Elise Feingold: Okay.
Thank you, Eric, for that really thorough introduction.
And I want to also welcome everybody here today and thank you for braving the heat and
for participating online as well.
So I want to give a little bit more of a background to the modENCODE Project, and hopefully that
will be a good lead-in to what we're going to hear about for the rest of the symposium.
So, as Eric was saying, way back in 2002 when we were anticipating the completion of the
human genome sequence we started to ask really in earnest how could we read the human genome
sequence.
I like to say there is no instruction manual.
We really don't know the language rules for the human genome.
And we know that evolutionary conservation can help to identify functionally important
regions.
About 5 percent of the genome is conserved; about 1.5 percent is protein coding.
We were moderately good at finding these protein-coding regions, but the fine structures were difficult
to predict just from the sequence alone.
We knew that regulatory regions can be very far away from genes, and so we felt we needed
an unbiased experimental investigation to really try to grapple with this challenge.
And so we did start this project called ENCODE, or Encyclopedia of DNA elements.
And the goal of this project is to compile a comprehensive encyclopedia of all the sequence
features in the human genome and in the genomes of selected model organisms.
As Eric pointed out, we felt that the use of these model organisms is very important
in being able to understand biology and understand the human genome sequence.
And the approach we took in the beginning of this project was to apply the lessons that
we learned from the success of the Human Genome Project.
We started with a well-defined pilot project, and we developed and tested high-throughput
technologies.
So, as Eric alluded to, there are several components of ENCODE.
We started, back in 2003, with a pilot project focused on 1 percent of the human genome sequence,
just to even see how we could approach this problem, how we would apply high-throughput
technologies to finding all the functional elements.
And based on the success of that pilot project, we then scaled up to the whole human genome
sequence in 2007, and then, at the same time, that's when we initiated the modENCODE project
to find all the functional elements in C.elegans and Drosophila melagonaster genomes.
In 2009 ,with help from the economic stimulus ARRA funding, we initiated a smaller effort
in mouse ENCODE, where we did a limited study, really trying to find functional elements
in the mouse genome as a way that we can help understand the human genome sequence.
And throughout this whole effort we have been working on technology development.
We really needed new technologies, new high-throughput technologies, that could be applied to really
tackle this problem.
We've had a series of initiatives in that area.
Most recently, we funded a group of proposals this past year, and interestingly, a number
of the technologies that were developed early on were then implemented in the production
activities.
And we're looking forward to the next phase of ENCODE starting this fall, and stay tuned
for information about that.
But those will include additional data production where there will be a collapse of these projects
into one large umbrella of human and bio-organism genomes, as well as the special data analysis
projects.
We're really looking at new ways that you can use the ENCODE data and the modENCODE
data to understand genomes.
So, as Eric also mentioned in his slide of people standing on top of each other, these
are really highly interactive research consortia.
We have monthly teleconference calls, actually, a lot more frequently than that.
We have a number of working groups who address specific problems and issues such as data
management, resources, and data release.
Each of the projects have a data analysis working group.
We have lots of annual meetings of the whole consortium as well as the analysis working
groups.
There are a lot of inter-consortia collaborations that you'll hear about, and also a number
of consortia publications.
We view the ENCODE projects as community resources, and so we really want to get all this information
out to the researches to use as best as they can, especially for the understanding of the
regulation of gene expression as well as the genetic basis of disease, especially from
the human data.
One of the hallmarks is rapid pre-publication data release.
And we also want to get the information out and how to use it through consortia publications.
The analysis of the data has required the development of common data reporting formats,
data standards, and analytical tools, and you're going to hear a little bit more about
those later.
We are very interested, as we said, in getting this data out to the community and so we have
a number of portals that you can use.
The first to gain access to the human data is through this portal at encodeproject.org,
through the UCSC group.
You can look at the data from the UCSC browser.
This is human analysis I should say, as well as Ensembl.
All the data is being pushed out to NCBI, and you'll hear today more about the modENCODE
portal, modENCODE.org and data is also going out to FlyBase and WormBase.
So we're trying to make this data as accessible to the community as possible.
The ENCODE pilot project, which I mentioned started in 2003 went to 2007, had published
a large number of papers back in 2007, a large paper in Nature as well as a number of companion
papers, including this one, a whole issue in Genome Research devoted to the ENCODE project,
and the pilot project.
And the ENCODE project -- now this is all getting focused in human -- is planning to
have a set of a large set of publications coming out early this fall, so give you a
heads up to be on the lookout for that.
ModENCODE group has done a number of publications as well.
The group published what we call a "marker" paper back in 2009, and this was to inform
the community about the plans for the modENCODE consortium, what types of data there were,
how to access the data, and really what the community can anticipate.
And you're going to hear a lot more about the data but I'll just highlight some of the
features here.
This is a figure from the paper that talks about data that you are going to get on transcription
factor bonding sites, histone modifications, origins of DNA replication, as well as extensive
analysis of transcription.
This is just a little preview of what you are going to hear about later.
Back in 2010, in December of 2010, there were a number of publications that have come out
from the modENCODE group.
There were two papers in Science; one focused on the integrative analysis of C.elegans data
and the other focused on integrative analysis of the Drosophila data.
And with that as well were a number of companion papers in Nature as well as this Genome Research
issue and in several other journals.
And you are going to hear about plans for additional publications in the future.
We're also trying to get the word out for social media.
Through social media we have a Facebook page now and a twitter feed, and you can be following
this symposium at #modSymp2012.
There are also efforts for education outreach.
There are several volunteer scientists from modENCODE and the Genomics Education Partnership
who've teamed up with Science and AAAS to create an education website.
And this is being led by Sally Elgin and Bob Waterston through modENCODE, and by Laura
Zahn and Stewart Wills at Science.
And the target audience is really the general public but with a specific emphasis on high
school students.
And this is going to have six segments which will provide a rich background on works in
both fly and worm, including an introduction to chromatin structure and eukaryotic transcription,
description of modern high-throughput genomic technologies as well as bioinformatics approach
to data analysis.
And this is not live yet, but if you want to receive notification when the beta test
site goes live, please email Stewart Wills.
You don't have to memorize this because there is a handout and a poster about this website
out in the front, at the front desk.
Okay, so today we're here to celebrate, as Eric said, the completion of this phase of
the project, modENCODE, as an entity; it has been a five-year project coming to a conclusion.
We do want to showcase the modENCODE findings and to celebrate the project.
We're going to hear today about data access and data analysis.
We're going to have two panel discussions discussing the utility of modENCODE data for
basic biological processes, as well as human biology and disease.
We have speakers both from within the modENCODE consortium as well as several outside speakers
who have been using the modENCODE data.
And we're happy that this meeting was being held in conjunction with the Genetic Society
of America Model Organism to Human Biology: Cancer Genomics meeting.
We welcome those of you who attended that meeting who are here as well.
So there are a number of people to acknowledge from the modENCODE consortium.
There were 10 data production groups.
I'm not going to go into details of all their work and all the people, but you can see here
that within each major project there were a number of co-PIs of these projects.
The main data production groups were from Sue Celniker's group, Steve Henikoff, Gary
Karpen, Eric Lai, Jason Lieb, Dave MacAlpine, Fabio Piano, Mike Snyder, Bob Waterston, and
Kevin White.
In addition, Manolis Kellis' led the data analysis center and Lincoln Stein's led the
data coordination center.
In addition to all the people listed here, there've been many additional senior scientists,
post-doc students, technicians, computer scientists, statisticians, and administrators from these
groups.
So it's been quite a large effort.
Here's a picture of many of them, and NHGRI would like to thank this whole group for their
very hard work in this endeavor.
It's been a lot of fun.
I also want to acknowledge my colleagues at NHGRI.
I want to give particular mention of Peter Good, who's been my collaborator and co-leading
this ENCODE and modENCODE effort for the past 10 years, and unfortunately he couldn't be
with us today.
As well as Mike Pazin, who joined us as a program director about 18 months ago.
Special thanks also to our division director, Mike Guyer, who's been great help with guiding
us through the management of this project and who's been a very strong proponent of
the ENCODE and modENCODE projects.
And particular thanks to our program analysts, Leslie Adams and Caroline Kelly, who've been
really keeping us on track and have been an enormous help in helping to run these consortia.
And I also want to mention some former program analysts, Laura Liefer Dillon, who is here
today, Rebecca Lowdon, Jessica Melone, Judith Wexler, and Julia Zhang who've been part of
ENCODE and modENCODE from the beginning.
Okay, so, does anyone have any questions?
I think we have time for a couple; if not, we can move on to the next speaker.
Okay.
So, thank you.
[applause]
So it is my pleasure to introduce the first speaker, Gos Micklem, who is director of the
Cambridge Computational Biology Institute and its group leader in the Department of
Genetics for the University of Cambridge, talking about modENCODE tools, data and tools
for the community.
[end of transcript]