The FaceBase Consortium: A comprehensive resource for craniofacial researchers

Brinkley, James F.; Fisher, Shannon; Harris, Matthew P.; Holmes, Greg; Hooper, Joan E.; Jabs, Ethylin Wang; Jones, Kenneth L.; Kesselman, Carl; Klein, Ophir D.; Maas, Richard L.; Marazita, Mary L.; Selleri, Licia; Spritz, Richard A.; van Bakel, Harm; Visel, Axel; Williams, Trevor J.; Wysocka, Joanna; Chai, Yang

doi:10.1242/dev.135434

Title: The FaceBase Consortium: A comprehensive resource for craniofacial researchers

Journal Article · 14 July 2016 · Development (Cambridge)

DOI: https://doi.org/10.1242/dev.135434 · OSTI ID:1904091

Brinkley, James F. ^[1]; Fisher, Shannon ^[2]; Harris, Matthew P. ^[3]; Holmes, Greg ^[4]; Hooper, Joan E. ^[5]; Jabs, Ethylin Wang ^[4]; Jones, Kenneth L. ^[5]; Kesselman, Carl ^[6]; Klein, Ophir D. ^[7]; Maas, Richard L. ^[8]; Marazita, Mary L. ^[9]; Selleri, Licia ^[7]; Spritz, Richard A. ^[5]; van Bakel, Harm ^[4]; Visel, Axel ^[10]; Williams, Trevor J. ^[5]; Wysocka, Joanna ^[11];

^[6]

University of Washington, Seattle, WA (United States); OSTI
Boston University, MA (United States). School of Mediciene, MA (United States)
Harvard Medical School, Boston, MA (United States)
Icahn School of Medicine at Mount Sinai, New York, NY (United States)
University of Colorado, Aurora, CO (United States)
University of Southern California, Los Angeles, CA (United States)
University of California, San Francisco, CA (United States)
Brigham and Women's Hospital (Harvard Medical School), Boston, MA (United States)
University of Pittsburgh, PA (United States)
Lawrence Berkeley National Laboratory, Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); University of California, Merced, CA (United States)
Stanford University, CA (United States). School of Medicine

The FaceBase Consortium, funded by the National Institute of Dental and Craniofacial Research, National Institutes of Health, is designed to accelerate understanding of craniofacial developmental biology by generating comprehensive data resources to empower the research community, exploring high-throughput technology, fostering new scientific collaborations among researchers and human/computer interactions, facilitating hypothesis-driven research, and translating science into improved health care to benefit patients. The resources generated by the FaceBase projects include a number of dynamic imaging modalities, genome-wide association studies, software tools for analyzing human facial abnormalities, detailed phenotyping, anatomical and molecular atlases, global and specific gene expression patterns, and transcriptional profiling over the course of embryonic and postnatal development in animal models and humans. The integrated data visualization tools, faceted search infrastructure, and curation provided by the FaceBase Hub offer flexible and intuitive ways to interact with these multidisciplinary data. In parallel, the datasets also offer unique opportunities for new collaborations and training for researchers coming into the field of craniofacial studies. Here we highlight the focus of each spoke project and the integration of datasets contributed by the spokes to facilitate craniofacial research.

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Research Organization:: USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; National Institute of Dental and Craniofacial Research

Contributing Organization:: FaceBase Consortium

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1904091

Journal Information:: Development (Cambridge), Journal Name: Development (Cambridge) Journal Issue: 14 Vol. 143; ISSN 0950-1991

Publisher:: Company of BiologistsCopyright Statement

Country of Publication:: United States

Language:: English

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Toward interoperable bioscience data Sansone, Susanna-Assunta; Rocca-Serra, Philippe; Field, Dawn Nature Genetics, Vol. 44, Issue 2 https://doi.org/10.1038/ng.1054	journal	January 2012
Genome-Wide Association Studies in Dogs and Humans Identify ADAMTS20 as a Risk Variant for Cleft Lip and Palate Wolf, Zena T.; Brand, Harrison A.; Shaffer, John R. PLOS Genetics, Vol. 11, Issue 3 https://doi.org/10.1371/journal.pgen.1005059	journal	March 2015
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Closing the Gap: Genetic and Genomic Continuum from Syndromic to Nonsyndromic Craniosynostoses Heuzé, Yann; Holmes, Gregory; Peter, Inga Current Genetic Medicine Reports, Vol. 2, Issue 3 https://doi.org/10.1007/s40142-014-0042-x	journal	June 2014
Facial morphometrics of children with non-syndromic orofacial clefts in Tanzania Manyama, Mange; Larson, Jacinda R.; Liberton, Denise K. BMC Oral Health, Vol. 14, Issue 1 https://doi.org/10.1186/1472-6831-14-93	journal	July 2014
Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest Prescott, Sara L.; Srinivasan, Rajini; Marchetto, Maria Carolina Cell, Vol. 163, Issue 1 https://doi.org/10.1016/j.cell.2015.08.036	journal	September 2015
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Evaluation and integration of disparate classification systems for clefts of the lip Wang, Kathie H.; Heike, Carrie L.; Clarkson, Melissa D. Frontiers in Physiology, Vol. 5 https://doi.org/10.3389/fphys.2014.00163	journal	May 2014
Modulation of noncanonical TGF-β signaling prevents cleft palate in Tgfbr2 mutant mice Iwata, Jun-ichi; Hacia, Joseph G.; Suzuki, Akiko Journal of Clinical Investigation, Vol. 122, Issue 3 https://doi.org/10.1172/JCI61498	journal	March 2012
Epigenomic Annotation of Enhancers Predicts Transcriptional Regulators of Human Neural Crest Rada-Iglesias, Alvaro; Bajpai, Ruchi; Prescott, Sara Cell Stem Cell, Vol. 11, Issue 5 https://doi.org/10.1016/j.stem.2012.07.006	journal	November 2012
Computer processable classification of craniofacial clefts Koul, Rakesh Frontiers in Physiology, Vol. 6 https://doi.org/10.3389/fphys.2015.00067	journal	March 2015
Identification of Novel Craniofacial Regulatory Domains Located far Upstream of SOX9 and Disrupted in Pierre Robin Sequence Gordon, Christopher T.; Attanasio, Catia; Bhatia, Shipra Human Mutation, Vol. 35, Issue 8 https://doi.org/10.1002/humu.22606	journal	July 2014
The FaceBase Consortium: A comprehensive program to facilitate craniofacial research Hochheiser, Harry; Aronow, Bruce J.; Artinger, Kristin Developmental Biology, Vol. 355, Issue 2 https://doi.org/10.1016/j.ydbio.2011.02.033	journal	July 2011
twist is required in head mesenchyme for cranial neural tube morphogenesis. Chen, Z. F.; Behringer, R. R. Genes & Development, Vol. 9, Issue 6 https://doi.org/10.1101/gad.9.6.686	journal	March 1995
Noncanonical Transforming Growth Factor β (TGFβ) Signaling in Cranial Neural Crest Cells Causes Tongue Muscle Developmental Defects Iwata, Jun-ichi; Suzuki, Akiko; Pelikan, Richard C. Journal of Biological Chemistry, Vol. 288, Issue 41 https://doi.org/10.1074/jbc.M113.493551	journal	October 2013
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Skeletogenic Fate of Zebrafish Cranial and Trunk Neural Crest Kague, Erika; Gallagher, Michael; Burke, Sally PLoS ONE, Vol. 7, Issue 11 https://doi.org/10.1371/journal.pone.0047394	journal	November 2012
Epigenomic Annotation of Enhancers Predicts Transcriptional Regulators of Human Neural Crest Rada-Iglesias, Alvaro; Bajpai, Ruchi; Prescott, Sara Cell Stem Cell, Vol. 11, Issue 5 https://doi.org/10.1016/j.stem.2012.07.006	journal	November 2012

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Network-based identification of critical regulators as putative drivers of human cleft lip Li, Aimin; Qin, Guimin; Suzuki, Akiko BMC Medical Genomics, Vol. 12, Issue S1 https://doi.org/10.1186/s12920-018-0458-3	journal	January 2019
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