TY - JOUR
T1 - Integration of heterogeneous functional genomics data in gerontology research to find genes and pathway underlying aging across species
AU - Bubier, Jason A.
AU - Sutphin, George L.
AU - Reynolds, Timothy J.
AU - Korstanje, Ron
AU - Fuksman-Kumpa, Axis
AU - Baker, Erich J.
AU - Langston, Michael A.
AU - Chesler, Elissa J.
N1 - Funding Information:
Funded by EJC AG038070 Nathan Shock Center of Excellence on the Biology of Aging. EJC AA018776 National Institute of Drug Abuse. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank Stephen Sampson for his feedback on this manuscript. We appreciate the contributions of previous Chesler lab members in the curation of the aging literature in GeneWeaver specifically; Kathryn Toal, Courtney M. Vaughn, Laura C. Anderson. This work was supported by NIH R01 AA018776 and Nathan Shock Center of Excellence on the Biology of Aging NIH AG038070.
Publisher Copyright:
© 2019 Bubier et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2019/4
Y1 - 2019/4
N2 - Understanding the biological mechanisms behind aging, lifespan and healthspan is becoming increasingly important as the proportion of the world’s population over the age of 65 grows, along with the cost and complexity of their care. BigData oriented approaches and analysis methods enable current and future bio-gerontologists to synthesize, distill and interpret vast, heterogeneous data from functional genomics studies of aging. GeneWeaver is an analysis system for integration of data that allows investigators to store, search, and analyze immense amounts of data including user-submitted experimental data, data from primary publications, and data in other databases. Aging related genome-wide gene sets from primary publications were curated into this system in concert with data from other model-organism and aging-specific databases, and applied to several questions in genrontology using. For example, we identified Cd63 as a frequently represented gene among aging-related genome-wide results. To evaluate the role of Cd63 in aging, we performed RNAi knockdown of the C. elegans ortholog, tsp-7, demonstrating that this manipulation is capable of extending lifespan. The tools in GeneWeaver enable aging researchers to make new discoveries into the associations between the genes, normal biological processes, and diseases that affect aging, healthspan, and lifespan.
AB - Understanding the biological mechanisms behind aging, lifespan and healthspan is becoming increasingly important as the proportion of the world’s population over the age of 65 grows, along with the cost and complexity of their care. BigData oriented approaches and analysis methods enable current and future bio-gerontologists to synthesize, distill and interpret vast, heterogeneous data from functional genomics studies of aging. GeneWeaver is an analysis system for integration of data that allows investigators to store, search, and analyze immense amounts of data including user-submitted experimental data, data from primary publications, and data in other databases. Aging related genome-wide gene sets from primary publications were curated into this system in concert with data from other model-organism and aging-specific databases, and applied to several questions in genrontology using. For example, we identified Cd63 as a frequently represented gene among aging-related genome-wide results. To evaluate the role of Cd63 in aging, we performed RNAi knockdown of the C. elegans ortholog, tsp-7, demonstrating that this manipulation is capable of extending lifespan. The tools in GeneWeaver enable aging researchers to make new discoveries into the associations between the genes, normal biological processes, and diseases that affect aging, healthspan, and lifespan.
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U2 - 10.1371/journal.pone.0214523
DO - 10.1371/journal.pone.0214523
M3 - Article
C2 - 30978202
AN - SCOPUS:85064347934
SN - 1932-6203
VL - 14
JO - PloS one
JF - PloS one
IS - 4
M1 - e0214523
ER -