References
Ashburner, Michael, Catherine A. Ball, Judith A. Blake, David Botstein,
Heather Butler, J. Michael Cherry, Allan P. Davis, et al. 2000.
“Gene Ontology: Tool for the Unification of Biology.”
Nature Genetics 25 (1): 25–29. https://doi.org/10.1038/75556.
Breitkreutz, Dylan, Lynn Hlatky, Edward Rietman, and Jack A. Tuszynski.
2012. “Molecular Signaling Network Complexity Is Correlated with
Cancer Patient Survivability.” Proceedings of the National
Academy of Sciences 109 (23): 9209–12. https://doi.org/10.1073/pnas.1201416109.
Carbon, Seth, Eric Douglass, Benjamin M Good, Deepak R Unni, Nomi L
Harris, Christopher J Mungall, Siddartha Basu, et al. 2020. “The
Gene Ontology Resource: Enriching a GOld Mine.” Nucleic Acids
Research 49 (D1): D325–34. https://doi.org/10.1093/nar/gkaa1113.
Fabregat, Antonio, Florian Korninger, Guilherme Viteri, Konstantinos
Sidiropoulos, Pablo Marin-Garcia, Peipei Ping, Guanming Wu, Lincoln
Stein, Peter D’Eustachio, and Henning Hermjakob. 2018. “Reactome
Graph Database: Efficient Access to Complex Pathway Data.” Edited
by Timothée Poisot. PLOS Computational Biology 14 (1):
e1005968. https://doi.org/10.1371/journal.pcbi.1005968.
Fabregat, Antonio, Konstantinos Sidiropoulos, Guilherme Viteri, Oscar
Forner, Pablo Marin-Garcia, Vicente Arnau, Peter D’Eustachio, Lincoln
Stein, and Henning Hermjakob. 2017. “Reactome Pathway Analysis: A
High-Performance in-Memory Approach.” BMC Bioinformatics
18 (1). https://doi.org/10.1186/s12859-017-1559-2.
Fabregat, Antonio, Konstantinos Sidiropoulos, Guilherme Viteri, Pablo
Marin-Garcia, Peipei Ping, Lincoln Stein, Peter D’Eustachio, and Henning
Hermjakob. 2017. “Reactome Diagram Viewer: Data Structures and
Strategies to Boost Performance.” Edited by Janet Kelso.
Bioinformatics 34 (7): 1208–14. https://doi.org/10.1093/bioinformatics/btx752.
Gillespie, Marc, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen
Rothfels, Andrea Senff-Ribeiro, Johannes Griss, et al. 2021. “The
Reactome Pathway Knowledgebase 2022.” Nucleic Acids
Research 50 (D1): D687–92. https://doi.org/10.1093/nar/gkab1028.
Griss, Johannes, Guilherme Viteri, Konstantinos Sidiropoulos, Vy Nguyen,
Antonio Fabregat, and Henning Hermjakob. 2020. “ReactomeGSA -
Efficient Multi-Omics Comparative Pathway Analysis.”
Molecular & Cellular Proteomics 19 (12): 2115–25. https://doi.org/10.1074/mcp.tir120.002155.
Herling, Therese W., David J. O’Connell, Mikael C. Bauer, Jonas Persson,
Ulrich Weininger, Tuomas P.J. Knowles, and Sara Linse. 2016. “A
Microfluidic Platform for Real-Time Detection and Quantification of
Protein-Ligand Interactions.” Biophysical Journal 110
(9): 1957–66. https://doi.org/10.1016/j.bpj.2016.03.038.
Imami, Ali Sajid. 2021. “Example Output from a PamChip
Asssay.” https://doi.org/10.5281/ZENODO.4639790.
Jassal, Bijay, Lisa Matthews, Guilherme Viteri, Chuqiao Gong, Pascual
Lorente, Antonio Fabregat, Konstantinos Sidiropoulos, et al. 2019.
“The Reactome Pathway Knowledgebase.” Nucleic Acids
Research, November. https://doi.org/10.1093/nar/gkz1031.
Kanehisa, M. 2000. “KEGG: Kyoto Encyclopedia of Genes and
Genomes.” Nucleic Acids Research 28 (1): 27–30. https://doi.org/10.1093/nar/28.1.27.
Kanehisa, Minoru. 2019. “Toward Understanding the Origin and
Evolution of Cellular Organisms.” Protein Science 28
(11): 1947–51. https://doi.org/10.1002/pro.3715.
Kanehisa, Minoru, Miho Furumichi, Yoko Sato, Masayuki Kawashima, and
Mari Ishiguro-Watanabe. 2022. “KEGG for Taxonomy-Based Analysis of
Pathways and Genomes.” Nucleic Acids Research 51 (D1):
D587–92. https://doi.org/10.1093/nar/gkac963.
Khatri, Purvesh, Marina Sirota, and Atul J. Butte. 2012. “Ten
Years of Pathway Analysis: Current Approaches and Outstanding
Challenges.” Edited by Christos A. Ouzounis. PLoS
Computational Biology 8 (2): e1002375. https://doi.org/10.1371/journal.pcbi.1002375.
Lee, Jeong Hoon, Benjamin D. Cosgrove, Douglas A. Lauffenburger, and
Jongyoon Han. 2009. “Microfluidic Concentration-Enhanced Cellular
Kinase Activity Assay.” Journal of the American Chemical
Society 131 (30): 10340–41. https://doi.org/10.1021/ja902594f.
Mann, Matthias, and Ole N. Jensen. 2003. “Proteomic Analysis of
Post-Translational Modifications.” Nature Biotechnology
21 (3): 255–61. https://doi.org/10.1038/nbt0303-255.
Manning, G., D. B. Whyte, R. Martinez, T. Hunter, and S. Sudarsanam.
2002. “The Protein Kinase Complement of the Human Genome.”
Science 298 (5600): 1912–34. https://doi.org/10.1126/science.1075762.
McBrayer, Samuel K., Javelin C. Cheng, Seema Singhal, Nancy L. Krett,
Steven T. Rosen, and Mala Shanmugam. 2012. “Multiple Myeloma
Exhibits Novel Dependence on GLUT4, GLUT8, and GLUT11: Implications for
Glucose Transporter-Directed Therapy.” Blood 119 (20):
4686–97. https://doi.org/10.1182/blood-2011-09-377846.
McLaggan, Debra, Noppadon Adjimatera, Kristina Sepčić, Marcel Jaspars,
David J MacEwan, Ian S Blagbrough, and Roderick H Scott. 2006.
“Pore Forming Polyalkylpyridinium Salts from Marine Sponges Versus
Synthetic Lipofection Systems: Distinct Tools for Intracellular Delivery
of cDNA and siRNA.” BMC Biotechnology 6 (1). https://doi.org/10.1186/1472-6750-6-6.
Mertins, Philipp, Feng Yang, Tao Liu, D. R. Mani, Vladislav A. Petyuk,
Michael A. Gillette, Karl R. Clauser, et al. 2014. “Ischemia in
Tumors Induces Early and Sustained Phosphorylation Changes in Stress
Kinase Pathways but Does Not Affect Global Protein Levels.”
Molecular & Cellular Proteomics 13 (7): 1690–1704. https://doi.org/10.1074/mcp.m113.036392.
PamGene Corporation. 2020. “Protocol 1140: Protocol for
Preparation of Tissue Sections,” September. https://pamgene.com/wp-content/uploads/2022/03/1160-Preparation-Lysates-of-Cell-Lines-or-Purified-Cells-V4.2-2022-03.pdf.
———. 2021. “Protocol 1150: Preparation of Lysates of Tissue
Sections,” December. https://pamgene.com/wp-content/uploads/2022/03/1160-Preparation-Lysates-of-Cell-Lines-or-Purified-Cells-V4.2-2022-03.pdf.
———. 2022. “Protocol 1160: Preparation of Lysates of Cell Lines or
Purified Cells,” March. https://pamgene.com/wp-content/uploads/2022/03/1160-Preparation-Lysates-of-Cell-Lines-or-Purified-Cells-V4.2-2022-03.pdf.
Sidiropoulos, Konstantinos, Guilherme Viteri, Cristoffer Sevilla, Steve
Jupe, Marissa Webber, Marija Orlic-Milacic, Bijay Jassal, et al. 2017.
“Reactome Enhanced Pathway Visualization.” Edited by Janet
Kelso. Bioinformatics 33 (21): 3461–67. https://doi.org/10.1093/bioinformatics/btx441.
Smail, Marissa A., James K. Reigle, and Robert E. McCullumsmith. 2021.
“Using Protein Turnover to Expand the Applications of
Transcriptomics.” Scientific Reports 11 (1). https://doi.org/10.1038/s41598-021-83886-7.
Sousa, André M. M., Ying Zhu, Mary Ann Raghanti, Robert R. Kitchen,
Marco Onorati, Andrew T. N. Tebbenkamp, Bernardo Stutz, et al. 2017.
“Molecular and Cellular Reorganization of Neural Circuits in the
Human Lineage.” Science 358 (6366): 1027–32. https://doi.org/10.1126/science.aan3456.
Stebbing, Justin, Keren Paz, Gary K. Schwartz, Leonard H. Wexler, Robert
Maki, Raphael E. Pollock, Ronnie Morris, et al. 2014.
“Patient-Derived Xenografts for Individualized Care
in Advanced Sarcoma.” Cancer 120 (13): 2006–15. https://doi.org/10.1002/cncr.28696.
Tacken, Paul J., I. Jolanda M. de Vries, Karlijn Gijzen, Ben Joosten,
Dayang Wu, Russell P. Rother, Susan J. Faas, et al. 2005.
“Effective Induction of Naive and Recall T-Cell Responses by
Targeting Antigen to Human Dendritic Cells via a Humanized
AntiDC-SIGN Antibody.” Blood 106 (4):
1278–85. https://doi.org/10.1182/blood-2005-01-0318.
Vepachedu, Ramarao, Sang-Wook Park, Neelam Sharma, and Jorge M. Vivanco.
2005. “Bacterial Expression and Enzymatic Activity Analysis of
ME1, a Ribosome-Inactivating Protein from Mirabilis Expansa.”
Protein Expression and Purification 40 (1): 142–51. https://doi.org/10.1016/j.pep.2004.12.005.
Wu, Guanming, and Robin Haw. 2017. “Functional Interaction Network
Construction and Analysis for Disease Discovery.” In, 235–53.
Springer New York. https://doi.org/10.1007/978-1-4939-6783-4_11.
Zhang, Jianming, Priscilla L. Yang, and Nathanael S. Gray. 2009.
“Targeting Cancer with Small Molecule Kinase Inhibitors.”
Nature Reviews Cancer 9 (1): 28–39. https://doi.org/10.1038/nrc2559.