Tag Archives: epigenomics

Video Tips of the Week: Annual Review IV, 2nd half

As you may know, we’ve been doing these video tips-of-the-week for FOUR years now. We have completed around 200 little tidbit introductions to various resources from last year, 2011 (yep, it’s 2012 now). 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.

You can see past years’ tips here: 2008 I2008 II2009 I2009 II2010 I2010 II. The summary of the first half of 2011 is available from last week.

July 2011

July 6: Prioritizing genes using the Gene Prioritization Portal

July 13: PolySearch, searching many databases at once

July 20: Human Epigenomics Visualization Hub

July 27: The new SIB Bioinformatics Resource Portal

 

August 2011

August 3: SNPexp, correlation between SNPs and gene expression 

August 10: CompaGB for comparing genome browser software

August 17: CoGe, comparing genomes revisited

August 24: Domain Draw for quick motif diagrams

August 31: From UniProt to the PSI SBKB and back again

 

September 2011

September 7: Plant comparative genomics using Plaza

September 14: phiGENOME for bacteriophage genome exploration

September 21: Getting flanking sequences of genomic locations

September 28: Introduction to R statistical software 

 

October 2011

October 5: VnD resource for genetic variation and drug information

October 12: Track Hubs in UCSC Genome Browser

October 19: Mitochondrial Transcriptome GBrowser 

October 26: Variation data from Ensembl

 

November 2011

November 2: MizBee Synteny Browser

November 9: The new database of genomic variants: DGV2

November 16: MapMi, automated mapping of microRNA loci

November 23: BioMart’s new central portal

November 30: Phosphida, a post-translational modification database

December 2011

December 7: VarSifter, for identifying key sequence variations

December 14: Big changes to NCBI’s genome resources

December 21: eggNOG for the Holidays (or to explore orthologous genes)

December 28: Video Tips of the Week: Annual Review IV (first half of 2011)

Tip of the Week: DAnCER for disease-annotated epigenetics data

Epigenetics and epigenomics are becoming more exciting areas of investigation, and we are seeing more requests for database resources to support them, and for the sources of data from these types of experiments. If you aren’t aware of these investigations at this point, check out their entries in the Talking Glossary of Genetic Terms:

Epigenetics: Epigenetics is an emerging field of science that studies heritable changes caused by the activation and deactivation of genes without any change in the underlying DNA sequence of the organism. The word epigenetics is of Greek origin and literally means over and above (epi) the genome.

Epigenome: The term epigenome is derived from the Greek word epi which literally means “above” the genome. The epigenome consists of chemical compounds that modify, or mark, the genome in a way that tells it what to do, where to do it, and when to do it. Different cells have different epigenetic marks. These epigenetic marks, which are not part of the DNA itself, can be passed on from cell to cell as cells divide, and from one generation to the next.

And for the talking part–you can hear Dr. Laura Elnitski talk about these in more detail–have a listen at each entry. And just today an article providing an epigenetics primer appeared in my inbox: Epigenetics: A Primer.

These intriguing–and sometimes puzzling–chromatin modification (CM) signals and leads that are being unveiled in many labs and projects now are becoming more widely available in different databases. For this week’s tip of the week I’ll introduce DAnCER: Disease-Annotated Chromatin Epigenetics Resource, one of the tools that is organizing this type of data and enabling additional explorations. You can find DAnCER here: http://wodaklab.org/dancer/

In the associated publication, the DAnCER team describes other useful resources that provide epigenetics data. These include ChromDB, ChromatinDB (for yeast), and the Human Histone Modification Database (HHMD), among others. I’m also aware of other sources. A few months back I introduced the NCBI Epigenomics resource as my tip-of-the-week. (At that time I promised that when the publication became available I’d mention it–that’s now at the bottom in the references section below.) There’s also quite a bit of this data flowing in to the UCSC Genome Browser ENCODE DCC. Including–may I add–some data from the very cool Elnitski bi-directional promoter studies.  You can find similar data types via the modENCODE project as well.

So, there are lots of resources out there. Each provider has different projects, species, goals, displays, etc. But the group that developed DAnCER wanted to fill a niche they didn’t see available already: linking these epigenetic changes to possible disease association data. Here’s how they describe their work:

Our research effort therefore strives to explore CM-related genes in the context of their protein-interaction network, their partnership in multi-protein complexes and cellular pathways, as well as their gene expression profiles….

They are well-suited to linking this kind of information. You may remember our previous explorations and discussions of iRefWeb. The kind of network and interaction data that they assemble in that context can be brought to the chromatin-modification arena. The point is that you can take steps beyond the modifications you know about, to explore their neighborhood of interactions, and potentially unearth important disease relationships from that.

The data includes several species, and because of that evolutionary conservation can also be explored.

So if you find that you are interested in exploring chromatin modifications, and want to take that data further, check out DAnCER, and the other tools and projects that are providing this type of information. If you have used the iRefWeb interface, you’ll see some similarities in structure. Search options with many filters are available. Color-coded and sortable results are provided. Links to gene details within the Wodak lab tools and external links are offered. On the gene pages at DAnCER you’ll have many types of annotations, including Gene Ontology descriptions, evidence type and references, neighbors, and protein domain information as well. And besides the texty-table based stuff, you can choose to load up the interactive network/interaction graphic, just like with the iRefWeb tool.

There’s a lot of opportunity to learn things from this tool. Try it out.

Quick Links and References:

DAnCER http://wodaklab.org/dancer/

Turinsky, A., Turner, B., Borja, R., Gleeson, J., Heath, M., Pu, S., Switzer, T., Dong, D., Gong, Y., On, T., Xiong, X., Emili, A., Greenblatt, J., Parkinson, J., Zhang, Z., & Wodak, S. (2010). DAnCER: Disease-Annotated Chromatin Epigenetics Resource Nucleic Acids Research, 39 (Database) DOI: 10.1093/nar/gkq857

Fingerman, I., McDaniel, L., Zhang, X., Ratzat, W., Hassan, T., Jiang, Z., Cohen, R., & Schuler, G. (2010). NCBI Epigenomics: a new public resource for exploring epigenomic data sets Nucleic Acids Research, 39 (Database) DOI: 10.1093/nar/gkq1146

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: NCBI Epigenomics “Beyond the Genome”

We spend a lot of time talking about sequence data: where to find it, how to analyze it, etc. But increasingly we are seeing more and more data that comes from epigenomics projects. Recently a tweet from NCBI got me to look at their Epigenetics site again.  http://www.ncbi.nlm.nih.gov/epigenomics

Their definition of epigenetics is:

What is Epigenetics?

Interest in epigenetics has exploded in recent years, but the central question it aims to answer has been with us for decades: how do the many cell types of the body maintain drastically different gene expression patterns while sharing exactly the same DNA?

Epigenetics refers to a gene activity state that may be stable over long periods of time, persist through many cell divisions, or even be inherited through several generations, all without any change to the primary DNA sequence (Roloff and Nuber 2005, Ng and Gurdon 2008, Probst, et al. 2009).

This is a nice site that offers a lot of helpful background, project information about the NIH Roadmap for Epigenomics, and then of course access to the data itself.  They have separate guidance on the types of data that you will find in here: About DNA Methylation, About Histone Modification, and About Chromatin Structure. So if you are ready to go “Beyond the Genome” as their tag line indicates, you can learn about the data types and find the data too.

This tip of the week will take a look at access to the data. I’ll be taking a look at what happens when you use the Sample Browser as a starting point to see some of the data via browsing. You can do more complex and custom queries with the Advanced Query form, which looks like other query building tools at NCBI. I won’t have time to cover that, but I wanted you to know it was available.

For my example I just chose the top sample that was in the list at the time I did this tip. And it was fortuitous for a couple of reasons.  First it was exactly the kind of paper that I was talking about in my recent post (The data isn’t in the papers anymore, you know.) This paper (referenced below) has a huge volume of data. It looks at 39 types of histone modifications, and looks at them genome wide.  There’s no way to publish all that as figures in this paper.  There are summary figures, but not individual ones for that data collection. You’d have to visualize this yourself elsewhere.  The second reason it was cool was because the data perfectly validates some of the data I’ve been using to develop the ENCODE project tutorial we’ve just created with the UCSC ENCODE team.

Anyway–check out the NCBI Epigenomics resource for a great way to visualize data on this topic. Data that you will not find in the papers.

Quick links:

NCBI Epigenomics (the tip site): http://www.ncbi.nlm.nih.gov/epigenomics

Roadmap: http://www.roadmapepigenomics.org/

Epigenome Browser: http://www.epigenomebrowser.org/

ENCODE: http://encodeproject.org/

By the way: I also asked the hive mind at BioStar what tools they are using for epigenomics or epigenetics, and you can go and see that question over there. People told me about the Epigenome Atlas and EPIGRAPH. And as I was researching this tip I came across a Roadmap Epigenomics site, that offers a link to a browser. It’s a UCSC Genome Browser framework focused on this kind of data: Epigenome Browser–but that’s a different installation than the main UCSC Genome Browser that I illustrate from this tip.

Reference for data used and shown in the tip:

Wang, Z., Zang, C., Rosenfeld, J., Schones, D., Barski, A., Cuddapah, S., Cui, K., Roh, T., Peng, W., Zhang, M., & Zhao, K. (2008). Combinatorial patterns of histone acetylations and methylations in the human genome Nature Genetics, 40 (7), 897-903 DOI: 10.1038/ng.154

Currently there’s isn’t a reference for NCBI Epigenomics. I contacted the Help Desk to be sure, and they told me it’s been submitted but isn’t out yet. I’ll update this when that reference becomes available.