kinase-TF-regulome

This repository contains the transcription factor and kinase target compendiums used in the hierarchical MARINa analysis of

@article{robertson_integrative_2017,
	title = {Integrative {Analysis} {Identifies} {Four} {Molecular} and {Clinical} {Subsets} in {Uveal} {Melanoma}},
	volume = {32},
	issn = {1535-6108, 1878-3686},
	url = {http://www.cell.com/cancer-cell/abstract/S1535-6108(17)30295-7},
	doi = {10.1016/j.ccell.2017.07.003},
	language = {English},
	number = {2},
	urldate = {2018-03-27},
	journal = {Cancer Cell},
	author = {Robertson, A. Gordon and Shih, Juliann and Yau, Christina and Gibb, Ewan A. and Oba, Junna and Mungall, Karen L. and Hess, Julian M. and Uzunangelov, Vladislav and Walter, Vonn and Danilova, Ludmila and Lichtenberg, Tara M. and Kucherlapati, Melanie and Kimes, Patrick K. and Tang, Ming and Penson, Alexander and Babur, Ozgun and Akbani, Rehan and Bristow, Christopher A. and Hoadley, Katherine A. and Iype, Lisa and Chang, Matthew T. and Abdel-Rahman, Mohamed H. and Akbani, Rehan and Ally, Adrian and Auman, J. Todd and Babur, Ozgun and Balasundaram, Miruna and Balu, Saianand and Benz, Christopher and Beroukhim, Rameen and Birol, Inanc and Bodenheimer, Tom and Bowen, Jay and Bowlby, Reanne and Bristow, Christopher A. and Brooks, Denise and Carlsen, Rebecca and Cebulla, Colleen M. and Chang, Matthew T. and Cherniack, Andrew D. and Chin, Lynda and Cho, Juok and Chuah, Eric and Chudamani, Sudha and Cibulskis, Carrie and Cibulskis, Kristian and Cope, Leslie and Coupland, Sarah E. and Danilova, Ludmila and Defreitas, Timothy and Demchok, John A. and Desjardins, Laurence and Dhalla, Noreen and Esmaeli, Bita and Felau, Ina and Ferguson, Martin L. and Frazer, Scott and Gabriel, Stacey B. and Gastier-Foster, Julie M. and Gehlenborg, Nils and Gerken, Mark and Gershenwald, Jeffrey E. and Getz, Gad and Gibb, Ewan A. and Griewank, Klaus G. and Grimm, Elizabeth A. and Hayes, D. Neil and Hegde, Apurva M. and Heiman, David I. and Helsel, Carmen and Hess, Julian M. and Hoadley, Katherine A. and Hobensack, Shital and Holt, Robert A. and Hoyle, Alan P. and Hu, Xin and Hutter, Carolyn M. and Jager, Martine J. and Jefferys, Stuart R. and Jones, Corbin D. and Jones, Steven J. M. and Kandoth, Cyriac and Kasaian, Katayoon and Kim, Jaegil and Kimes, Patrick K. and Kucherlapati, Melanie and Kucherlapati, Raju and Lander, Eric and Lawrence, Michael S. and Lazar, Alexander J. and Lee, Semin and Leraas, Kristen M. and Lichtenberg, Tara M. and Lin, Pei and Liu, Jia and Liu, Wenbin and Lolla, Laxmi and Lu, Yiling and Iype, Lisa and Ma, Yussanne and Mahadeshwar, Harshad S. and Mariani, Odette and Marra, Marco A. and Mayo, Michael and Meier, Sam and Meng, Shaowu and Meyerson, Matthew and Mieczkowski, Piotr A. and Mills, Gordon B. and Moore, Richard A. and Mose, Lisle E. and Mungall, Andrew J. and Mungall, Karen L. and Murray, Bradley A. and Naresh, Rashi and Noble, Michael S. and Oba, Junna and Pantazi, Angeliki and Parfenov, Michael and Park, Peter J. and Parker, Joel S. and Penson, Alexander and Perou, Charles M. and Pihl, Todd and Pilarski, Robert and Protopopov, Alexei and Radenbaugh, Amie and Rai, Karan and Ramirez, Nilsa C. and Ren, Xiaojia and Reynolds, Sheila M. and Roach, Jeffrey and Robertson, A. Gordon and Roman-Roman, Sergio and Roszik, Jason and Sadeghi, Sara and Saksena, Gordon and Sastre, Xavier and Schadendorf, Dirk and Schein, Jacqueline E. and Schoenfield, Lynn and Schumacher, Steven E. and Seidman, Jonathan and Seth, Sahil and Sethi, Geetika and Sheth, Margi and Shi, Yan and Shields, Carol and Shih, Juliann and Shmulevich, Ilya and Simons, Janae V. and Singh, Arun D. and Sipahimalani, Payal and Skelly, Tara and Sofia, Heidi and Soloway, Matthew G. and Song, Xingzhi and Stern, Marc-Henri and Stuart, Joshua and Sun, Qiang and Sun, Huandong and Tam, Angela and Tan, Donghui and Tang, Ming and Tang, Jiabin and Tarnuzzer, Roy and Taylor, Barry S. and Thiessen, Nina and Thorsson, Vesteinn and Tse, Kane and Uzunangelov, Vladislav and Veluvolu, Umadevi and Verhaak, Roel G. W. and Voet, Doug and Walter, Vonn and Wan, Yunhu and Wang, Zhining and Weinstein, John N. and Wilkerson, Matthew D. and Williams, Michelle D. and Wise, Lisa and Woodman, Scott E. and Wong, Tina and Wu, Ye and Yang, Liming and Yang, Lixing and Yau, Christina and Zenklusen, Jean C. and Zhang, Jiashan and Zhang, Hailei and Zmuda, Erik and Cherniack, Andrew D. and Benz, Christopher and Mills, Gordon B. and Verhaak, Roel G. W. and Griewank, Klaus G. and Felau, Ina and Zenklusen, Jean C. and Gershenwald, Jeffrey E. and Schoenfield, Lynn and Lazar, Alexander J. and Abdel-Rahman, Mohamed H. and Roman-Roman, Sergio and Stern, Marc-Henri and Cebulla, Colleen M. and Williams, Michelle D. and Jager, Martine J. and Coupland, Sarah E. and Esmaeli, Bita and Kandoth, Cyriac and Woodman, Scott E.},
	month = aug,
	year = {2017},
	pmid = {28810145},
	keywords = {EIF1AX, GNA11, GNAQ, molecular subtypes, monosomy 3, noncoding RNA, SF3B1, SRSF2, TCGA, uveal melanoma},
	pages = {204--220.e15},
}

PMID:28810145

For file derivations, see the Supplementary Methods of Roberston et. al (2017). All files are in .listt format - each line begins with a regulator followed by all its targets in a tab-delimited manner.

Files:

• kinase_targets.listt - kinase targets
• tf_targets.listt - TF targets
• tf_targets_filtered_min_15.listt - retains only TFs with >=15 targets from tf_targets.listt. This is the file used for all downstream analysis in Robertson et. al (2017).