Tag Archives: ctd

Tip of the Week: A year in tips III (last half of 2010)

As you may know, we’ve been doing tips-of-the-week for three years now. We have completed around 150 little tidbit introductions to various resources. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

Here are the tips from the first half of the year, and below you will find the tips from the last half of 2010 (you can see past years’ tips here: 2008 I2008 II2009 I2009 II):

July

July 7: Mint for Protein Interactions, an introduction to MINT to study protein-protein interactions
July 14: Introduction to Changes to NCBI’s Protein Database, as it states :D
July 21: 1000 Genome Project Browser, 1000 Genomes project has pilot data out, this is the browser.
July 28: R Genetics at Galaxy, the Galaxy analysis and workflow tool added R genetics analysis tools.

August

August 4: YeastMine, SGD adds an InterMine capability to their database search.
August 11: Gaggle Genome Browser, a tool to allow for the visualization of genomic data, part of the “gaggle components”
August 18: Brenda, comprehensive enzyme information.
August 25: Mouse Genomic Pathology, unlike other tips, this is not a video but rather a detailed introduction to a new website.

September

September 1: Galaxy Pages, and introduction to the new community documentation and sharing capability at Galaxy.
September 8: Varitas. A Plaid Database. A resource that integrates human variation data such as SNPs and CNVs.
September 15: CircuitsDB for TF/miRNA/gene regulation networks.
September 21: Pathcase for pathway data.
September 29: Comparative Toxicogenomics Database (CTD), VennViewer. A new tool to create Venn diagrams to compare associated datasets for genes, diseases or chemicals.

October

October 6: BioExtract Server, a server that allows researcher to store data, analyze data and create workflows of data.
October 13: NCBI Epigenomics, “Beyond the Genome” NCBI’s site for information and data on epigenetics.
October 20: Comparing Microbial Databases including IMG, UCSC Microbial and Archeal browsers, CMR and others.
October 27: iTOL, interactive tree of life

November

November 3: VISTA Enhancer Browser explore possible regulatory elements with comparative genomics
November 10: Getting canonical gene info from the UCSC Browser. Need one gene version to ‘rule them all’?
November 17: ENCODE Data in the UCSC Genome Browser, an entire 35 minute tutorial on the ENCODE project.
November 24: FLink. A tool that links items in one NCBI database to another in a meaningful and weighted manner.

December

December 1: PhylomeDB. A database of gene phylogenies of many species.
December 8: BioGPS for expression data and more.
December 15: RepTar, a database of miRNA target sites.

Tip of the Week: Comparative Toxicogenomics Database (CTD), VennViewer

ResearchBlogging.org

A couple years ago (yes, we’ve been doing tips for almost 3 years now!) I did a tip on CTD, introducing the database to new users. As I stated then, CTD:

…is an excellent database to find information on chemical-gene-disease interactions. It is a manually curated database of chemical-gene interactions, chemical-disease and gene-disease associations.

Well, the developers of CTD have been busy. CTD has had a few interface changes that will make it a bit simpler to navigate. The tip linked above still stands as a pretty good introduction to what CTD is and does, but they’ve also added a few very nice features for comparisons and more. You can read a lot more about it in their recent NAR database issue article. Reading that article, I found that there are a lots of new tools and features. Can’t do them all :), so in today’s tip I present you with a very brief re-introduction to CTD and an introduction to one of the several new features at CTD, VennViewer. VennViewer creates a Venn Diagram “to compare associated data sets for up to three chemicals, diseases or genes.” A useful way to compare interactions.

Read the paper and explore the database to find more!

Davis AP, King BL, Mockus S, Murphy CG, Saraceni-Richards C, Rosenstein M, Wiegers T, & Mattingly CJ (2010). The Comparative Toxicogenomics Database: update 2011. Nucleic acids research PMID: 20864448

Guest Post: New features at CTD – Allan Peter Davis

This next post in our continuing semi-regular Guest Post series is from Allen Peter Davis, of Comparative Toxicogenomics Database (CTD) at Mount Desert Island Biological Laboratory (MDIBL). If you are a provider of a free, publicly available genomics tool, database or resource and would like to convey something to users on our guest post feature, please feel free to contact us at wlathe AT openhelix DOT com.

The Comparative Toxicogenomics Database (CTD) is a free, public resource that promotes understanding about the effects of environmental chemicals on human health.  Since Trey’s original Tip of the Week about CTD, we’ve added many new features we’d like to highlight.

* The redesigned CTD homepage makes navigation easier and more intuitive.  Check out the keyword quick search box on every page, and try the “All” setting to see the scope of information available at CTD.

* A new Data Status page uses tag clouds to display the updated content for that month.

* We are particularly pleased to announce new statistical analyses of CTD data.  Chemical pages now feature enriched Gene Ontology (GO) terms, garnered from the genes that interact with a chemical.  In this release, CTD connects over 5,000 enriched GO terms to more than 4,500 chemicals.  As well, now our inferred chemical-disease relationships are also statistically scored and ranked.  Both new features will help users explore and generate testable hypotheses about the biological effects of chemicals.

* GeneComps and ChemComps discover genes or chemicals with a similar toxicogenomic profile to your molecule of interest.  Learn more about this feature in our recent publication.

* Reactome data are now also included with KEGG, for a more comprehensive view of pathways affected by chemicals.

VennViewer and MyGeneVenn are new tools that compare datasets for chemicals, diseases, or genes (including your own gene list) using Venn diagrams to discover shared and unique information.  These two visualization tools are a nice accompaniment to our original Batch Query tool for meta-analysis.

* The FAQ section under the “Help” menu provides examples of how to maximize your experience with CTD.

* Download our Resource Guide (pdf link) to keep as a handy reference card for CTD.

From the homepage, you can also subscribe to our monthly email newsletter to keep current with CTD’s growing content and features.  You can always contact us to request curation of your favorite chemical or paper.  And with our new “Author Alert” email program, we’ll even contact you to let you know when we’ve curated data from one of your publications in CTD.

We strive to be the best possible resource of chemical-gene-disease networks for the biological community, so feedback and input from users are of great importance to us.

- Allan Peter Davis

Tip of the Week: Discovering Chemicals-Gene-Diseases Interactions w/ CTD (or Google)

ctdThe Comparative Toxicogenomics Database (or CTD) is an excellent database to find information on chemical-gene-disease interactions. It is a manually curated database of chemical-gene interactions, chemical-disease and gene-disease associations. At your fingertips you can find information about chemicals, interacting gnees, inferred diseases, pathways, references and news. It’s worth a look. And you can use Google to quickly search the database. Check out this week’s tip to find out more about the database and using Google to search it quickly.