Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types

Cory C. Funk; Alex M. Casella; Segun Jung; Matthew A. Richards; Alex Rodriguez; Paul Shannon; Rory Donovan-Maiye; Ben Heavner; Kyle Chard; Yukai Xiao; Gustavo Glusman; Nilufer Ertekin-Taner; Todd E. Golde; Arthur Toga; Leroy Hood; John D. Van Horn; Carl Kesselman; Ian Foster; Ravi Madduri; Nathan D. Price; Seth A. Ament

doi:10.1016/j.celrep.2020.108029

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types

Cory C. Funk, Alex M. Casella, Segun Jung, Matthew A. Richards, Alex Rodriguez, Paul Shannon, Rory Donovan-Maiye, Ben Heavner, Kyle Chard, Yukai Xiao, Gustavo Glusman, Nilufer Ertekin-Taner, Todd E. Golde, Arthur Toga, Leroy Hood, John D. Van Horn, Carl Kesselman, Ian Foster, Ravi Madduri, Nathan D. PriceSeth A. Ament

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

DNase-seq footprinting provides a means to predict genome-wide binding sites for hundreds of transcription factors (TFs) simultaneously. Funk et al. analyze data from the ENCODE consortium to create a resource of footprints in 27 human tissues, demonstrating associations of tissue-specific TF occupancy with gene regulation and disease risk.

Original language	English (US)
Article number	108029
Journal	Cell reports
Volume	32
Issue number	7
DOIs	https://doi.org/10.1016/j.celrep.2020.108029
State	Published - Aug 18 2020

Keywords

DNase-seq
ENCODE
footprinting
gene regulation
motifs
psychiatric genetics
transcription factors

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)

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10.1016/j.celrep.2020.108029

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Funk, C. C., Casella, A. M., Jung, S., Richards, M. A., Rodriguez, A., Shannon, P., Donovan-Maiye, R., Heavner, B., Chard, K., Xiao, Y., Glusman, G., Ertekin-Taner, N., Golde, T. E., Toga, A., Hood, L., Van Horn, J. D., Kesselman, C., Foster, I., Madduri, R., ... Ament, S. A. (2020). Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types. Cell reports, 32(7), Article 108029. https://doi.org/10.1016/j.celrep.2020.108029

Funk, CC, Casella, AM, Jung, S, Richards, MA, Rodriguez, A, Shannon, P, Donovan-Maiye, R, Heavner, B, Chard, K, Xiao, Y, Glusman, G, Ertekin-Taner, N, Golde, TE, Toga, A, Hood, L, Van Horn, JD, Kesselman, C, Foster, I, Madduri, R, Price, ND & Ament, SA 2020, 'Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types', Cell reports, vol. 32, no. 7, 108029. https://doi.org/10.1016/j.celrep.2020.108029

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abstract = "DNase-seq footprinting provides a means to predict genome-wide binding sites for hundreds of transcription factors (TFs) simultaneously. Funk et al. analyze data from the ENCODE consortium to create a resource of footprints in 27 human tissues, demonstrating associations of tissue-specific TF occupancy with gene regulation and disease risk.",

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note = "Funding Information: This work was supported by the BDDS Center of the NIH Big Data to Knowledge program ( U54 EB020406 to N.D.P. and L.H.), the National Institute of Aging ( U01 AG046139 to N.D.P.; RF1 AG057443 to N.D.P.), the National Institute for General Medical Sciences Center for Systems Biology at the Institute for Systems Biology ( P50 GM07654 to L.H. and N.D.P.), and the national Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative ( R24MH114788 , Owen White, PI; R24MH114815 , Owen White and Ronna Hertzano, PIs; the National Human Genome Research Institute ( 5R01HG009018 to I.F. and R.M.,); and the National Institute of Mental Health ( F30 MH120910 to A.M.C.). Publisher Copyright: {\textcopyright} 2020 The Authors",

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AU - Donovan-Maiye, Rory

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AU - Chard, Kyle

AU - Xiao, Yukai

AU - Glusman, Gustavo

AU - Ertekin-Taner, Nilufer

AU - Golde, Todd E.

AU - Toga, Arthur

AU - Hood, Leroy

AU - Van Horn, John D.

AU - Kesselman, Carl

AU - Foster, Ian

AU - Madduri, Ravi

AU - Price, Nathan D.

AU - Ament, Seth A.

N1 - Funding Information: This work was supported by the BDDS Center of the NIH Big Data to Knowledge program ( U54 EB020406 to N.D.P. and L.H.), the National Institute of Aging ( U01 AG046139 to N.D.P.; RF1 AG057443 to N.D.P.), the National Institute for General Medical Sciences Center for Systems Biology at the Institute for Systems Biology ( P50 GM07654 to L.H. and N.D.P.), and the national Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative ( R24MH114788 , Owen White, PI; R24MH114815 , Owen White and Ronna Hertzano, PIs; the National Human Genome Research Institute ( 5R01HG009018 to I.F. and R.M.,); and the National Institute of Mental Health ( F30 MH120910 to A.M.C.). Publisher Copyright: © 2020 The Authors

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Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types

Abstract

Keywords

ASJC Scopus subject areas

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