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2. AXL-initiated paracrine activation of pSTAT3 enhances mesenchymal and vasculogenic supportive features of tumor-associated macrophages

Author

Hung, Chia-Nung, Chen, Meizhen, DeArmond, Daniel T., Chiu, Cheryl H.-L., Limboy, Catherine A., Tan, Xi, Kusi, Meena, Chou, Chih-Wei, Lin, Li-Ling, Zhang, Zhao, Wang, Chiou-Miin, Chen, Chun-Liang, Mitsuya, Kohzoh, Osmulski, Pawel A., Gaczynska, Maria E., Kirma, Nameer B., Vadlamudi, Ratna K., Gibbons, Don L., Warner, Steve, Brenner, Andrew J., Mahadevan, Daruka, Michalek, Joel E., Huang, Tim H.-M., and Taverna, Josephine A.

Published
2023
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5. Diverse AR-V7 cistromes in castration-resistant prostate cancer are governed by HoxB13

Author

Chen, Zhong, Wu, Dayong, Thomas-Ahner, Jennifer M., Lu, Changxue, Zhao, Pei, Zhang, Qingfu, Geraghty, Connor, Yan, Pearlly S., Hankey, William, Sunkel, Benjamin, Cheng, Xiaolong, Antonarakis, Emmanuel S., Wang, Qi-En, Liu, Zhihua, Huang, Tim H.-M., Jin, Victor X., Clinton, Steven K., Luo, Jun, Huang, Jiaoti, and Wang, Qianben

Published
2018

12. Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming

Author

Xiong, Lei, Wu, Feng, Wu, Qiong, Xu, Liangliang, Cheung, Otto K., Kang, Wei, Mok, Myth T., Szeto, Lemuel L. M., Lun, Cheuk-Yin, Lung, Raymond W., Zhang, Jinglin, Yu, Ken H., Lee, Sau-Dan, Huang, Guangcun, Wang, Chiou-Miin, Liu, Joseph, Yu, Zhuo, Yu, Dae-Yeul, Chou, Jian-Liang, Huang, Wan-Hong, Feng, Bo, Cheung, Yue-Sun, Lai, Paul B., Tan, Patrick, Wong, Nathalie, Chan, Michael W., Huang, Tim H., Yip, Kevin Y., Cheng, Alfred S., and To, Ka-Fai

Published
2019
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13. CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome

Author

Heisler, Lawrence E, Torti, Dax, Boutros, Paul C, Watson, John, Chan, Charles, Winegarden, Neil, Takahashi, Mark, Yau, Patrick, Huang, Tim H-M, Farnham, Peggy J, Jurisica, Igor, Woodgett, James R, Bremner, Rod, Penn, Linda Z, and Der, Sandy D

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Base Sequence, Chromosome Mapping, CpG Islands, DNA Probes, Databases, Nucleic Acid, Genome, Human, Genomic Library, Humans, Oligonucleotide Array Sequence Analysis, Sequence Alignment, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

An effective tool for the global analysis of both DNA methylation status and protein-chromatin interactions is a microarray constructed with sequences containing regulatory elements. One type of array suited for this purpose takes advantage of the strong association between CpG Islands (CGIs) and gene regulatory regions. We have obtained 20,736 clones from a CGI Library and used these to construct CGI arrays. The utility of this library requires proper annotation and assessment of the clones, including CpG content, genomic origin and proximity to neighboring genes. Alignment of clone sequences to the human genome (UCSC hg17) identified 9595 distinct genomic loci; 64% were defined by a single clone while the remaining 36% were represented by multiple, redundant clones. Approximately 68% of the loci were located near a transcription start site. The distribution of these loci covered all 23 chromosomes, with 63% overlapping a bioinformatically identified CGI. The high representation of genomic CGI in this rich collection of clones supports the utilization of microarrays produced with this library for the study of global epigenetic mechanisms and protein-chromatin interactions. A browsable database is available on-line to facilitate exploration of the CGIs in this library and their association with annotated genes or promoter elements.

Published
2005

14. Targeting hepatic serine-arginine protein kinase 2 ameliorates alcohol-associated liver disease by alternative splicing control of lipogenesis

Author

Li, Guannan, primary, Chen, Hanqing, additional, Shen, Feng, additional, Smithson, Steven Blake, additional, Shealy, Gavyn Lee, additional, Ping, Qinggong, additional, Liang, Zerong, additional, Han, Jingyan, additional, Adams, Andrew C., additional, Li, Yu, additional, Feng, Dechun, additional, Gao, Bin, additional, Morita, Masahiro, additional, Han, Xianlin, additional, Huang, Tim H., additional, Musi, Nicolas, additional, and Zang, Mengwei, additional

Published
2023
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21. Supplementary Table S1 from Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle–Related Transcription and Attenuated Androgen Response

Author

Horning, Aaron M., primary, Wang, Yao, primary, Lin, Che-Kuang, primary, Louie, Anna D., primary, Jadhav, Rohit R., primary, Hung, Chia-Nung, primary, Wang, Chiou-Miin, primary, Lin, Chun-Lin, primary, Kirma, Nameer B., primary, Liss, Michael A., primary, Kumar, Addanki P., primary, Sun, LuZhe, primary, Liu, Zhijie, primary, Chao, Wei-Ting, primary, Wang, Qianben, primary, Jin, Victor X., primary, Chen, Chun-Liang, primary, and Huang, Tim H.-M., primary

Published
2023
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22. Data from A First-in-Class Inhibitor of ER Coregulator PELP1 Targets ER+ Breast Cancer

Author

Altwegg, Kristin A., primary, Viswanadhapalli, Suryavathi, primary, Mann, Monica, primary, Chakravarty, Dimple, primary, Krishnan, Samaya, primary, Liu, Zexuan, primary, Liu, Junhao, primary, Pratap, Uday P., primary, Ebrahimi, Behnam, primary, Sanchez, John R., primary, Li, Xiaonan, primary, Ma, Shihong, primary, Park, Ben H., primary, Santhamma, Bindu, primary, Chen, Yidong, primary, Lai, Zhao, primary, Raj, Ganesh V., primary, Yuan, Yaxia, primary, Zhou, Daohong, primary, Sareddy, Gangadhara R., primary, Tekmal, Rajeshwar R., primary, McHardy, Stan, primary, Huang, Tim H.-M., primary, Rao, Manjeet K., primary, Vankayalapati, Hariprasad, primary, and Vadlamudi, Ratna K., primary

Published
2023
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23. Data from Contacts with Macrophages Promote an Aggressive Nanomechanical Phenotype of Circulating Tumor Cells in Prostate Cancer

Author

Osmulski, Pawel A., primary, Cunsolo, Alessandra, primary, Chen, Meizhen, primary, Qian, Yusheng, primary, Lin, Chun-Lin, primary, Hung, Chia-Nung, primary, Mahalingam, Devalingam, primary, Kirma, Nameer B., primary, Chen, Chun-Liang, primary, Taverna, Josephine A., primary, Liss, Michael A., primary, Thompson, Ian M., primary, Huang, Tim H.-M., primary, and Gaczynska, Maria E., primary

Published
2023
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24. Supplementary Figure S1-10 from Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle–Related Transcription and Attenuated Androgen Response

Author

Horning, Aaron M., primary, Wang, Yao, primary, Lin, Che-Kuang, primary, Louie, Anna D., primary, Jadhav, Rohit R., primary, Hung, Chia-Nung, primary, Wang, Chiou-Miin, primary, Lin, Chun-Lin, primary, Kirma, Nameer B., primary, Liss, Michael A., primary, Kumar, Addanki P., primary, Sun, LuZhe, primary, Liu, Zhijie, primary, Chao, Wei-Ting, primary, Wang, Qianben, primary, Jin, Victor X., primary, Chen, Chun-Liang, primary, and Huang, Tim H.-M., primary

Published
2023
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25. Data from Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle–Related Transcription and Attenuated Androgen Response

Author

Horning, Aaron M., primary, Wang, Yao, primary, Lin, Che-Kuang, primary, Louie, Anna D., primary, Jadhav, Rohit R., primary, Hung, Chia-Nung, primary, Wang, Chiou-Miin, primary, Lin, Chun-Lin, primary, Kirma, Nameer B., primary, Liss, Michael A., primary, Kumar, Addanki P., primary, Sun, LuZhe, primary, Liu, Zhijie, primary, Chao, Wei-Ting, primary, Wang, Qianben, primary, Jin, Victor X., primary, Chen, Chun-Liang, primary, and Huang, Tim H.-M., primary

Published
2023
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26. Supplementary Data from A First-in-Class Inhibitor of ER Coregulator PELP1 Targets ER+ Breast Cancer

Author

Altwegg, Kristin A., primary, Viswanadhapalli, Suryavathi, primary, Mann, Monica, primary, Chakravarty, Dimple, primary, Krishnan, Samaya, primary, Liu, Zexuan, primary, Liu, Junhao, primary, Pratap, Uday P., primary, Ebrahimi, Behnam, primary, Sanchez, John R., primary, Li, Xiaonan, primary, Ma, Shihong, primary, Park, Ben H., primary, Santhamma, Bindu, primary, Chen, Yidong, primary, Lai, Zhao, primary, Raj, Ganesh V., primary, Yuan, Yaxia, primary, Zhou, Daohong, primary, Sareddy, Gangadhara R., primary, Tekmal, Rajeshwar R., primary, McHardy, Stan, primary, Huang, Tim H.-M., primary, Rao, Manjeet K., primary, Vankayalapati, Hariprasad, primary, and Vadlamudi, Ratna K., primary

Published
2023
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27. Data from PRC2-Mediated Epigenetic Suppression of Type I IFN-STAT2 Signaling Impairs Antitumor Immunity in Luminal Breast Cancer

Author

Hong, Juyeong, primary, Lee, Ji Hoon, primary, Zhang, Zhao, primary, Wu, Yanming, primary, Yang, Mei, primary, Liao, Yiji, primary, de la Rosa, Richard, primary, Scheirer, Jessica, primary, Pechacek, Douglas, primary, Zhang, Nu, primary, Xu, Zhenming, primary, Curiel, Tyler, primary, Tan, Xi, primary, Huang, Tim H.-M., primary, and Xu, Kexin, primary

Published
2023
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28. Supplementary Methods, Figure Legend, Table 1 from Mapping Geographic Zones of Cancer Risk with Epigenetic Biomarkers in Normal Breast Tissue

Author

Yan, Pearlly S., primary, Venkataramu, Chinnambally, primary, Ibrahim, Ashraf, primary, Liu, Joseph C., primary, Shen, Rulong Z., primary, Diaz, Nils M., primary, Centeno, Barbara, primary, Weber, Frank, primary, Leu, Yu-Wei, primary, Shapiro, Charles L., primary, Eng, Charis, primary, Yeatman, Timothy J., primary, and Huang, Tim H.-M., primary

Published
2023
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29. Supplementary Data from Contacts with Macrophages Promote an Aggressive Nanomechanical Phenotype of Circulating Tumor Cells in Prostate Cancer

Author

Osmulski, Pawel A., primary, Cunsolo, Alessandra, primary, Chen, Meizhen, primary, Qian, Yusheng, primary, Lin, Chun-Lin, primary, Hung, Chia-Nung, primary, Mahalingam, Devalingam, primary, Kirma, Nameer B., primary, Chen, Chun-Liang, primary, Taverna, Josephine A., primary, Liss, Michael A., primary, Thompson, Ian M., primary, Huang, Tim H.-M., primary, and Gaczynska, Maria E., primary

Published
2023
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31. Supplementary Table S1 from Prognostic DNA Methylation Biomarkers in Ovarian Cancer

Author

Wei, Susan H., primary, Balch, Curtis, primary, Paik, Henry H., primary, Kim, Yoo-Sung, primary, Baldwin, Rae Lynn, primary, Liyanarachchi, Sandya, primary, Li, Lang, primary, Wang, Zailong, primary, Wan, Joseph C., primary, Davuluri, Ramana V., primary, Karlan, Beth Y., primary, Gifford, Gillian, primary, Brown, Robert, primary, Kim, Sun, primary, Huang, Tim H-M., primary, and Nephew, Kenneth P., primary

Published
2023
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33. Supplementary Figure 1 from Mapping Geographic Zones of Cancer Risk with Epigenetic Biomarkers in Normal Breast Tissue

Author

Yan, Pearlly S., primary, Venkataramu, Chinnambally, primary, Ibrahim, Ashraf, primary, Liu, Joseph C., primary, Shen, Rulong Z., primary, Diaz, Nils M., primary, Centeno, Barbara, primary, Weber, Frank, primary, Leu, Yu-Wei, primary, Shapiro, Charles L., primary, Eng, Charis, primary, Yeatman, Timothy J., primary, and Huang, Tim H.-M., primary

Published
2023
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34. Supplementary Data from Modulation of Genetic and Epigenetic Biomarkers of Colorectal Cancer in Humans by Black Raspberries: A Phase I Pilot Study

Author

Wang, Li-Shu, primary, Arnold, Mark, primary, Huang, Yi-Wen, primary, Sardo, Christine, primary, Seguin, Claire, primary, Martin, Edward, primary, Huang, Tim H.-M., primary, Riedl, Ken, primary, Schwartz, Steven, primary, Frankel, Wendy, primary, Pearl, Dennis, primary, Xu, Yiqing, primary, Winston, John, primary, Yang, Guang-Yu, primary, and Stoner, Gary, primary

Published
2023
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35. Supplementary Figure from A First-in-Class Inhibitor of ER Coregulator PELP1 Targets ER+ Breast Cancer

Author

Altwegg, Kristin A., primary, Viswanadhapalli, Suryavathi, primary, Mann, Monica, primary, Chakravarty, Dimple, primary, Krishnan, Samaya, primary, Liu, Zexuan, primary, Liu, Junhao, primary, Pratap, Uday P., primary, Ebrahimi, Behnam, primary, Sanchez, John R., primary, Li, Xiaonan, primary, Ma, Shihong, primary, Park, Ben H., primary, Santhamma, Bindu, primary, Chen, Yidong, primary, Lai, Zhao, primary, Raj, Ganesh V., primary, Yuan, Yaxia, primary, Zhou, Daohong, primary, Sareddy, Gangadhara R., primary, Tekmal, Rajeshwar R., primary, McHardy, Stan, primary, Huang, Tim H.-M., primary, Rao, Manjeet K., primary, Vankayalapati, Hariprasad, primary, and Vadlamudi, Ratna K., primary

Published
2023
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36. Supplementary Data from PRC2-Mediated Epigenetic Suppression of Type I IFN-STAT2 Signaling Impairs Antitumor Immunity in Luminal Breast Cancer

Author

Hong, Juyeong, primary, Lee, Ji Hoon, primary, Zhang, Zhao, primary, Wu, Yanming, primary, Yang, Mei, primary, Liao, Yiji, primary, de la Rosa, Richard, primary, Scheirer, Jessica, primary, Pechacek, Douglas, primary, Zhang, Nu, primary, Xu, Zhenming, primary, Curiel, Tyler, primary, Tan, Xi, primary, Huang, Tim H.-M., primary, and Xu, Kexin, primary

Published
2023
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37. Data from Targeted Methylation of Two Tumor Suppressor Genes Is Sufficient to Transform Mesenchymal Stem Cells into Cancer Stem/Initiating Cells

Author

Teng, I-Wen, primary, Hou, Pei-Chi, primary, Lee, Kuan-Der, primary, Chu, Pei-Yi, primary, Yeh, Kun-Tu, primary, Jin, Victor X., primary, Tseng, Min-Jen, primary, Tsai, Shaw-Jenq, primary, Chang, Yu-Sun, primary, Wu, Chi-Sheng, primary, Sun, H. Sunny, primary, Tsai, Kuen-daw, primary, Jeng, Long-Bin, primary, Nephew, Kenneth P., primary, Huang, Tim H.-M., primary, Hsiao, Shu-Huei, primary, and Leu, Yu-Wei, primary

Published
2023
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40. Supplementary Table 2 from Diverse Gene Expression and DNA Methylation Profiles Correlate with Differential Adaptation of Breast Cancer Cells to the Antiestrogens Tamoxifen and Fulvestrant

Author

Fan, Meiyun, primary, Yan, Pearlly S., primary, Hartman-Frey, Cori, primary, Chen, Lei, primary, Paik, Henry, primary, Oyer, Samuel L., primary, Salisbury, Jonathan D., primary, Cheng, Alfred S.L., primary, Li, Lang, primary, Abbosh, Phillip H., primary, Huang, Tim H-M., primary, and Nephew, Kenneth P., primary

Published
2023
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42. Supplementary Table 4 from Diverse Gene Expression and DNA Methylation Profiles Correlate with Differential Adaptation of Breast Cancer Cells to the Antiestrogens Tamoxifen and Fulvestrant

Author

Fan, Meiyun, primary, Yan, Pearlly S., primary, Hartman-Frey, Cori, primary, Chen, Lei, primary, Paik, Henry, primary, Oyer, Samuel L., primary, Salisbury, Jonathan D., primary, Cheng, Alfred S.L., primary, Li, Lang, primary, Abbosh, Phillip H., primary, Huang, Tim H-M., primary, and Nephew, Kenneth P., primary

Published
2023
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43. Data from Breast Cancer–Associated Fibroblasts Confer AKT1-Mediated Epigenetic Silencing of Cystatin M in Epithelial Cells

Author

Lin, Huey-Jen L., primary, Zuo, Tao, primary, Lin, Ching-Hung, primary, Kuo, Chieh Ti, primary, Liyanarachchi, Sandya, primary, Sun, Shuying, primary, Shen, Rulong, primary, Deatherage, Daniel E., primary, Potter, Dustin, primary, Asamoto, Lisa, primary, Lin, Shili, primary, Yan, Pearlly S., primary, Cheng, Ann-Lii, primary, Ostrowski, Michael C., primary, and Huang, Tim H.-M., primary

Published
2023
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45. Data from EZH2-Mediated Concordant Repression of Wnt Antagonists Promotes β-Catenin–Dependent Hepatocarcinogenesis

Author

Cheng, Alfred S.L., primary, Lau, Suki S., primary, Chen, Yangchao, primary, Kondo, Yutaka, primary, Li, May S., primary, Feng, Hai, primary, Ching, Arthur K., primary, Cheung, Kin F., primary, Wong, Hoi K., primary, Tong, Joanna H., primary, Jin, Hongchuan, primary, Choy, Kwong W., primary, Yu, Jun, primary, To, Ka F., primary, Wong, Nathalie, primary, Huang, Tim H.-M., primary, and Sung, Joseph J.Y., primary

Published
2023
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46. Supplementary Table 3 from Diverse Gene Expression and DNA Methylation Profiles Correlate with Differential Adaptation of Breast Cancer Cells to the Antiestrogens Tamoxifen and Fulvestrant

Author

Fan, Meiyun, primary, Yan, Pearlly S., primary, Hartman-Frey, Cori, primary, Chen, Lei, primary, Paik, Henry, primary, Oyer, Samuel L., primary, Salisbury, Jonathan D., primary, Cheng, Alfred S.L., primary, Li, Lang, primary, Abbosh, Phillip H., primary, Huang, Tim H-M., primary, and Nephew, Kenneth P., primary

Published
2023
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47. Supplementary Table 7 from EZH2-Mediated Concordant Repression of Wnt Antagonists Promotes β-Catenin–Dependent Hepatocarcinogenesis

Author

Cheng, Alfred S.L., primary, Lau, Suki S., primary, Chen, Yangchao, primary, Kondo, Yutaka, primary, Li, May S., primary, Feng, Hai, primary, Ching, Arthur K., primary, Cheung, Kin F., primary, Wong, Hoi K., primary, Tong, Joanna H., primary, Jin, Hongchuan, primary, Choy, Kwong W., primary, Yu, Jun, primary, To, Ka F., primary, Wong, Nathalie, primary, Huang, Tim H.-M., primary, and Sung, Joseph J.Y., primary

Published
2023
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48. Data from Epithelial Progeny of Estrogen-Exposed Breast Progenitor Cells Display a Cancer-like Methylome

Author

Cheng, Alfred S.L., primary, Culhane, Aedín C., primary, Chan, Michael W.Y., primary, Venkataramu, Chinnambally R., primary, Ehrich, Mathias, primary, Nasir, Aejaz, primary, Rodriguez, Benjamin A.T., primary, Liu, Joseph, primary, Yan, Pearlly S., primary, Quackenbush, John, primary, Nephew, Kenneth P., primary, Yeatman, Timothy J., primary, and Huang, Tim H-M., primary

Published
2023
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49. Supplementary Figure Legends 1-3 from Diverse Gene Expression and DNA Methylation Profiles Correlate with Differential Adaptation of Breast Cancer Cells to the Antiestrogens Tamoxifen and Fulvestrant

Author

Fan, Meiyun, primary, Yan, Pearlly S., primary, Hartman-Frey, Cori, primary, Chen, Lei, primary, Paik, Henry, primary, Oyer, Samuel L., primary, Salisbury, Jonathan D., primary, Cheng, Alfred S.L., primary, Li, Lang, primary, Abbosh, Phillip H., primary, Huang, Tim H-M., primary, and Nephew, Kenneth P., primary

Published
2023
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50. Supplementary Methods, Figures 1-9, Tables 2-6 from EZH2-Mediated Concordant Repression of Wnt Antagonists Promotes β-Catenin–Dependent Hepatocarcinogenesis

Author

Cheng, Alfred S.L., primary, Lau, Suki S., primary, Chen, Yangchao, primary, Kondo, Yutaka, primary, Li, May S., primary, Feng, Hai, primary, Ching, Arthur K., primary, Cheung, Kin F., primary, Wong, Hoi K., primary, Tong, Joanna H., primary, Jin, Hongchuan, primary, Choy, Kwong W., primary, Yu, Jun, primary, To, Ka F., primary, Wong, Nathalie, primary, Huang, Tim H.-M., primary, and Sung, Joseph J.Y., primary

Published
2023
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