Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

Mumbach, Maxwell R, Satpathy, Ansuman T, Boyle, Evan A, Dai, Chao, Gowen, Benjamin G, Cho, Seung Woo, Nguyen, Michelle L, Rubin, Adam J +19 more·2017·Nature Genetics
DOI 10.1038/ng.3963

Cited by (509)

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  18. Faculty Opinions recommendation of The chromatin accessibility landscape of primary human cancers.
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  30. Additional file 2 of CRISPR screens identify gene targets at breast cancer risk loci
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  31. Additional file 7 of CRISPR screens identify gene targets at breast cancer risk loci
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  32. Additional file 4 of 3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk
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  33. Additional file 5 of CRISPR screens identify gene targets at breast cancer risk loci
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  34. Additional file 3 of CRISPR screens identify gene targets at breast cancer risk loci
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  35. Additional file 6 of CRISPR screens identify gene targets at breast cancer risk loci
    Natasha Tuano, Jonathan Beesley, Murray Manning, Wei Shi, Laura Perlaza-Jiménez, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue et al. · 2023 · Figshare
  36. Additional file 8 of CRISPR screens identify gene targets at breast cancer risk loci
    Natasha Tuano, Jonathan Beesley, Murray Manning, Wei Shi, Laura Perlaza-Jiménez, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue et al. · 2023 · Figshare
  37. Additional file 3 of 3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk
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  38. Additional file 4 of Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies
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  39. Additional file 2 of 3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk
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  40. Additional file 4 of CRISPR screens identify gene targets at breast cancer risk loci
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  42. Additional file 3 of Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies
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  53. Additional file 10 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
    Helen F. Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P. Morris, Antony D. Adamson et al. · 2020 · Figshare
  54. Additional file 1 of 3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk
    Liu, Ning, Timothy J. Sadlon, Ying Y. Wong, Stephen Pederson, Breen, James, Barry, Simon C. · 2022 · Figshare
  55. Additional file 9 of CRISPR screens identify gene targets at breast cancer risk loci
    Natasha Tuano, Jonathan Beesley, Murray Manning, Shi, Wei, Laura Perlaza-Jiménez, Luis Fernando Malaver-Ortega, Jacob M. Paynter, Debra M. Black, Andrew Civitarese, Karen McCue et al. · 2023 · Figshare
  56. Additional file 1 of Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation
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  57. Additional file 4 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
    Helen F. Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P. Morris, Antony D. Adamson et al. · 2020 · Figshare
  58. Additional file 4 of CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms
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  59. Additional file 5 of Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies
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  60. Additional file 1 of HiCoP, a simple and robust method for detecting interactions of regulatory regions
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  61. Additional file 4 of Chromatin activity identifies differential gene regulation across human ancestries
    Kade P. Pettie, Maxwell R. Mumbach, Lea, Amanda J., Julien F. Ayroles, Howard Y. Chang, Maya M. Kasowski, Hunter B. Fraser · 2024 · Figshare
  62. Additional file 8 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
    Helen F. Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P. Morris, Antony D. Adamson et al. · 2020 · Figshare
  63. Additional file 14 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
    Helen F. Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P. Morris, Antony D. Adamson et al. · 2020 · Figshare
  64. Additional file 2 of GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
    Lee, Da-Inn, Sushmita Roy · 2021 · Figshare
  65. Additional file 2 of Chromatin activity identifies differential gene regulation across human ancestries
    Kade P. Pettie, Maxwell R. Mumbach, Lea, Amanda J., Julien F. Ayroles, Howard Y. Chang, Maya M. Kasowski, Hunter B. Fraser · 2024 · Figshare
  66. Additional file 1 of Chromatin activity identifies differential gene regulation across human ancestries
    Kade P. Pettie, Maxwell R. Mumbach, Lea, Amanda J., Julien F. Ayroles, Howard Y. Chang, Maya M. Kasowski, Hunter B. Fraser · 2024 · Figshare
  67. Additional file 2 of CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms
    Li, Yongge, Ju, Fusong, Chen, Zhiyuan, Yiming Qu, Xia, Huanhuan, He, Liang, Wu, Lijun, Zhu, Jianwei, Shao, Bin, Deng, Pan · 2024 · Figshare
  68. Additional file 1 of Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies
    Tang, Li, Matthew C. Hill, Patrick T. Ellinor, Li, Min · 2022 · Figshare
  69. Additional file 6 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
    Helen F. Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P. Morris, Antony D. Adamson et al. · 2020 · Figshare
  70. Additional file 7 of Chromatin activity identifies differential gene regulation across human ancestries
    Kade P. Pettie, Maxwell R. Mumbach, Lea, Amanda J., Julien F. Ayroles, Howard Y. Chang, Maya M. Kasowski, Hunter B. Fraser · 2024 · Figshare
  71. Additional file 13 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
    Helen F. Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P. Morris, Antony D. Adamson et al. · 2020 · Figshare
  72. Additional file 11 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
    Helen F. Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P. Morris, Antony D. Adamson et al. · 2020 · Figshare
  73. Additional file 6 of Chromatin activity identifies differential gene regulation across human ancestries
    Kade P. Pettie, Maxwell R. Mumbach, Lea, Amanda J., Julien F. Ayroles, Howard Y. Chang, Maya M. Kasowski, Hunter B. Fraser · 2024 · Figshare
  74. Additional file 1 of CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms
    Li, Yongge, Ju, Fusong, Chen, Zhiyuan, Yiming Qu, Xia, Huanhuan, He, Liang, Wu, Lijun, Zhu, Jianwei, Shao, Bin, Deng, Pan · 2023 · Figshare
  75. Additional file 2 of Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation
    Abbas Roayaei Ardakany, Halil Tuvan Gezer, Lonardi, Stefano, Ay, Ferhat · 2020 · Figshare
  76. Additional file 1 of CRISPR screens identify gene targets at breast cancer risk loci
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  77. Additional file 1 of GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
    Lee, Da-Inn, Sushmita Roy · 2021 · Figshare
  78. Additional file 9 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
    Helen F. Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P. Morris, Antony D. Adamson et al. · 2020 · Figshare
  79. Additional file 5 of Chromatin activity identifies differential gene regulation across human ancestries
    Kade P. Pettie, Maxwell R. Mumbach, Lea, Amanda J., Julien F. Ayroles, Howard Y. Chang, Maya M. Kasowski, Hunter B. Fraser · 2024 · Figshare
  80. Additional file 2 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
    Helen F. Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P. Morris, Antony D. Adamson et al. · 2020 · Figshare
  81. Additional file 4 of GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
    Lee, Da-Inn, Sushmita Roy · 2021 · Figshare
  82. Additional file 1 of Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress
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  83. Additional file 2 of Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress
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  84. Additional file 3 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
    Helen F. Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P. Morris, Antony D. Adamson et al. · 2020 · Figshare
  85. Additional file 3 of Chromatin activity identifies differential gene regulation across human ancestries
    Kade P. Pettie, Maxwell R. Mumbach, Amanda J. Lea, Julien F. Ayroles, Howard Y. Chang, Maya M. Kasowski, Hunter B. Fraser · 2024 · Figshare
  86. Additional file 3 of CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms
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