NOVELTIES
The International Cancer Genome Consortium (ICGC) Data Portal allows researchers to access mutation and expression data for specific genes, or to scroll through data sets collected so far on 24 types of cancers by project teams in 9 countries. It represents a good starting point to check for known mutations and other aberrations in a gene of interest. Registration not required.
Click here for more informationsPublished on 2012-04-12 09:03:50
The Genomics of Drug Sensitivity in Cancer project from Weelcome Trust is an academic research program to identify molecular features of cancers that predict response to anti-cancer drugs. Participants are performing a large-scale drug screen incorporating detailed genomic and gene expression analyses to systematically identify drug response biomarkers. Registration not required.
Click here for more informationsPublished on 2012-04-12 08:56:29
It's a simple Excel spreadsheet from Jon Wittwer of Vertex42 for constructin box-plots by inputing single subject values. In addition the spreadsheet includes examples for generating a random number from a Normal distribution, for calculating cumulative probabilities and for shading a portion of the distribution. Registration not required.
Click here for more informationsPublished on 2012-04-10 10:23:54
It's a simple and well constructed Excel spreadsheet from Jon Wittwer of Vertex42 for graphing a Normal distribution curve by inputing either a mean & SD or single subject values. In addition the spreadsheet includes examples for generating a random number from a Normal distribution, for calculating cumulative probabilities and for shading a portion of the distribution. Registration not required.
Click here for more informationsPublished on 2012-04-10 10:14:10
The Broad-Novartis Cancer Cell Line Encyclopedia (CCLE) is an ongoing project from collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access analysis and visualization of DNA copy number, mRNA expression and mutation data for about 1000 cell lines. Registration required.
Click here for more informationsPublished on 2012-04-09 03:25:40
The server from MSKCC predicts the functional impact (high, medium, low, or neutral) of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. MutationAssessor looks at conservation across all the homologs of a protein and also it takes into account the conservation within just the closest homologs, which is called “specificity.” This gives the tool an advantage in predicting mutations that have a functional impact, particularly those that lead to a change in function rather than a loss or gain of function Registration not required.
Click here for more informationsPublished on 2012-03-19 11:28:46
The Common Fund's Human Microbiome Project (HMP) aims to characterize the microbial communities found at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract, and to analyze the role of these microbes in human health and disease. HMP includes the following initiatives Registration not required.
Click here for more informationsPublished on 2012-03-16 05:12:06
TargetScan (Whitehead Institute) predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA Registration not required.
Click here for more informationsPublished on 2012-03-09 12:39:31
The Vertebrate Genome Annotation (VEGA) genome browser is a central repository for high quality manual annotation of vertebrate finished genome sequence. The majority of the annotation is from the HAVANA group at the Welcome Trust Sanger Institute. Registration not required.
Click here for more informationsPublished on 2012-03-02 12:12:28
LRG sequence format has been designed for the specific purpose of gene variant reporting. LRGs have fixed sequences that are independent of the genome so that they provide a stable framework for reporting variants. The data base provides a single-file record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants.
Click here for more informationsPublished on 2012-03-02 11:46:13
The HUGO Gene Nomenclature Committee (HGNC) has assigned unique gene symbols and names to over 33,000 human loci, of which around 19,000 are protein coding. http://genenames.org is a curated online repository of HGNC-approved gene nomenclature and associated resources including links to genomic, proteomic and phenotypic information, as well as dedicated gene family pages. Registration not required.
Click here for more informationsPublished on 2012-03-02 11:13:08
The Participant Portal is the single-entry point for interactions with the research and innovation programmes of the European Commission. It offers you the possibility to use a great variety of services and tools that facilitate the monitoring and the management of your proposals and projects throughout their lifecycle. Registration required.
Click here for more informationsPublished on 2012-03-02 10:12:08
ESF is a strong international network of 75 research funding, performing organisations and academics. ESF offers a number of opportunities, scientific and non-scientific, and provides career opportunities that could progress in management and administrative science activities. Registration required.
Click here for more informationsPublished on 2012-03-02 10:06:18
The UCSC Genome Browser is an on-line genome browser hosted by the University of California, Santa Cruz (UCSC).[2] [3] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. Registration not required.
Click here for more informationsPublished on 2012-03-02 05:29:50
BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. Registration not required.
Click here for more informationsPublished on 2012-02-29 12:12:49
The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. Registration required.
Click here for more informationsPublished on 2012-02-29 12:01:55
PMP gives access to various models computed by comparative modeling methods provided by different partner sites, and provides access to various interactive services for model building, and quality assessment.Protein Model Portal is a component of the Nature PSI Structural Biology Knowledgebase Registration not required.
Click here for more informationsPublished on 2012-02-27 10:47:19
ExPASy is the Swiss Institute of Bioinformatics (SIB)Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. (see Categories in the left menu). On this portal you find resources from many different SIB groups as well as external institutions. Registration not required.
Click here for more informationsPublished on 2012-02-27 09:23:18
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Category: Gene information search, Gene expression
WashU Human Epigenome Browser allows: Epigenome
The browser currently hosts Human (and other species) Epigenome Atlas data produced by the Roadmap Epigenomics project,but lets users diverge from the strict genome-centric view of the UCSC browser to, for instance, view all genes (or promoters, or 3’ UTRs) in a given pathway side by side. “You can do lots of Google Maps-style operations, and you can look at your data in the context of their metadata.
Click here for more informationsPublished on 2012-02-27 09:21:04
Engine for Protein Similarity Search. SSearch is optimal for short peptides, GGsearch is optimal to find sequences similar (>80%) in length to the guery sequence, GLsearch is fine to match a short sequence or domain to the full protein. Registration not required.
Click here for more informationsPublished on 2012-02-27 09:10:36
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