Links

Bioinformatics & Gene Expression

ArrayExpress at the EBI ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with MGED recommendations.The ArrayExpress Data Warehouse stores gene-indexed expression profiles from a curated subset of experiments in the repository.
Bioinformatics Links Directory The Bioinformatics Links Directory features curated links to molecular resources, tools and databases.
CIBEX Center for Information Biology gene EXpression database.
DAVID Database for Annotation, Visualization and Integrated Discovery.
GEO (NCBI) Gene Expression Omnibus: a gene expression/molecular abundance repository supporting MIAME compliant data submissions, and a curated, online resource for gene expression data browsing, query and retrieval.
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.
Human Protein Atlas The human protein atlas displays expression and localization of proteins in a large variety of normal human tissues and cancer cells.
Onto-Tools Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments.
PathVisio PathVisio is a pathway visualization and editing program using pathways in the GPML format. It is meant to be flexible enough to display many different types of data, such as microarray data and proteomics data, on familiar biological pathways. The available GPML pathways are converted directly from GenMAPP pathways, and should appear exactly the same.
PubGene PubGene is a text mining tools which helps you retrieve information on genes and proteins.
Public Expression Profiling Resource (PEPR) PEPR is an experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform.
PubMatrix PubMatrix is a simple way to rapidly and systematically compare any list of terms against any other list of terms in PubMed. It reports back the frequency of co-occurrence between all pairwise comparisons between the two lists as a matrix table.
RefExA Reference database for gene Expression Analysis
SISTA SISTA’s major research objective is to contribute to the development of improved digital (control and signal processing) systems, that incorporate advanced mathematical modeling techniques as a crucial new ingredient.To achieve this goal, a variety of research activities are set up, ranging from fundamental/theoretical work (signal theory, linear and nonlinear systems – including complex systems and neural networks – theory, circuit theory and control theory), to applications driven algorithm design and implementation.
BioGPS A web-application for publishing experimental gene functionalization datasets integrated with a flexibly searchable gene-centric database of public and proprietary annotations.
TIGR The Institute for Genomic Research (TIGR) is a not-for-profit center dedicated to deciphering and analyzing genomes – the complexmolecular chains that constitute each organism’s unique genetic heritage.
TOUCAN TOUCAN is a workbench for regulatory sequence analysis on metazoan genomes : comparative genomics, detection of significant transcription factor binding sites, and detection of cis-regulatory modules (combinations of binding sites) in sets of coexpressed/coregulated genes.
TXTgate TXTGate is a literature index database and is part of an experimental platform to evaluate (combinations of) information extraction and indexing from a variety of biological annotation databases. It is designed towards the summarization and analysis of groups of genes based on text.

 

Gene Ontology & Annotation

AmiGO AmiGO is the official tool for searching and browsing the Gene Ontology database, which consists of a controlled vocabulary of terms covering biological concepts, and a large number of genes or gene products whose attributes have been annotated using GO terms.
Babelomics Babelomics is a complete suite of web tools for functional analysis of genome-scale experiments.Babelomics includes tools for functional annotation of pre-selected sets of genes, such as FatiGO+, Tissue Mining Tool and MARMITE. It also includes the FatiScan tool and an improved GSEA module to find blocks of functionally related genes.
Gene Ontology Consortium The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
GeneAnnot GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 andHG-U133 Plus2.0.
GeneCards GeneCards® is an integrated database of human genes that includes automatically-mined genomic, proteomic and transcriptomic information, as well as orthologies, disease relationships, SNPs, gene expression, gene function, and service links for ordering assays and antibodies.
GeneLynx GeneLynx is a portal to a collection of hyperlinks for each gene within three different genomes (human, rat, and mouse). It is implemented as an easily extensible relational database with a straightforward user interface.
GeneTools GENETOOLS is a collection of web-based tools on top of a database that brings together information from a broad range of resources, and provides this in a manner particularly useful for genome-wide analyses.
iHOP A network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function.iHOP provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research.
IMAGE The I.M.A.G.E. Consortium has arrayed cDNA clones for various EST projects. A majority of the clones arrayed by I.M.A.G.E. are available royalty-free through our distributors (see the FAQ for more information), and all sequences obtained are submitted immediately to dbEST. The I.M.A.G.E. team at Lawrence Livermore National Laboratory is supported by the U.S. Department of Energy (Office of Biological and Environmental Research) and the National Institutes of Health.
KEGG KEGG: Kyoto Encyclopedia of Genes and Genomes
MGI Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
SOURCE SOURCE is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports.
UniGene Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.

 

Literature

Entrez-Pubmed
Google Scholar (Beta) Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: peer-reviewed papers, theses, books, abstracts and articles, from academic publishers, professional societies, preprint repositories, universities and other scholarly organizations. Google Scholar helps you identify the most relevant research across the world of scholarly research.
Journal Citation Reports
Journal Abbreviation Index

 

Statistics & Data Analysis

Bioconductor Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
Bioconfuctor Mailing List Archives
BRB-Tools BRB ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data. It was developed by professional statisticians experienced in the analysis of microarray data and involved in the development of improved methods for the design and analysis of microarray based experiments. The array tools package utilizes an Excel front end.
caGEDA A web application for the integrated analysis of global gene expression patterns in cancer.
Gene Set Enrichment Analysis Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).
GEPAS The Gene Expression Pattern Analysis Suite is an integrated web-based pipeline for the analysis of gene expression patterns. GEPAS includes tools for normalization, clustering, differential gene expression, predictors, array CGH and functional annotation.
GeneMaths XT GeneMaths XT is a complete and professional software package for microarray analysis. Its advanced concept of layers and subsets makes it is possible to work with different layers for different data outputs, for example Cy3 and Cy5, standard deviations, error values, etc., as well as different subsets of genes and/or arrays.
R-project R is a free software environment for statistical computing and graphics.
Statistics in Dutch Electronic Statistics Textbook in Dutch
StatSoft Electronic Statistics Textbook