBLAST server as a sequence-level entry point into the MGI Database.
MTB
integrates data on the frequency, incidence, genetics, and pathology
of neoplastic disorders, emphasizing data on tumors that develop characteristically
in different genetically defined strains of mice.
Promoters
TRANSFAC® System
comprising 5 independent databases helps researchers to understand the transcriptional control
of genes, and the signaling pathways through which control occurs.
Tri's Comment: TRANSFAC is the commercial version of TFSEARCH (with more features but not free)
TRANSPATH® describes
the signal transduction from the ligand at the surface of a cell up to the transcription factor.
Cytomer® is a database on cells,
organs, tissues and developmental stages and it is needed
to link all cellular processes to a specific expression profile.
TFSEARCH
The TFSEARCH searches highly correlated sequence fragments
against TFMATRIX transcription factor binding site profile database
in the 'TRANSFAC' databases by GBF-Braunschweig.
MatInspector
MatInspector professional is a tool that utilizes a library of matrix descriptions for transcription
factor binding sites to locate matches in sequences of unlimited length.
Tri's comment: free for academic scientists