Perturbation Detection Through Modeling of Gene Expression on a Latent Biological Pathway Network: A Bayesian Hierarchical Approach

REFERENCES

• Abbas, T., Olivier, M., Lopez, J., Houser, S., Xiao, G., Suresh-Kumar, G., Tomasz, M., Bargonetti, J. (2002), Differential Activation of p53 by the Various Adducts of Mitomycin C, The Journal of Biological Chemistry, 277, 40513–40519.
   PubMed Web of Science ®Google Scholar
• Allingham, J.S., Smith, R., Rayment, I. (2005), The Structural Basis of Blebbistatin Inhibition and Specificity for Myosin II, Nature Structural & Molecular Biology, 12, 378–379.
   PubMed Web of Science ®Google Scholar
• Alqurashi, N., Hashimi, S.M., Wei, M.Q. (2013), Chemical Inhibitors and microRNAs (miRNA) Targeting the Mammalian Target of Rapamycin (mTOR) Pathway: Potential for Novel Anticancer Therapeutics, International Journal of Molecular Sciences, 14, 3874–3900.
   PubMed Web of Science ®Google Scholar
• Bansal, M., Yang, J., Karan, C., Menden, M.P., Costello, J.C., Tang, H., Xiao, G., Li, Y., Allen, J., Zhong, R., Chen, B., Kim, M., Wang, T., Heiser, L.M., Realubit, R., Mattioli, M., Alvarez, M.J., Shen, Y., NCI-DREAM Community, Gallahan, D., Singer, D., Saez-Rodriguez, J., Xie, Y., Stolovitzky, G., and Califano, A., NCI-DREAM Community. (2014), A Community Computational Challenge to Predict the Activity of Pairs of Compounds.” Nature Biotechnology, 32, 1213–1222.
   Google Scholar
• Bollen, K.A. (1989), Structural Equations With Latent Variables, Hoboken, NJ: Wiley-Interscience.
   Google Scholar
• Braunstein, A., McShane, B., Piette, J., Jensen, S. (2011), A Hierarchical Bayesian Variable Selection Approach to Major League Baseball Hitting Metrics, Journal of Quantitative Analysis in Sports, 7, Article 2.
   Google Scholar
• Carvalho, C., Chang, J., Lucas, J., Wang, Q., Nevins, J., West, M. (2008), High-Dimensional Sparse Factor Modelling: Applications in Gene Expression Genomics, Journal of the American Statistical Association, 103, 1438–1456.
   PubMed Web of Science ®Google Scholar
• Carvalho, L.E., Lawrence, C.E. (2008), Centroid Estimation in Discrete High-Dimensional Spaces With Applications in Biology, Proceedings of the National Academy of Sciences, 105, 3209–3214.
   PubMed Web of Science ®Google Scholar
• Chuang, H.Y., Lee, E., Liu, Y.T., Lee, D., Ideker, T. (2007), Network-Based Classification of Breast Cancer Metastasis, Molecular Systems Biology, 3, 140.
   PubMed Web of Science ®Google Scholar
• Cosgrove, E.J., Yingchun, Z., Gardner, T.S., Kolaczyk, E.D. (2008), Predicting Gene Targets of Perturbations via Network-Based Filtering of mRNA Expression Compendia, BMC Bioinformatics, 24, 2482–2490.
   Web of Science ®Google Scholar
• Cressie, N. A. C. (1993), Statistics for Spatial Data, New York: Wiley.
   Google Scholar
• de Oliveira, V. (2012), Bayesian Analysis of Conditional Autoregressive Models, Annals of the Institute of Statistical Mathematics, 64, 107–133.
   Web of Science ®Google Scholar
• Bernardo, D., Thompson, M., Gardner, T., Chobot, S.E., Eastwood, E.L., Wojtovich, A.P., Elliott, S.J., Schaus, S.E., and Collins, J.J. (2005), Chemogenomic Profiling On A Genome-Wide Scale Using Reverse-Engineered Gene Networks, Nature Biotechnology, 23, 377–383.
   PubMed Web of Science ®Google Scholar
• Draghici, S., Khatri, P., Tarca, A.L., Amin, K., Done, A., Voichita, C., Georgescu, C., Romero, R. (2007), A Systems Biology Approach for Pathway Level Analysis, Genome Research, 17, 1537–1545.
   PubMed Web of Science ®Google Scholar
• Dudoit, S., Shaffer, J.P., Boldrick, J.C. (2003), Multiple Hypothesis Testing in Microarray Experiments, Statistical Science, 18, 71–103.
   Web of Science ®Google Scholar
• Faulon, J.L., Misra, M., Martin, S., Sale, K., Sapra, R. (2008), Genome Scale Enzyme-Metabolite and Drug-Target Interaction Predictions Sing the Signature Molecular Descriptor, Bioinformatics, 24, 225–233.
   PubMed Web of Science ®Google Scholar
• Figueiredo-Pereira, M.E., Chen, W.E., Li, J., Johdo, O. (1996), The Antitumor Drug Aclacinomycin A, which Inhibits the Degradation of Ubiquitinated Proteins, Shows Selectivity for the Chymotrypsin-Like Activity of the Bovine Pituitary 20 S Proteasome, Journal of Biological Chemistry, 271, 16455–16459.
   PubMed Web of Science ®Google Scholar
• Fritsche, M., Haessler, C., Brandner, G. (1993), Induction of Nuclear Accumulation of the Tumor-Suppressor Protein p53 by DNA Damaging Agents, Oncogene, 8, 307–318.
   PubMed Web of Science ®Google Scholar
• Gandhi, T., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Nagaraju, S., Periaswamy, B., Mishra, G., Nandakumar, K., Shen, B., Deshpande, N., Nayak, R., Sarker, M., Boeke, J. D., Parmigiani, G., Schultz, J., Bader, J. S., and Pandey, A. (2006), Analysis of the Human Protein Interactome and Comparison With Yeast, Worm and Fly Interaction Datasets, Nature Genetics, 38, 285–293.
   PubMed Web of Science ®Google Scholar
• Gelman, A. (2006), Prior Distributions for Variance Parameters in Hierarchical Models, Bayesian Analysis, 1, 515–533.
   Web of Science ®Google Scholar
• Gelman, A., Carlin, J.B., Stern, H.S., and Rubin, D.B. (2004), Bayesian Data Analysis, New York: Chapman & Hall/CRC.
   Google Scholar
• George, E.I., McCulloch, R.E. (1997), Approaches for Bayesian Variable Selection, Statistica Sinica, 7, 339–373.
   Web of Science ®Google Scholar
• Goodsell, D.S. (1999), The Molecular Perspective: Methotrexate, The Oncologist, 4, 340–341.
   PubMedGoogle Scholar
• Grandela, C., Pera, M.F., Grimmond, S.M., Kolle, G., Wolvetang, E.J. (2007), p53 is Required for Etoposide-Induced Apoptosis of Human Embryonic Stem Cells, Stem Cell Research, 1, 116–128.
   PubMed Web of Science ®Google Scholar
• Grenert, J.P., Sullivan, W. P., Fadden, P., Haystead, T. A., Clark, J., Mimnaugh, E., Krutzsch, H., Ochel, H. J., Schulte T. W., Sausville, E., Neckers, L. M., and Toft, D. O. (1997), The Amino-Terminal Domain of Heat Shock Protein 90 (hsp90) That Binds Geldanamycin is an ATP/ADP Switch Domain That Regulates hsp90 Conformation, Journal of Biological Chemistry, 272, 23843–23850.
   PubMed Web of Science ®Google Scholar
• Gu, J., Chen, Y., Li, S., Li, Y. (2010), Identification of Responsive Gene Modules by Network-Based Gene Clustering and Extending: Application to Inflammation and Angiogenesis, BMC Systems Biology, 4, 47.
   PubMed Web of Science ®Google Scholar
• Gupta, M., Fan, S., Zhan, Q., Kohn, K.W., O’Connor, P.M., Pommier, Y. (1997), Inactivation of p53 Increases the Cytotoxicity of Camptothecin in Human Colon HCT116 and Breast MCF-7 Cancer Cells, Clinical Cancer Research, 3, 1653–1660.
   PubMed Web of Science ®Google Scholar
• Hidaka, H., Inagaki, M., Kawamoto, S., and Sasaki, Y. (1984), Isoquinolinesulfonamides, Novel and Potent Inhibitors of Cyclic Nucleotide Dependent Protein Kinase and Protein Kinase C, Biochemistry, 23, 5036.
   PubMed Web of Science ®Google Scholar
• Huang, W.Y., Yang, P.M., Chang, Y.F., Marquez, V.E., Chen, C.C. (2011), Methotrexate Induces Apoptosis Through p53/p21-Dependent Pathway and Increases E-Cadherin Expression Through Downregulation of HDAC/EZH2, Biochemical Pharmacology, 81, 510–517.
   PubMed Web of Science ®Google Scholar
• Ideker, T., Ozier, O., Schwikowski, B., Siegel, A.F. (2002), Discovering Regulatory and Signalling Circuits in Molecular Interaction Networks, Bioinformatics, 18, S233–S240.
   PubMedGoogle Scholar
• Jaks, V., Jers, A., Kristjuhan, A., Maimets, T. (2001), p53 Protein Accumulation in Addition to the Transactivation Activity is Required for p53-Dependent Cell Cycle Arrest After Treatment of Cells With Camptothecin, Oncogene, 20, 1212–1219.
   PubMed Web of Science ®Google Scholar
• Jiang, Z., Gentleman, R. (2007), Extensions to Gene Set Enrichment, Bioinformatics, 23, 306–313.
   PubMed Web of Science ®Google Scholar
• Kanehisa, M., Goto, S. (2000), KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, 28, 27–30.
   PubMed Web of Science ®Google Scholar
• Kanehisa, M., Wasner, M., Reinhard, W., Haugwitz, U., Dohna, C. L., Mössner, J., and Engeland, K. (2006), From Genomics to Chemical Genomics: New Developments in KEGG, Nucleic Acids Research, 34, 354–357.
   PubMed Web of Science ®Google Scholar
• Karpinich, N.O., Tafani, M., Rothman, R.J., Russo, M.A., Farber, J.L. (2002), The Course of Etoposide-Induced Apoptosis From Damage to DNA and p53 Activation to Mitochondrial Release of Cytochrome c, Journal of Biological Chemistry, 277, 16547–16552.
   PubMed Web of Science ®Google Scholar
• Khatri, P., Draghici, S. (2005), Ontological Analysis of Gene Expression Data: Current Tools, Limitations, and Open Problems, Bioinformatics, 21, 3587–3595.
   PubMed Web of Science ®Google Scholar
• Krause, K., Wasner, M., Reinhard, W., Haugwitz, U., Dohna, C. L., Mössner, J., and Engeland, K. (2002), The Tumour Suppressor Protein p53 Can Repress Transcription of Cyclin B, Nucleic Acids Research, 22, 4410–4441.
   Google Scholar
• Kurz, E.U., Douglas, P., Lees-Miller, S.P. (2004), Doxorubicin Activates ATM-Dependent Phosphorylation of Multiple Downstream Targets in Part Through the Generation of Reactive Oxygen Species, Journal of Biological Chemistry, 279, 53272–53281.
   PubMed Web of Science ®Google Scholar
• Liao, J., Boscolo, R., Yang, Y., Tran, L. M., Sabatti, C., and Roychowdhury, V. P. (2003), Network Component Analysis: Reconstruction of Regulatory Signals in Biological Systems, Proceedings of the National Academy of Sciences, 100, 15522–15527.
   PubMed Web of Science ®Google Scholar
• Lindley, D.V., Smith, A.F. (1972), Bayes Estimates for the Linear Model, Journal of the Royal Statistical Society, Series B, 34, 1–41.
   Google Scholar
• Ling, B., Wei-Guo, Z. (2006), p53: Structure, Function and Therapeutic Applications, Journal of Cancer Molecules, 2, 141–153.
   Google Scholar
• Ling, Y.H., Naggar, A.K., Priebe, W., Perez-Soler, R. (1996), Cell Cycle-Dependent Cytotoxicity, G2/M Phase Arrest, and Disruption of p34cdc2/cyclin B1 Activity Induced by Doxorubicin in Synchronized P388 Cells, Molecular Pharmacology, 49, 832–841.
   PubMed Web of Science ®Google Scholar
• Liu, M., Liberzon, A., Kong, S. W., Lai, W. R., Park, P. J., Kohane, I. S., and Kasif, S. (2007), Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Model, PLoS Genetics, 3 e96.
   PubMedGoogle Scholar
• Lucas, J., Carvalho, C.M., Wang, Q., Bild, A., Nevins, J.R., West, M. (2006), Sparse Statistical Modelling in Gene Expression Genomics, Bayesian Inference for Gene Expression and Proteomics, 14, 155–176.
   Google Scholar
• Lucas, J.E., Kung, H.-N., Chi, J.-T. (2010), Latent Factor Analysis to Discover Pathway-Associated Putative Segmental Aneuploidies in Human Cancers, PLoS Computational Biology, 6, e1000920.
   Google Scholar
• Ma, H., Zhao, H. (2012), iFad: An Integrative Factor Analysis Model for Drug-Pathway Association Inference, Bioinformatics, 28, 1911–1918.
   PubMed Web of Science ®Google Scholar
• Maliga, Z., Kapoor, T.M., Mitchison, T.J. (2002), Evidence That Monastrol is an Allosteric Inhibitor of the Mitotic Kinesin Eg5, Chemical Biology, 9, 989–996.
   PubMed Web of Science ®Google Scholar
• Malik, M., Nitiss, K.C., Enriques-Rios, V., Nitiss, J.L. (2006), Roles of Nonhomlogous End-Joinng Pathways in Surviving Topoisomerase II-Mediated DNA Damage, Molecular Cancer Therapeutics, 5, 1405–1414.
   Google Scholar
• Marbach, D., Costello, C.J., Küffner, R., Nicole, M.V., Prill, R., Camacho, D., Allison, K., Consortium, T.D., Kellis, M., Collins, J.J., Stolovitzky, G.. (2012), Wisdom of Crowds for Robust Gene Network Inference, Nature Methods, 9, 796–804.
   PubMed Web of Science ®Google Scholar
• Nakada, S., Katsuki, Y., Imoto, I., Yokoyama, T., Nagasawa, M., Inazawa, J., Mizutani, S. (2006), Early G2/M Checkpoint Failure as a Molecular Mechanism Underlying Etoposide-Induced Chromosomal Aberrations, Journal of Clinical Investigation, 116, 80–89.
   PubMed Web of Science ®Google Scholar
• Nam, D., Kim, S.Y. (2008), Gene-Set Approach for Expression Pattern Analysis, Briefings in Bioinformatics, 9, 189–197.
   PubMed Web of Science ®Google Scholar
• Neckers, L., Schulte, T.W., Mimnaugh, E. (1999), Geldanamycin as a Potential Anti-Cancer Agent: Its Molecular Target and Biochemical Activity, Investigational New Drugs, 17, 361–373.
   PubMed Web of Science ®Google Scholar
• Obrig, T.G., Culp, W.J., McKeehan, W.L., Hardesty, B. (1971), The Mechanism by Which Cycloheximide and Related Glutarimide Antibiotics Inhibit Peptide Synthesis on Reticulocyte Ribosomes, Journal of Biological Chemistry, 246, 174–181.
   PubMed Web of Science ®Google Scholar
• Pham, L., Christadore, L., Schaus, S., Kolaczyk, E.D. (2011), Network-Based Prediction for Sources of Transcriptional Dysregulation via Latent Pathway Identification Analysis, Proceedings of the National Academy of Sciences, 108, 13347–13352.
   PubMed Web of Science ®Google Scholar
• Pommier, Y., Leo, E., Zhang, H., Marchand, C. (2012), DNA Topoisomerases and Their Poisoning by Anticancer and Antibacterial Drugs, Chemical Biology, 17, 421–433.
   Web of Science ®Google Scholar
• Prill, R.J., Saez-Rodriguez, J., Alexopoulos, L.G., Sorger, P.K., Stolovitzky, G. (2011), Crowdsourcing Network Inference: The DREAM4 Predictive Signaling Network Challenge, Science, 4, mr7.
   Google Scholar
• Rao, C.V., Kurkjian, C.D., Yamada, H.Y. (2012), Mitosis-Targeting Natural Products for Cancer Prevention and Therapy, Current Drug Targets, 13, 1820–1830.
   PubMed Web of Science ®Google Scholar
• Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B. J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., Stark, C., Ho, Y., Botstein, D., Andrews, B., Boone, C., Troyanskya, O. G., Ideker, T., Dolinski, K., Batada, N. N., and Tyers, M. (2006), Comprehensive Curation and Analysis of Global Interaction Networks in Saccharomyces Cerevisiae, Journal of Biology, 5, 11.
   PubMedGoogle Scholar
• Rivals, I., Personnaz, L., Taing, L., and (2007), Enrichment or Depletion of a GO Category Within a Class of Genes: Which Test? Bioinformatics, 23, 401–407.
   PubMed Web of Science ®Google Scholar
• Roguev, A., Bandyopadhyay, S., Zofall, M., Zhang, K., Fischer, T., Collins, S. R., Qu, H., Shales, M., Park, H. O., Hayles, J., Hoe, K. L., Kim, D. U., Ideker, T., Grewal, S. I., Weissman, J. S., and Krogan, N. J. (2008), Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast, Science, 322, 405–410.
   PubMed Web of Science ®Google Scholar
• Storey, J.D., Tibshirani, R. (2003), Statistical Significance for Genome-Wide Studies, Proceedings of the National Academy of Sciences, 100, 9440–9445.
   Google Scholar
• Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., and Mesirov, J. P. (2005), Gene Set Enrichment Analysis: A Knowledge-Based Approach for Interpreting Genome-Wised Expression Profiles, Proceedings of the National Academy of Sciences of the United States of America, 102, 15545–15550.
   PubMed Web of Science ®Google Scholar
• Terstappen, G.C., Schlüpen, C., Raggiaschi, R., Gaviraghi, G. (2007), Target Deconvolution Strategies in Drug Discovery, Nature Reviews, 6, 891–903.
   Web of Science ®Google Scholar
• (2000), Gene Ontology: Tool for the Unification of Biology, Nature Genetics, 25, 25–29.
   PubMed Web of Science ®Google Scholar
• Tomasz, M. (1995), Mitomycin C: Small, Fast and Deadly (But Very Selective), Chemical Biology, 2, 575–579.
   PubMed Web of Science ®Google Scholar
• van Dyk, D.A., Park, T. (2008), Partially Collapsed Gibbs Samplers: Theory and Methods, Journal of the American Statistical Association, 482, 790–796.
   Web of Science ®Google Scholar
• Vanhaecke, T., Papeleu, P., Elaut, G., Rogiers, V. (2004), Trichostatin A-Like Hydroxamate Histone Deacetylase Inhibitors as Therapeutic Agents: Toxicological Point of View, Current Medicinal Chemistry, 11, 1629–1643.
   PubMed Web of Science ®Google Scholar
• Verweij, J., Pinedo, H.M. (1990), Mitomycin C: Mechanism of Action, Usefulness and Limitations, Anticancer Drugs, 1, 5–13.
   PubMedGoogle Scholar
• Vogelstein, B., Kinzler, K.W. (2004), Cancer Genes and the Pathways They Control, Nature Medicine, 10, 789–799.
   PubMed Web of Science ®Google Scholar
• Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S., and Bork, P. (2002), Comparative Assessment of Large-Scale Data Sets of Protein-Protein Interactions, Nature, 417, 6887.
   Google Scholar
• Wall, M.M. (2004), A Close Look at the Spatial Structure Implied by the CAR and SAR Models, Journal of Statistical Planning and Inference, 121, 311–324.
   Web of Science ®Google Scholar
• Wang, S., Konorev, E., Kotamraju, S., Joseph, J., Kalivendi, S., Kalyanaraman, B. (2004), Doxorubicin Induces Apoptosis in Normal and Tumor Cells via Distinctly Different Mechanisms, Journal of Biological Chemistry, 279, 25535–25543.
   PubMed Web of Science ®Google Scholar
• Wei, P., Pan, W. (2008), Incorporating Gene Networks Into Statistical Tests for Genomic Data via a Spatially Correlated Mixture Model, Bioinformatics, 24, 404–411.
   PubMed Web of Science ®Google Scholar
• Yamanishi, Y., Araki, M., Gutteridge, A., Honda, W., Kanehisa, M. (2008), Prediction of Drug-Target Interaction Networks From the Integration of Chemical and Genomic Spaces, Bioinformatics, 24, 232–240.
   PubMed Web of Science ®Google Scholar
• Zhou, M., Gu, L., Li, F., Zhu, Y., Woods, W.G., Findley, H.W. (2002), DNA Damage Induces a Novel p53-Survivin Signaling Pathway Regulating Cell Cycle and Apoptosis in Acute Lymphoblastic Leukemia Cells, Molecular Pharmacology, 303, 124–131.
   Google Scholar