Next Steps for Functional Genomics Proceedings of a Workshop (2020) / Chapter Skim
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10 Future of Functional Genomics
10 Future of Functional Genomics
Pages 145-152
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From page 145... ...
The second part was a "town hall" in which everyone had the chance to address the points heard during the meeting or bring up issues that had not been discussed. Moderator Emma Farley of the University of California, San Diego, opened the first part of the session by describing its format and providing a list of issues and questions for each breakout group to address: • List 5 to 10 research and knowledge goals for the field of functional genomics.
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From page 146... ...
A second goal would be to develop tools to manipulate networks in graded ways to be able to exert minor perturbations to nodes, both for validation purposes and for prediction. A third goal is to be able to distinguish the different forms of "functional." The word "functional" has different meanings, Robinson noted.
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From page 147... ...
Finally, the group offered a number of specific goals concerning how genes work; how they are organized, both in two and three dimensions; what they do; and when and where they are expressed. Among the obstacles the group listed, Benfey said, was "the impossibility of doing a totally comprehensive analysis of anything," which arises from the fact that even reasonably simple systems have far too many possible combinations to completely analyze every one.
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From page 148... ...
Finally, more diverse models could be useful, moving beyond those such as the typical inbred mouse models. Concerning obstacles, the group pointed toward the usefulness of interoperability of technologies across organisms and the fact that proteomics technology is not yet sufficiently mature or robust.
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From page 149... ...
"We do know that about 80 percent of these, at least in yeast and some other organisms, make proteins," Wurtele said. The bottom line, she said, is that there is a dark transcriptome that includes not only many orphan protein-coding genes but also non-coding genes as well, "and all this is probably intimately involved in functional genomics." The next speaker touched on several topics including the observation that as sample sizes become increasingly large, it is inevitable that more and more genes will be found to have a connection with a particular phenotype.
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From page 150... ...
"But," he said, "if we're interested in function, natural genetic variation may not be ideally distributed in natural populations." And that is why it is important to have constructs like the Drosophila melanogaster Genetic Reference Panel and various other panels such as those involving mice, corn, and Arabidopsis "where we can bring together genetic variation and use it as a tool." Next, Emma Farley of the University of California, San Diego, made a comment about what people mean by "functional genomics." "I'm wondering if maybe I don't understand what functional genomics is," she said. "Two people have said to me that functional genomics is a set of tools and functional genomics is generating large datasets.
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From page 151... ...
"Let's start trying to make the case that one reason the science of biology is so dominant in the 21st century is that we're starting to get our heads around scales of numbers that were just completely unheard of 10, 20, 30 years ago," he said. Similarly, the group has no fear in moving from one area to the next -- from molecular biology to cell biology, to organismal biology, to considerations of diversity in model systems, all put in an evolutionary context as the need arises.
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