The DOI matches its Crossref record; 128 of the 129 references it cites were found in a registry or an index.
An Integrated Approach to Uncover Drivers of Cancer
Open accessAbstract
Systematic characterization of cancer genomes has revealed a staggering number of diverse aberrations that differ among individuals, such that the functional importance and physiological impact of most tumor genetic alterations remain poorly defined. We developed a computational framework that integrates chromosomal copy number and gene expression data for detecting aberrations that promote cancer progression. We demonstrate the utility of this framework using a melanoma data set. Our analysis correctly identified known drivers of melanoma and predicted multiple tumor dependencies. Two dependencies, TBC1D16 and RAB27A, confirmed empirically, suggest that abnormal regulation of protein trafficking contributes to proliferation in melanoma. Together, these results demonstrate the ability of integrative Bayesian approaches to identify candidate drivers with biological, and possibly therapeutic, importance in cancer.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Similarly, CONEXIC (Akavia et al., 2010) also uses a BN to integrate gene expression and copy number variation from tumour samples to identify driver mutations.”
From Using machine learning approaches for multi-omics data analysis: A review (2021) · cites this paper as Akavia et al., 2010
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
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., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
Bootstrap methods: another look at the jackknife
Efron, B. (1979) · The Annals of Statistics · doi:10.1214/aos/1176344552 · Cited by 17,602
Causality: Models, Reasoning, and Inference
Pearl, J. (2009) · doi:10.1017/cbo9780511803161 · Cited by 11,653
Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., et al. (1999) · Science · doi:10.1126/science.286.5439.531 · Cited by 11,516
Term-Weighting Approaches in Automatic Text Retrieval
Salton, G., & Buckley, C. (1988) · Information Processing & Management · doi:10.1016/0306-4573(88)90021-0 · Cited by 11,421
In silico prediction of protein-protein interactions in human macrophages
Souiai, O., Guerfali, F. Z., Miled, S. B., Brun, C., & Benkahla, A. (2014) · BMC Research Notes · doi:10.1186/1756-0500-7-157 · Cited by 10,785
Significance analysis of microarrays applied to the ionizing radiation response
Tusher, V. G., Tibshirani, R., & Chu, G. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.091062498 · Cited by 10,568
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
CAUSALITY: MODELS, REASONING AND INFERENCE
Hitchcock, C., & Pearl, J. (2001) · The Philosophical Review · doi:10.2307/3182612 · Cited by 4,827
The landscape of somatic copy-number alteration across human cancers
Beroukhim, R., Mermel, C. H., Porter, D., Wei, G., Raychaudhuri, S., Donovan, J., Barretina, J., Boehm, J. S., Dobson, J., Urashima, M., et al. (2010) · Nature · doi:10.1038/nature08822 · Cited by 4,017
Stratton, M. R., Campbell, P. J., & Futreal, P. A. (2009) · Nature · doi:10.1038/nature07943 · Cited by 3,625
Using Bayesian Networks to Analyze Expression Data
Friedman, N., Michal Linial, B., Nachman, I., & Pe’er, D. (2000) · Journal of Computational Biology · doi:10.1089/106652700750050961 · Cited by 3,248
Causality: models, reasoning, and inference
(2000) · Choice Reviews Online · doi:10.5860/choice.38-1494a · Cited by 2,968
Baumann, H., & Gauldie, J. (1994) · Immunology Today · doi:10.1016/0167-5699(94)90137-6 · Cited by 2,907
Pinkel, D., Segraves, R., Sudar, D., Clark, S. M., Poole, I., Kowbel, D., Collins, C. C., Kuo, W.-L., Chen, C., Zhai, Y., et al. (1998) · Nature Genetics · doi:10.1038/2524 · Cited by 2,238
A comprehensive catalogue of somatic mutations from a human cancer genome
Pleasance, E. D., Cheetham, R. K., Stephens, P. J., McBride, D. J., Humphray, S. J., Greenman, C. D., Varela, I., Lin, M.-L., Ordóñez, G. R., Bignell, G. R., et al. (2010) · Nature · doi:10.1038/nature08658 · Cited by 1,696
Osborn, L., Hession, C. A., Tizard, R., Vassallo, C., Luhowskyj, S., Rosso, G. C., & Lobb, R. R. (1989) · Cell · doi:10.1016/0092-8674(89)90775-7 · Cited by 1,690
Segal, E., Shapira, M., Regev, A., Pe’er, D., Botstein, D., Koller, D., & Friedman, N. (2003) · Nature Genetics · doi:10.1038/ng1165 · Cited by 1,678
Witten, D., Tibshirani, R. J., & Hastie, T. J. (2009) · Biostatistics · doi:10.1093/biostatistics/kxp008 · Cited by 1,549
Garraway, L. A., Widlund, H. R., Rubin, M. A., Getz, G., Berger, A. J., Ramaswamy, S., Beroukhim, R., Milner, D. A., Granter, S. R., Du, J., et al. (2005) · Nature · doi:10.1038/nature03664 · Cited by 1,548
Self-citationTHE SIGNIFICANCE OF THE DIFFERENCE BETWEEN TWO MEANS WHEN THE POPULATION VARIANCES ARE UNEQUAL
Welch, B. L. (1938) · Biometrika · doi:10.1093/biomet/29.3-4.350 · Cited by 1,506
The transcriptional network for mesenchymal transformation of brain tumours
Carro, M. S., Lim, W. K., Alvarez, M. J., Bollo, R. J., Zhao, X., Snyder, E. Y., Sulman, E. P., Anne, S. L., Doetsch, F. K., Colman, H., et al. (2009) · Nature · doi:10.1038/nature08712 · Cited by 1,268
MITF: master regulator of melanocyte development and melanoma oncogene
Levy, C., Khaled, M., & Fisher, D. E. (2006) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2006.07.008 · Cited by 1,169
Beroukhim, R., Getz, G. A., Nghiemphu, L., Barretina, J., Hsueh, T., Linhart, D., Vivanco, I., Lee, J. C., Huang, J. H. Y., Alexander, S., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0710052104 · Cited by 1,076
Control of Macroautophagy by Calcium, Calmodulin-Dependent Kinase Kinase-β, and Bcl-2
Høyer-Hansen, M., Bastholm, L., Szyniarowski, P., Campanella, M., Szabadkai, G., Farkas, T., Bianchi, K., Fehrenbacher, N., Elling, F., Rizzuto, R., et al. (2007) · Molecular Cell · doi:10.1016/j.molcel.2006.12.009 · Cited by 1,072
Promiscuous Mutations Activate the Noncanonical NF-κB Pathway in Multiple Myeloma
Keats, J. J., Fonseca, R., Chesi, M., Schop, R., Baker, A., Chng, W.-J., Van Wier, S., Tiedemann, R., Shi, C.-X., Sebag, M., et al. (2007) · Cancer Cell · doi:10.1016/j.ccr.2007.07.003 · Cited by 983
Annunziata, C. M., Davis, R. E., Demchenko, Y., Bellamy, W., Gabrea, A., Zhan, F., Lenz, G., Hanamura, I., Wright, G., Xiao, W., et al. (2007) · Cancer Cell · doi:10.1016/j.ccr.2007.07.004 · Cited by 952
Trevisani, M., Siemens, J., Materazzi, S., Bautista, D. M., Nassini, R., Campi, B., Imamachi, N., Andrè, E., Patacchini, R., Cottrell, G. S., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0705923104 · Cited by 775
Melanocytes and theMicrophthalmiaTranscription Factor Network
Steingrı́msson, E., Copeland, N. G., & Jenkins, N. A. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.38.072902.092717 · Cited by 762
McGill, G. G., Horstmann, M. A., Widlund, H. R., Du, J., Motyckova, G., Nishimura, E. K., Lin, Y., Ramaswamy, S., Avery, W., Ding, H., et al. (2002) · Cell · doi:10.1016/s0092-8674(02)00762-6 · Cited by 760
In vivo Switching of Human Melanoma Cells between Proliferative and Invasive States
Hoek, K. S., Eichhoff, O. M., Schlegel, N. C., Döbbeling, U., Kobert, N., Schaerer, L., Hemmi, S., & Dummer, R. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-2491 · Cited by 743
A module map showing conditional activity of expression modules in cancer
Segal, E., Friedman, N., Koller, D., & Regev, A. (2004) · Nature Genetics · doi:10.1038/ng1434 · Cited by 685
Pankiv, S., Alemu, E. A., Brech, A., Bruun, J., Lamark, T., Øvervatn, A., Bjørkøy, G., & Johansen, T. (2010) · The Journal of Cell Biology · doi:10.1083/jcb.200907015 · Cited by 684
Pratilas, C. A., Taylor, B. S., Ye, Q., Viale, A. J., Sander, C., Solit, D. B., & Rosen, N. X. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900780106 · Cited by 626
Vallabhapurapu, S., Matsuzawa, A., Zhang, W., Tseng, P., Keats, J. J., Wang, H., Vignali, D. A. A., Bergsagel, P. L., & Karin, M. (2008) · Nature Immunology · doi:10.1038/ni.1678 · Cited by 605
Hoek, K. S., Schlegel, N. C., Brafford, P. A., Sucker, A., Ugurel, S., Kumar, R., Weber, B. L., Nathanson, K. L., Phillips, D. J., Herlyn, M., et al. (2006) · Pigment Cell Research · doi:10.1111/j.1600-0749.2006.00322.x · Cited by 579
PTEN-deficient cancers depend on PIK3CB
Wee, S., Wiederschain, D., Maira, S., Loo, A. T., Miller, C., deBeaumont, R. S., Stegmeier, F., Yao, Y.-M. M., & Lengauer, C. (2008) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0802655105 · Cited by 565
Malignant melanoma: genetics and therapeutics in the genomic eraPreprint
Chin, L., Garraway, L. A., & Fisher, D. E. (2006) · Genes & Development · doi:10.1101/gad.1437206 · Cited by 524
Fischer, T., Stone, R. M., DeAngelo, D. J., Galinsky, I., Estey, E., Lanza, C., Fox, E., Ehninger, G., Feldman, E. J., Schiller, G. J., et al. (2010) · Journal of Clinical Oncology · doi:10.1200/jco.2010.28.9678 · Cited by 504
Nielsen, M. S., Madsen, P., Christensen, E. I., Nykjær, A., Gliemann, J., Kasper, D., Pohlmann, R., & Petersen, C. M. (2001) · The EMBO Journal · doi:10.1093/emboj/20.9.2180 · Cited by 457
KLF6 , a Candidate Tumor Suppressor Gene Mutated in Prostate Cancer
Narla, G., Heath, K. E., Reeves, H. L., Li, D., Giono, L. E., Kimmelman, A. C., Glucksman, M., Narla, J., Eng, F. J., Chan, A. M.-L., et al. (2001) · Science · doi:10.1126/science.1066326 · Cited by 442
An Oncogenomics-Based In Vivo RNAi Screen Identifies Tumor Suppressors in Liver Cancer
Zender, L., Xue, W., Zuber, J. A., Semighini, C. P., Krasnitz, A., Ma, B., Zender, P., Kubicka, S., Luk, J. M., Schirmacher, P., et al. (2008) · Cell · doi:10.1016/j.cell.2008.09.061 · Cited by 428
Raychaudhuri, S., Plenge, R. M., Rossin, E. J., Ng, A., Purcell, S., Sklar, P. B., Scolnick, E. M., Xavier, R. J., Altshuler, D., & Daly, M. J. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000534 · Cited by 427
Goedert, M., Cuenda, A., Craxton, M., Jakes, R., & Cohen, P. (1997) · The EMBO Journal · doi:10.1093/emboj/16.12.3563 · Cited by 420
Du, J., Widlund, H. R., Horstmann, M. A., Ramaswamy, S., Ross, K. N., Huber, W. E., Nishimura, E. K., Golub, T. R., & Fisher, D. E. (2004) · Cancer Cell · doi:10.1016/j.ccr.2004.10.014 · Cited by 420
Turner, N. C., Lambros, M. B. K., Horlings, H. M., Pearson, A., Sharpe, R., Natrajan, R., Geyer, F. C., van Kouwenhove, M., Kreike, B., Mackay, A. G., et al. (2010) · Oncogene · doi:10.1038/onc.2009.489 · Cited by 420
Beroukhim, R., Brunet, J.-P., Napoli, A. D., Mertz, K. D., Seeley, A., Pires, M. M., Linhart, D., Worrell, R., Moch, H., Rubin, M. A., et al. (2009) · Cancer Research · doi:10.1158/0008-5472.can-09-0146 · Cited by 413
The Cl-/H+ antiporter ClC-7 is the primary chloride permeation pathway in lysosomes
Graves, A. R., Curran, P. K., Smith, C. L., & Mindell, J. A. (2008) · Nature · doi:10.1038/nature06907 · Cited by 399
GOLPH3 modulates mTOR signalling and rapamycin sensitivity in cancer
Scott, K. L., Kabbarah, O., Liang, M., Ivanova, E. V., Anagnostou, V., Wu, J., Dhakal, S., Wu, M., Chen, S., Feinberg, T. Y., et al. (2009) · Nature · doi:10.1038/nature08109 · Cited by 354
Yang, R., Lee, M., Hu, H., Pollin, T. I., Ryan, A. S., Nicklas, B. J., Snitker, S., Horenstein, R. B., Hull, K., Goldberg, N. H., et al. (2006) · PLoS Medicine · doi:10.1371/journal.pmed.0030287 · Cited by 354
Pielberg, G., Golovko, A., Sundström, E., Čurik, I., Lennartsson, J., Seltenhammer, M. H., Druml, T., Binns, M. M., Fitzsimmons, C., Lindgren, G., et al. (2008) · Nature Genetics · doi:10.1038/ng.185 · Cited by 335
Automated Network Analysis Identifies Core Pathways in Glioblastoma
Cerami, E. G., Demir, E., Schultz, N. D., Taylor, B. S., & Sander, C. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008918 · Cited by 331
Itoh, S., Kim, H. W., Nakagawa, O., Ozumi, K., Lessner, S. M., Aoki, H., Akram, K., McKinney, R. D., Ushio‐Fukai, M., & Fukai, T. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m709463200 · Cited by 323
Probabilistic models of indexing and searching
Robertson, S. E., van Rijsbergen, C. J., & Porter, M. (1980) · doi:10.5555/636669.636673 · Cited by 314
Identification of Common Transcriptional Regulatory Elements in Interleukin-17 Target Genes
Shen, F., Hu, Z., Goswami, J., & Gaffen, S. L. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m604597200 · Cited by 299
Modeling Genomic Diversity and Tumor Dependency in Malignant Melanoma
Lin, W. M., Baker, A. C., Beroukhim, R., Winckler, W., Feng, W., Marmion, J. M., Laine, E., Greulich, H. E., Tseng, H., Gates, C., et al. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-2615 · Cited by 296
Oncogenic BRAF Regulates Melanoma Proliferation through the Lineage Specific Factor MITF
Wellbrock, C., Rana, S., Paterson, H., Pickersgill, H., Brummelkamp, T. R., & Marais, R. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002734 · Cited by 289
Novel MITF targets identified using a two‐step DNA microarray strategy
Hoek, K. S., Schlegel, N. C., Eichhoff, O. M., Widmer, D. S., Praetorius, C., Einarsson, S. O., Valgeirsdóttir, S., Bergsteinsdóttir, K., Schepsky, A., Dummer, R., et al. (2008) · Pigment Cell & Melanoma Research · doi:10.1111/j.1755-148x.2008.00505.x · Cited by 276
Acquired copy number alterations in adult acute myeloid leukemia genomes
Walter, M. J., Payton, J. E., Ries, R. E., Shannon, W. D., Deshmukh, H., Zhao, Y., Baty, J., Heath, S. E., Westervelt, P., Watson, M. A., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903091106 · Cited by 251
GREB1 is a critical regulator of hormone dependent breast cancer growth
Rae, J. M., Johnson, M. D., Scheys, J. O., Cordero, K. E., Larios, J. M., & Lippman, M. E. (2005) · Breast Cancer Research and Treatment · doi:10.1007/s10549-005-1483-4 · Cited by 251
The metallochaperone Atox1 plays a critical role in perinatal copper homeostasis
Hamza, I., Faisst, A. M., Prohaska, J. R., Chen, J., Gruß, P., & Gitlin, J. D. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.111058498 · Cited by 246
Wang, K., Saito, M., Bisikirska, B. C., Alvarez, M. J., Lim, W. K., Rajbhandari, P., Shen, Q. “., Nemenman, I. M., Basso, K., Margolin, A. A., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1563 · Cited by 239
Genetic regulators of large-scale transcriptional signatures in cancer
Adler, A. S., Lin, M., Horlings, H. M., Nuyten, D. S. A., van de Vijver, M. J., & Chang, H. Y. (2006) · Nature Genetics · doi:10.1038/ng1752 · Cited by 232
Lipocalin 2 Is Required for Pulmonary Host Defense against Klebsiella Infection
Chan, Y. R., Liu, J. S., Pociask, D. A., Zheng, M., Mietzner, T. A., Berger, T., Mak, T. W., Clifton, M. C., Strong, R. K., Ray, P., et al. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0803282 · Cited by 219
Hanein, S., Martin, E., Boukhris, A., Byrne, P. C., Goizet, C., Hamri, A., Benomar, A., Lossos, A., Denora, P. S., Fernández, J. C. F., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.03.004 · Cited by 217
Influence of mate drinking, hot beverages and diet on esophageal cancer risk in south america
Castellsagué, X., Mu�oz, N., Stéfani, E. D., Victora, C. G., Castelletto, R. H., & Rol�n, P. A. (2000) · International Journal of Cancer · doi:10.1002/1097-0215(20001115)88:4 · Cited by 205
Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians
Nan, H., Kraft, P., Hunter, D. J., & Han, J. (2009) · International Journal of Cancer · doi:10.1002/ijc.24327 · Cited by 205
Essential role for Atox1 in the copper-mediated intracellular trafficking of the Menkes ATPase
Hamza, I., Prohaska, J., & Gitlin, J. D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0336230100 · Cited by 203
Yoshida, H., Jono, H., Kai, H., & Li, J. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m509526200 · Cited by 199
Suzuki, T., Li, W., Zhang, Q. H., Karim, A., Novak, E. K., Sviderskaya, E. V., Hill, S. P., Bennett, D. C., Levin, A. V., Nieuwenhuis, H. K., et al. (2002) · Nature Genetics · doi:10.1038/ng835 · Cited by 187
Zhang, R., Xu, Y., Ekman, N., Wu, Z., Wu, J., Alitalo, K. K., & Wang, M. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m310678200 · Cited by 173
Ueda, Y., & Richmond, A. J. (2006) · Pigment Cell Research · doi:10.1111/j.1600-0749.2006.00304.x · Cited by 164
Bric, A., Miething, C., Bialucha, C. U., Scuoppo, C., Zender, L., Krasnitz, A., Xuan, Z., Zuber, J. A., Wigler, M. H., Hicks, J. B., et al. (2009) · Cancer Cell · doi:10.1016/j.ccr.2009.08.015 · Cited by 162
Itoh, T., Satoh, M., Kanno, E., & Fukuda, M. (2006) · Genes to Cells · doi:10.1111/j.1365-2443.2006.00997.x · Cited by 158
Li, Y., Li, L., Brown, T. J., & Heldin, P. (2007) · International Journal of Cancer · doi:10.1002/ijc.22550 · Cited by 155
Structural basis for recognition of acidic-cluster dileucine sequence by GGA1
Shiba, T., Takatsu, H., Nogi, T., Matsugaki, N., Kawasaki, M., Igarashi, N., Suzuki, M., Kato, R., Earnest, T. N., Nakayama, K., et al. (2002) · Nature · doi:10.1038/415937a · Cited by 146
Lee, S., Pe’er, D., Dudley, A. M., Church, G. M., & Koller, D. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601852103 · Cited by 132
Learning Module NetworksPreprint
Segal, E., Pe’er, D., Regev, A., Koller, D., & Friedman, N. (2012) · arXiv (Cornell University) · doi:10.48550/arxiv.1212.2517 · Cited by 131
Mig-6 controls EGFR trafficking and suppresses gliomagenesis
Ying, H., Zheng, H., Scott, K. L., Wiedemeyer, R., Yan, H., Lim, C., Huang, J. S., Dhakal, S., Ivanova, E. V., Xiao, Y., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914930107 · Cited by 131
Nomiyama, T., Nakamachi, T., Gizard, F., Heywood, E. B., Jones, K. L., Ohkura, N., Kawamori, R., Conneely, O. M., & Bruemmer, D. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m603436200 · Cited by 127
Seye, C. I., Yu, N., JAIN, R. K., Kong, Q., Minor, T., Newton, J., Erb, L., González, F. A., & Weisman, G. A. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m301439200 · Cited by 122
Chiavérini, C., Beuret, L., Flori, E., Buscà, R., Abbe, P., Bille, K., Bahadoran, P., Ortonne, J. P., Bertolotto, C., & Ballotti, R. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m800130200 · Cited by 120
Satijn, D. P. E., Olson, D. J., van der Vlag, J., Hamer, K. M., Lambrechts, C., Masselink, H., Gunster, M. J., Sewalt, R. G. A. B., DRIEL, R. V., & Otte, A. P. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.10.6076 · Cited by 114
Dynek, J. N., Chan, S. M., Liu, J., Zha, J., Fairbrother, W. J., & Vucic, D. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-6622 · Cited by 113
Taub, N., Teis, D., Ebner, H. L., Hess, M. W., & Huber, L. A. (2007) · Molecular Biology of the Cell · doi:10.1091/mbc.e07-02-0098 · Cited by 113
Wang, J.-S., Wang, F.-B., Zhang, Q., Shen, Z., & Shao, Z. (2008) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-07-0162 · Cited by 110
Chiang, P. W., Oiso, N., Gautam, R., Suzuki, T., Swank, R. T., & Spritz, R. A. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m300090200 · Cited by 108
Hunziker, W., & Peters, P. J. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.25.15734 · Cited by 107
Knecht, W., Cottrell, G. S., Amadesi, S., Mohlin, J., Skåregärde, A., Gedda, K., Peterson, A., Chapman, K., Hollenberg, M. D., Vergnolle, N., et al. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m703840200 · Cited by 104
A genomic screen identifies TYRO3 as a MITF regulator in melanoma
Zhu, S., Wurdak, H., Wang, Y., Galkin, A., Tao, H., Li, J., Lyssiotis, C. A., Yan, F., Tu, B. P., Miraglia, L. J., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909292106 · Cited by 101
Rab7 and Rab27a control two motor protein activities involved in melanosomal transport
Jordens, I., Westbroek, W., Marsman, M., Rocha, N., Mommaas, M., Huizing, M., Lambert, J., Naeyaert, J. M., & Neefjes, J. (2006) · Pigment Cell Research · doi:10.1111/j.1600-0749.2006.00329.x · Cited by 98
Ludwig, R. J., Zollner, T. M., Santoso, S., Hardt, K., Gille, J., Baatz, H., Johann, P. S., Pfeffer, J., Radeke, H. H., Schön, M. P., et al. (2005) · Journal of Investigative Dermatology · doi:10.1111/j.0022-202x.2005.23912.x · Cited by 97
Piaggi, S., Raggi, C., Corti, A., Pitzalis, E., Mascherpa, M. C., Saviozzi, M., Alfonso Pompella, C., & Casini, A. (2010) · Carcinogenesis · doi:10.1093/carcin/bgq031 · Cited by 96
MC1R Variants Increase Risk of Melanomas Harboring BRAF Mutations
Fargnoli, M. C., Pike, K. M., Pfeiffer, R. M., Tsang, S. X., Rozenblum, E., Munroe, D. J., Golubeva, Y. G., Calista, D., Seidenari, S., Massi, D., et al. (2008) · Journal of Investigative Dermatology · doi:10.1038/jid.2008.67 · Cited by 95
GREB1 is a novel androgen‐regulated gene required for prostate cancer growth
Rae, J. M., Johnson, M. D., Cordero, K. E., Scheys, J. O., Larios, J. M., Gottardis, M. M., Pienta, K. J., & Lippman, M. E. (2006) · The Prostate · doi:10.1002/pros.20403 · Cited by 87
SCOTT, G. A., McClelland, L. A., Fricke, A. F., & Fender, A. B. (2008) · Journal of Investigative Dermatology · doi:10.1038/jid.2008.329 · Cited by 86
Revised Nomenclature for Mammalian Vacuolar-Type H+-ATPase Subunit Genes
Smith, A. N., Lovering, R. C., Futai, M., Takeda, J., Brown, D., & Karet, F. E. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00397-6 · Cited by 86
Confirmation of a BRAF mutation‐associated gene expression signature in melanoma
Johansson, P. A., Pavey, S. J., & Hayward, N. K. (2007) · Pigment Cell Research · doi:10.1111/j.1600-0749.2007.00375.x · Cited by 83
Knebel, A., Haydon, C. E., MORRICE, N. A., & Cohen, P. (2002) · Biochemical Journal · doi:10.1042/bj20020916 · Cited by 80
Analysis of a Truncated Form of Cathepsin H in Human Prostate Tumor Cells
Waghray, A., Keppler, D., Sloane, B. F., Schuger, L. A., & Chen, Y. Q. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m109557200 · Cited by 74
Vetrini, F., Auricchio, A., Du, J., Angeletti, B., Fisher, D. E., Ballabio, A., & Marigo, V. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.15.6550-6559.2004 · Cited by 74
Palmer, C. D., Mutch, B. E., Workman, S., McDaid, J., Horwood, N. J., & Foxwell, B. M. J. (2007) · Blood · doi:10.1182/blood-2007-07-102343 · Cited by 73
Novel Role for RGS1 in Melanoma Progression
Rangel, J., Nosrati, M., Leong, S. P. L., Haqq, C., Miller, J. R., Sagebiel, R. W., & Kashani–Sabet, M. (2008) · The American Journal of Surgical Pathology · doi:10.1097/pas.0b013e31816fd53c · Cited by 72
Identification of Survival Genes in Human Glioblastoma Cells by Small Interfering RNA Screening
Thaker, N. G., Zhang, F., McDonald, P. R., Shun, T. Y., Lewen, M. D., Pollack, I. F., & Lazo, J. S. (2009) · Molecular Pharmacology · doi:10.1124/mol.109.058024 · Cited by 72
Zou, L., Zhou, J., Zhang, J., Li, J., Liu, N., Chai, L., Li, N., Liu, T., Li, L., Xie, Z., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0905684106 · Cited by 69
The MICAL proteins and rab1: a possible link to the cytoskeleton?
Fischer, J., Weide, T., & Barnekow, A. (2005) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2004.12.182 · Cited by 67
CK2 phosphorylation of eukaryotic translation initiation factor 5 potentiates cell cycle progression
Homma, M. K., Wada, I., Suzuki, T., Yamaki, J., Krebs, E. G., & Homma, Y. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506791102 · Cited by 64
Comparative evolutionary analysis of VPS33 homologues: genetic and functional insights
Gissen, P., Johnson, C. A., Gentle, D., Hurst, L. D., Doherty, A. J., O’Kane, C. J., Kelly, D. A., & Maher, E. R. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi137 · Cited by 61
Bellanger, S., Gramont, A. D. E., & Sobczak‐Thépot, J. (2007) · Oncogene · doi:10.1038/sj.onc.1210539 · Cited by 56
Wang, L., Cao, X., Chen, Q., Zhu, T., Zhu, H., & Li, Z. (2009) · Cancer Science · doi:10.1111/j.1349-7006.2009.01246.x · Cited by 55
Munc18-Syntaxin Complexes and Exocytosis in Human Platelets
Houng, A. K., Polgár, J., & Reed, G. L. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m212465200 · Cited by 52
Schallreuter, K. U., Rübsam, K., Chavan, B., Zothner, C., Gillbro, J. M., Spencer, J. D., & Wood, J. M. (2006) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2006.01.124 · Cited by 52
Simplet controls cell proliferation and gene transcription during zebrafish caudal fin regeneration
Kızıl, Ç., Otto, G., Geisler, R., Nüsslein‐Volhard, C., & Antos, C. L. (2008) · Developmental Biology · doi:10.1016/j.ydbio.2008.09.032 · Cited by 47
JISTIC: Identification of Significant Targets in Cancer
Sanchez-Garcia, F., Akavia, U. D., Mozes, E., & Pe’er, D. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-189 · Cited by 46
γ‐BAR, a novel AP‐1‐interacting protein involved in post‐Golgi trafficking
Neubrand, V. E., Will, R. D., Möbius, W., Poustka, A., Wiemann, S., Schu, P. V., Dotti, C. G., Pepperkok, R., & Simpson, J. C. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600600 · Cited by 46
GTP-dependent Secretion from Neutrophils Is Regulated by Cdk5
Rosales, J. L., Ernst, J., Hallows, J. L., & Lee, K. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m408467200 · Cited by 45
Nomura, T., Huang, W., Seo, S., Zhau, H. E., Mimata, H., & Chung, L. W. K. (2007) · The Journal of Urology · doi:10.1016/j.juro.2007.03.007 · Cited by 44
RING-dependent tumor suppression and G2/M arrest induced by the TRC8 hereditary kidney cancer gene
Brauweiler, A. M., Lorick, K. L., Lee, J. P., Tsai, Y. C., Chan, D., Weissman, A. M., Drabkin, H. A., & Gemmill, R. M. (2006) · Oncogene · doi:10.1038/sj.onc.1210017 · Cited by 41
Miccoli, L., Frouin, I., Novac, O., Paola, D. D., Harper, F., Zannis‐Hadjopoulos, M., Maga, G., Biard, D. S. F., & Angulo, J. F. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.9.3814-3830.2005 · Cited by 35
Protein phosphatase 1H, overexpressed in colon adenocarcinoma, is associated with CSE1L
Sugiura, T., Noguchi, Y., Sakurai, K., & Hattori, C. (2008) · Cancer Biology & Therapy · doi:10.4161/cbt.7.2.5302 · Cited by 30
Characterisation of the human APC1 , the largest subunit of the anaphase-promoting complex
Jørgensen, P., Gräslund, S., Betz, R. C., Ståhl, S., Larsson, C., & Höög, C. (2001) · Gene · doi:10.1016/s0378-1119(00)00511-4 · Cited by 29
Appel, S., Bringmann, A., Grünebach, F., Weck, M., Bauer, J., & Brossart, P. (2006) · Blood · doi:10.1182/blood-2005-06-2480 · Cited by 28
Endo, R., Saito, T., Asada, A., Kawahara, H., Ohshima, T., & Hisanaga, S. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.026443 · Cited by 27
Short-hairpin RNA-mediated stable silencing of Grb2 impairs cell growth and DNA synthesis
Fulvio, M. D., Henkels, K. M., & Gómez-Cambronero, J. (2007) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2007.04.013 · Cited by 18
KLF6 Gene and Early Melanoma Development in a Collagen I-Rich Extracellular Environment
Huh, S. J., Chen, Y.-L., Friedman, S. L., Liao, J., Huang, H., Cavenee, W. K., & Robertson, G. P. (2010) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djq218 · Cited by 16
Weidle, U. H., Evtimova, V., Alberti, S., Guerra, E., Fersis, N., & Kaul, S. (2009) · PubMed · Cited by 15
CDK5 activator p35 downregulates E‐cadherin precursor independently of CDK5
Lin, S., Wang, J., Ye, Z., Ip, N. Y., & Lin, S. (2008) · FEBS Letters · doi:10.1016/j.febslet.2008.02.053 · Cited by 12
New mutations identified in the ocular albinism type 1 gene
Roma, C., Ferrante, P., Guardiola, O., Ballabio, A., & Zollo, M. (2007) · Gene · doi:10.1016/j.gene.2007.07.020 · Cited by 5
Research works printed but not linked: 18
- Adler, A.S., Lin, M., Horlings, H., Nuyten, D.S., van de Vijver, M.J., and Chang, H.Y. (2006). Genetic regulators of large-scale transcriptional signatures in cancer. Nat. Genet. 38, 421–430. · DOI
- Beroukhim, R., Brunet, J.-P., Di Napoli, A., Mertz, K.D., Seeley, A., Pires, M.M., Linhart, D., Worrell, R.A., Moch, H., Rubin, M.A., et al. (2009). Patterns of gene expression and copy-number alterations in von-hippel lindau disease-associated and sporadic clear cell carcinoma of the kidney. Cancer Res. 69, 4674–4681. · DOI
- Beroukhim, R., Getz, G., Nghiemphu, L., Barretina, J., Hsueh, T., Linhart, D., Vivanco, I., Lee, J.C., Huang, J.H., Alexander, S., et al. (2007). Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc. Natl. Acad. Sci. USA 104, 20007–20012. · DOI
- Beroukhim, R., Mermel, C.H., Porter, D., Wei, G., Raychaudhuri, S., Donovan, J., Barretina, J., Boehm, J.S., Dobson, J., Urashima, M., et al. (2010). The landscape of somatic copy-number alteration across human cancers. Nature 463, 899–905. · DOI · Paper page
- Chiaverini, C., Beuret, L., Flori, E., Busca, R., Abbe, P., Bille, K., Bahadoran, P., Ortonne, J.-P., Bertolotto, C., and Ballotti, R. (2008). Microphthalmia-associated transcription factor regulates RAB27A gene expression and controls melanosome transport. J. Biol. Chem. 283, 12635–12642. · DOI
- Garraway, L.A., Widlund, H.R., Rubin, M.A., Getz, G., Berger, A.J., Ramaswamy, S., Beroukhim, R., Milner, D.A., Granter, S.R., Du, J., et al. (2005). Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 436, 117–122. · DOI · Paper page
- Hoek, K.S., Schlegel, N.C., Brafford, P., Sucker, A., Ugurel, S., Kumar, R., Weber, B.L., Nathanson, K.L., Phillips, D.J., Herlyn, M., et al. (2006). Metastatic potential of melanomas defined by specific gene expression profiles with no BRAF signature. Pigment Cell Res. 19, 290–302. · DOI
- Hoek, K.S., Schlegel, N.C., Eichhoff, O.M., Widmer, D.S., Praetorius, C., Einarsson, S.O., Valgeirsdottir, S., Bergsteinsdottir, K., Schepsky, A., Dummer, R., and Steingrimsson, E. (2008). Novel MITF targets identified using a two-step DNA microarray strategy. Pigment Cell Melanoma Res 21, 665–676. · DOI
- Johansson, P., Pavey, S., and Hayward, N. (2007). Confirmation of a BRAF mutation-associated gene expression signature in melanoma. Pigment Cell Res. 20, 216–221. · DOI
- Lee, S.-I., Pe'er, D., Dudley, A.M., Church, G.M., and Koller, D. (2006). Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc. Natl. Acad. Sci. USA 103, 14062–14067. · DOI
- Levy, C., Khaled, M., and Fisher, D.E. (2006). MITF: master regulator of melanocyte development and melanoma oncogene. Trends Mol. Med. 12, 406–414. · DOI · Paper page
- Lin, W.M., Baker, A.C., Beroukhim, R., Winckler, W., Feng, W., Marmion, J.M., Laine, E., Greulich, H., Tseng, H., Gates, C., et al. (2008b). Modeling genomic diversity and tumor dependency in malignant melanoma. Cancer Res. 68, 664–673. · DOI
- Pratilas, C.A., Taylor, B.S., Ye, Q., Viale, A., Sander, C., Solit, D.B., and Rosen, N. (2009). (V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway. Proc. Natl. Acad. Sci. USA 106, 4519–4524. · DOI
- Sanchez-Garcia, F., Akavia, U.D., Mozes, E., and Pe'er, D. (2010). JISTIC: identification of significant targets in cancer. BMC Bioinformatics 11, 189. · DOI
- Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D., and Friedman, N. (2003). Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 34, 166–176. · DOI
- Steingrímsson, E., Copeland, N.G., and Jenkins, N.A. (2004). Melanocytes and the microphthalmia transcription factor network. Annu. Rev. Genet. 38, 365–411. · DOI
- 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-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545–15550. · DOI · Paper page
- Wang, L., Cao, X.X., Chen, Q., Zhu, T.F., Zhu, H.G., and Zheng, L. (2009). DIXDC1 targets p21 and cyclin D1 via PI3K pathway activation to promote colon cancer cell proliferation. Cancer Sci. 100, 1801–1808. · DOI
Cited by
Sorted by citations
Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET
Peinado, H., Alečković, M., Lavotshkin, S., Matei, I., Costa-Silva, B., Moreno-Bueno, G., Hergueta-Redondo, M., Williams, C., García-Santos, G., Ghajar, C. M., et al. (2012) · Nature Medicine · doi:10.1038/nm.2753 · Cited by 3,715
Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis
Levine, J. H., Simonds, E. F., Bendall, S. C., Davis, K. L., Amir, E.-A. D., Tadmor, M. D., Litvin, O., Fienberg, H. G., Jager, A., Zunder, E. R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.047 · Cited by 2,303
Multi-Omics Factor Analysis—a framework for unsupervised integration of multi-omics data sets
Argelaguet, R., Velten, B., Arnol, D., Dietrich, S., Zenz, T., Marioni, J. C., Buettner, F., Huber, W., & Stegle, O. (2018) · Molecular Systems Biology · doi:10.15252/msb.20178124 · Cited by 1,510
Methods of integrating data to uncover genotype-phenotype interactions
Ritchie, M. D., Holzinger, E. R., Li, R., Pendergrass, S. A., & Kim, D. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3868 · Cited by 1,085
Next-Generation Machine Learning for Biological Networks
Camacho, D. M., Collins, K. M., Powers, R. K., Costello, J. C., & Collins, J. J. (2018) · Cell · doi:10.1016/j.cell.2018.05.015 · Cited by 1,012
Metadata
- Authors
- Akavia, U. D., Litvin, O., Kim, J., Sanchez-Garcia, F., Kotliar, D., Causton, H. C., Pochanard, P., Mozes, E., Garraway, L. A., & Pe'er, D.
- Affiliations
- Columbia University (US)
- Broad Institute (US)
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2010-12
- Volume
- 143
- Issue
- 6
- Pages
- 1005-1017
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3013278
- OpenAlex
- W1968667083
- Cited by
- 484
- References
- 129
- Citations by year
- 2026: 5 · 2025: 5 · 2024: 14 · 2023: 21 · 2022: 18 · 2021: 17 · 2020: 30 · 2019: 28 · 2018: 24 · 2017: 33 · 2016: 42 · 2015: 51 · 2014: 47 · 2013: 60 · 2012: 56
- FWCI
- 14.99
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Burroughs Wellcome Fund
- National Institutes of Health (DP2OD002414)
- National Cancer Institute (U54CA121852)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- cancer driver genes, melanoma, chromosomal copy number alterations, gene expression, tumor dependency, Rab27a, protein trafficking, tumor progression, therapeutic target
- MeSH terms
- rab27 GTP-Binding Proteins, Bayes Theorem, Humans, Melanoma, GTPase-Activating Proteins, rab GTP-Binding Proteins, Gene Expression Profiling, Protein Transport, Microphthalmia-Associated Transcription Factor
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review