BIOINFORMATICS DATABASES

DISCLAIMER:

THE FOLLOWING LINKS TO DATABASES PROVIDE A STARTING POINT FOR VARIOUS BIOINFORMATICS QUERIES. IF ANY OF THE LINKS IS NOT CURRENT, USE A SEARCH ENGINE TO FIND THE CURRENT LINK. SOME OF THE DATABASE PROVIDER MAY REQUIRE REGISTRATION. COMMERCIAL USE OF ANY OF THESE DATABASES MAY ALSO REQUIRE SPECIAL LICENSE. INQUIRE THE DATABASE PROVIDER.

General:

Human genome project (HGP)http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml

Explore this site for information about the Human Genome Project (1990-2003).

HGNC http://www.gene.ucl.ac.uk/nomenclature/aboutHGNC.html -       For each known human gene HGNC approves a gene name and symbol (short-form abbreviation).  All approved symbols are stored in the HGNC database.  Each symbol is unique and is ensured that each gene is only given one approved gene symbol.  In preference each symbol maintains parallel construction in different members of a gene family and can also be used in other species, especially the mouse.

NHGRI http://www.genome.gov/ -       The Human Genome Project (HGP) was one of the great feats of exploration in history - an inward voyage of discovery rather than an outward exploration of the planet or the cosmos; an international research effort to sequence and map all of the genes - together known as the genome - of members of our species, Homo sapiens. Completed in April 2003, the HGP gave us the ability to, for the first time, to read nature's complete genetic blueprint for building a human being.

EMBL http://www.ebi.ac.uk/index.html- The European Bioinformatics Institute (EBI) is a non-profit academic organization that forms part of the European Molecular Biology Laboratory (EMBL).

The EBI is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.

DNA/Protein databases:

NCBI http://www.ncbi.nlm.nih.gov/ -       Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease. 

Eukaryotic promoter database (EPD) http://www.epd.isb-sib.ch/

The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.

The Transcript Sequence Retreiver (TRASER- see http://genome-www6.stanford.edu/cgi-bin/Traser/traser)  provides rapid retrieval of transcript and upstream (putative promoter-containing) sequences for predicted human genome mRNAs. The underlying database is built using the human genome annotation files provided by the National Center for Biotechnology Information.

TRANSFAC is the database on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles. http://www.gene-regulation.com/pub/databases.html#transfac or seehttp://www.cbrc.jp/research/db/TFSEARCH.html

TIGR http://www.tigr.org/ -       The new J. Craig Venter Institute was formed in October 2006 through the merger of several affiliated and legacy organizations--The Institute for Genomic Research (TIGR) and The Center for the Advancement of Genomics (TCAG), The J. Craig Venter Science Foundation, The Joint Technology Center, and the Institute for Biological Energy Alternatives (IBEA). Today all these organizations have become one large multidisciplinary genomic-focused organization. With more than 500 scientists and staff, more than 250, 000 square feet of laboratory space, and locations in Rockville, Maryland and La Jolla, California, the new JCVI is a world leader in genomic research. 

For protein datamining tools see Expasy http://ca.expasy.org/ -       The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE -       Proteomic tools at Expacy. See http://ca.expasy.org/tools/

UCSC genome browser http://genome.ucsc.edu/- This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE project.

Gene http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene

Entrez Gene (previously Locus Link) is a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer.

Genes to information:Genecards http://www.genecards.org/index.shtml -       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.

CGAP http://cgap.nci.nih.gov/ -       The goal of the NCI's Cancer Genome Anatomy Project is to determine the gene expression profiles of normal, precancer, and cancer cells, leading eventually to improved detection, diagnosis, and treatment for the patient. By collaborating with scientists worldwide, CGAP seeks to increase its scientific expertise and expand its databases for the benefit of all cancer researchers.Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find "in silico" answers to biological questions in a fraction of the time it once took in the laboratory.

Source http://smd-www.stanford.edu/cgi-bin/source/sourceSearch -      

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. -      

Aceview provides intron exon information along with a comprehensive summary for a gene on the genome. See http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi? -      

GeneAtlas provides an alternative view for genomic information, upstream promoter region in a highly integrated form with other relevant links. See http://www.dsi.univ-paris5.fr/genatlas/ -      

The Alternative Splicing Database (ASD) Project aims to understand the mechanism of alternative splicing on a genome-wide scale by creating a database of alternative splice events and the resultant isoform splice patterns of genes from human, and other model species.  See http://www.ebi.ac.uk/asd/. Also see http://hollywood.mit.edu/Dgene.php -      

UniGene: An Organized View of the Transcriptome.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.  See http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene

-       OMIM- online Mendalian inheritance in man database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information and references. It also contains copious links to MEDLINE and sequence records in the Entrez system, and links to additional related resources at NCBI and elsewhere. See http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

-       NCBI Map Viewer for chromosomal position of a gene in a graphical display. See http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606

-        Molecular targets http://dtp.nci.nih.gov/mtargets/mt_index.html -       Thousands of molecular targets have been measured in the NCI panel of 60 human tumor cell lines. Measurements include protein levels, RNA measurements, mutation status and enzyme activity levels. You can choose to search for a target of interest, or you may browse through a list of targets. Follow the links for a target to retrieve the 60 cell line data (either text or graphical), to run COMPARE (find Targets or Compounds whose patterns correlate with a Target of interest) and to link to various databases with information (function, sequences, disease associations) about the target.

Genatlas http://www.dsi.univ-paris5.fr/genatlas/- GENATLAS contains relevant information with respect to gene mapping and genetic diseases. The database was created in 1986 by Jean FrŽzal and is located on INSERM U781.

Microarray and Proteome databases:ArrayExpress http://www.ebi.ac.uk/arrayexpress/ -       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.

-       MIAME (Minimum Information About a Microarray Experiment) is a community standard for microarray data developed by the MGED (Microarray Gene Expression Data) Society (http://www.mged.org/miame). ArrayExpress and related tools are MIAME supportive. You can find a publication on MIAME here: Nature Genetics 29(4): 365-371. MIAME is a developing standard.

Novartis microarray http://www.gnf.org/ -       SymAtlas. This online tool is a public installation of the gene-centric database of integrated gene and genome annotation.  SymAtlas presents annotation collated from the public domain alongside gene expression data generated at GNF from humans and various rodents.  In particular, the ÒGeneAtlasÓ data set displays the expression pattern for > 20,000 transcripts across an anatomically diverse panel of tissues .  This application has been widely used as a candidate gene prioritization tool for gene expression and genetics studies.

-       SNPview. Browse or search the large-scale SNP collections GNF researchers generated for most of the commonly used in-bred laboratory strains. These SNP collections are a key tool towards the goal of in-silico mapping phenotypic and complex disease traits.

-       Druggable Genome BLAT.It provides a convenient interface to search against our expanded dataset of slightly more than 3000 unique human protein-encoding "druggable" genes.

Affymetrix http://www.affymetrix.com/index.affx

-       Comprehensive microarray services

Stanford microarray http://genome-www5.stanford.edu/

Oncomine http://www.oncomine.org/main/index.jsp

-       Oncomine combines a rapidly growing compendium of 20,000+ cancer transcriptome profiles with a sophisticated analysis engine and a powerful web application for data-mining and visualization. Oncomine facilitates rapid and reliable biomarker and therapeutic target discovery, validation and prioritization.

-        Open Proteomic database (OPD) is a public database for storing and disseminating mass spectrometry based proteomics data. The database currently contains roughly 3,000,000 spectra representing experiments from 5 different organisms. See http://bioinformatics.icmb.utexas.edu/OPD/

Other Protein Expression Data

2D Gel Databases

-       Partial List of Web 2D Electrophoretic Gel Databases

-       NCI 2DWG Image Meta-Database

-       SWISS-2DPAGE

-       Argonne National Lab Protein Mapping Group Gelbank

-       Weinstein: NCI-60 cancer cell lines

-       A Protein Expression Database for the Molecular Pharmacology of Cancer

-       http://www.proteomicsresearch.org/

-       http://www.bio-computing.org/

SNP/pharmacogenomics:

SNP Hap maphttp://www.hapmap.org/

-       The International HapMap Project is a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals. See "About the International HapMap Project" for more information.dbSNP. See http://www.ncbi.nlm.nih.gov/projects/SNP/

-       The Single Nucleotide Polymorphism database (dbSNP) is a public-domain archive for a broad collection of simple genetic polymorphisms.Pharmacogenomics http://www.pharmgkb.org/- PharmGKB curates information that establishes knowledge about the relationships among drugs, diseases and genes, including their variations and gene products. Our mission is to catalyze pharmacogenomics research.

PCR primer design:

Primer 3 http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi

Tm calculator: http://www.appliedbiosystems.com/support/techtools/calc/

-       To calculate the Tm of your primers please fillout the requested information for Primer #1 (Yellow) and Primer #2 (Grey). Upon submission you will be presented with a summary of the values you've submitted in addition to the optimized Tm calculated for Applied Biosystems products.

Clones/tissues/cDNA libraries:

ATCC, a comprehensive collection of cell, bacteria and cDNA repository. See  http://www.atcc.org/. 

MGC (Mammalian gene collection) full length clones- http://mgc.nci.nih.gov/

-       The goal of the Mammalian Gene Collection (MGC), a trans-NIH initiative, is to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes. In 2005, the project added the cow cDNAs generated by Genome Canada.

Initially, cDNA libraries provided the source of the clones. Recently, alternative methods based on gene-specific amplification have been developed to target the recovery of human and mouse genes absent from the MGC collection.

CHTN http://www-chtn.ims.nci.nih.gov/

- The Cooperative Human Tissue Network (CHTN) was initiated by the Cancer Diagnosis Program of the National Cancer Institute (NCI) in 1987 to provide increased access to human cancer tissue for basic and applied scientist from academia and industry to accelerate the advancement of discoveries in cancer diagnosis and treatment. The CHTN provides prospective investigator-defined procurement of malignant, benign, diseased and uninvolved (normal adjacent) tissues. The investigator can also choose from several methods to fix the specimen such as fresh, frozen, or chemically fixed. The CHTN also produces tissue microarrays (TMA) representing multiple tissue types to disease-specific blocks. Recently, the CHTN has approved the development within the divisions to isolate and distribute the raw nucleic acid to expand resources and to more readily serve investigatorÕs interest. Tissues are annotated with patient demographics including gender, age, and race. Additional patient information can be requested where applicable.

NIGMS Human Genetic Cell Repository

- By providing the resources for human genome research, the HUMAN GENETIC CELL REPOSITORY, sponsored by the National Institute of General Medical Sciences (NIGMS), supplies scientists with the materials for accelerating disease gene discovery. The resources available include highly-characterized, viable, and contaminant-free cell cultures and high quality, well-characterized DNA samples derived from these cultures, both subjected to rigorous quality control.  

If you are looking for additional links or alternatives see Biotool kit http://www.biosupplynet.com/biotoolkit/

-       The revised and updated BioToolKit provides access to over 1200 bioinformatics and neuroinformatics resources for the analysis and visualization of the genome, transcriptome, and proteome, and to neuroinformatics tools enabling visualization of neuroanatomic structure

.- Nucleic Acid Analysis Primer design and restriction site analysis tools. Literature gateways and sequence retrieval programs. Applications for multiple sequence alignment, the analysis of gene expression regulation, localization of transcription promoter sites, and identification of exons and alternative splice sites.

-  Genomics Resources Genomics and gene expression databases. Bioinformatics resources. Applications for resolving gene symbols and synonyms, and for the annotation of genes. Tools for comparing genomes and visualizing phylogenomic relationships.

- Protein Structural Imaging and Analysis Tools for predicting, classifying, comparing and visualizing protein structures. Proteome databases. Applications for motif identification, sequence alignment, and the analysis of protein-protein interactions. Small molecule and metabolomics resources.

-  Neuroinformatics Neuroimaging resources, including multi-scale imaging. Connectivity databases and applications for interactive display of the neuroanatomy of gene expression. Neuroinformatics databases and software.Micro RNA databases- RNAi resources-http://www.rnaiweb.com/

-       miRBase (http://microrna.sanger.ac.uk/) is the new home of microRNA data on the web, providing data previously accessible from the miRNA Registry.

• RNAi Database  (rnai.org) - Worm RNAi data including assay, resulting phenotypes, dsRNA target location.

• RNAi Phenotypes  (Wormbase) - Collection of RNAi experimental data on worms.

• SiRNA Database - The siRNA Database is the first complete database of pregenerated siRNA targets against all known genes throughout a variety of organisms. The targets have been generated using the Tuschl method. These siRNA targets have been statistically validated through comparison of experimentally tested siRNA targets.

•  siRNA design tools http://www.ambion.com/techlib/misc/siRNA_tools.html ,

• http://www.idtdna.com/Scitools/Applications/RNAi/RNAi.aspx ,

• siRNA Database - A collection of SiRNAs obtained from published data with references and sequences (some). Maintained by Michael McManus at MIT.

• The RNAi Consortium shRNA Library  (The RNAi Consortium) - Short hairpin RNA (shRNA) clones produced by the TRC, as well as protocols for handling and conducting screens with shRNA molecules. The RNAi consortium shRNA library is distributed as bacterial glycerol stocks, plasmid DNA or lentiviral particles by Sigma-Aldrich and as bacterial glycerol stocks by Open Biosystems.

• Tronolab SiRNA Database - A small collection of working SiRNAs collected from publications.