A human functional protein interaction network and its application to cancer data analysis
Open accessAbstract
Background: One challenge facing biologists is to tease out useful information from massive data sets for further analysis. A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system. Results: We have constructed a protein functional interaction network by extending curated pathways with non-curated sources of information, including protein-protein interactions, gene coexpression, protein domain interaction, Gene Ontology (GO) annotations and text-mined protein interactions, which cover close to 50% of the human proteome. By applying this network to two glioblastoma multiforme (GBM) data sets and projecting cancer candidate genes onto the network, we found that the majority of GBM candidate genes form a cluster and are closer than expected by chance, and the majority of GBM samples have sequence-altered genes in two network modules, one mainly comprising genes whose products are localized in the cytoplasm and plasma membrane, and another comprising gene products in the nucleus. Both modules are highly enriched in known oncogenes, tumor suppressors and genes involved in signal transduction. Similar network patterns were also found in breast, colorectal and pancreatic cancers. Conclusions: We have built a highly reliable functional interaction network upon expert-curated pathways and applied this network to the analysis of two genome-wide GBM and several other cancer data sets. The network patterns revealed from our results suggest common mechanisms in the cancer biology. Our system should provide a foundation for a network or pathway-based analysis platform for cancer and other diseases.
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Multiple groups found tumor associated mutations are significantly related by pathway information.
“Multiple groups have found that tumor associated mutations are significantly related by pathway information47,48.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [48]
A number of recent papers have used pathway analysis workflow to highlight genes and pathways active in specific model organisms or diseased tissues.
“A number of recent papers have used this pathway analysis workflow to highlight genes and pathways that are active in specific model organisms or diseased tissues, such as breast cancer, using gene and protein expression, copy number variants (CNVs) and SNPs19,44-49.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [48]
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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 · see citing works
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888 · see citing works
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206 · see citing works
Collective dynamics of ‘small-world’ networks
Watts, D. J., & Strogatz, S. H. (1998) · Nature · doi:10.1038/30918 · Cited by 43,060 · see citing works
Emergence of Scaling in Random Networks
Barabási, A.-L., & Albert, R. (1999) · Science · doi:10.1126/science.286.5439.509 · Cited by 36,135 · see citing works
Hanahan, D., & Weinberg, R. A. (2000) · Cell · doi:10.1016/s0092-8674(00)81683-9 · Cited by 29,219 · see citing works
Data Mining: Practical Machine Learning Tools and Techniques
Witten, I. H., Frank, E., & Hall, M. A. (2011) · Elsevier eBooks · doi:10.1016/c2009-0-19715-5 · Cited by 25,493 · see citing works
Community structure in social and biological networks
Girvan, M., & Newman, M. E. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.122653799 · Cited by 15,502 · see citing works
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
The Cancer Genome Atlas Research Network (2008) · Nature · doi:10.1038/nature07385 · Cited by 7,735 · see citing works
An Integrated Genomic Analysis of Human Glioblastoma Multiforme
Parsons, D. W., Jones, S., Zhang, X., Lin, J. C.-H., Leary, R. J., Angenendt, P., Mankoo, P., Carter, H., Siu, I.-M., Gallia, G. L., et al. (2008) · Science · doi:10.1126/science.1164382 · Cited by 5,857 · see citing works
The KEGG resource for deciphering the genome
Kanehisa, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh063 · Cited by 5,121 · see citing works
Cancer genes and the pathways they control
Vogelstein, B., & Kinzler, K. W. (2004) · Nature Medicine · doi:10.1038/nm1087 · Cited by 4,245 · see citing works
Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses
Jones, S., Zhang, X., Parsons, D. W., Lin, J. C.-H., Leary, R. J., Angenendt, P., Mankoo, P., Carter, H., Kamiyama, H., Jimeno, A., et al. (2008) · Science · doi:10.1126/science.1164368 · Cited by 3,969 · see citing works
Massagué, J. (2008) · Cell · doi:10.1016/j.cell.2008.07.001 · Cited by 3,907 · see citing works
Goh, K.-I., Cusick, M. E., Valle, D., Childs, B., Vidal, M., & Barabási, A.-L. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701361104 · Cited by 3,242 · see citing works
The Consensus Coding Sequences of Human Breast and Colorectal Cancers
Sjöblom, T., Jones, S., Wood, L. D., Parsons, D. W., Lin, J., Barber, T. D., Mandelker, D. L., Leary, R. J., Ptak, J., Silliman, N., et al. (2006) · Science · doi:10.1126/science.1133427 · Cited by 3,161 · see citing works
The Genomic Landscapes of Human Breast and Colorectal Cancers
Wood, L. D., Parsons, D. W., Jones, S., Lin, J., Sjöblom, T., Leary, R. J., Shen, D., Boca, S. M., Barber, T., Ptak, J., et al. (2007) · Science · doi:10.1126/science.1145720 · Cited by 2,833 · see citing works
Somatic mutations affect key pathways in lung adenocarcinoma
Ding, L., Getz, G., Wheeler, D. A., Mardis, E. R., McLellan, M. D., Cibulskis, K., Sougnez, C., Greulich, H., Muzny, D. M., Morgan, M. B., et al. (2008) · Nature · doi:10.1038/nature07423 · Cited by 2,681 · see citing works
The R Project in Statistical Computing
Ripley, B. D. (2001) · MSOR Connections · doi:10.11120/msor.2001.01010023 · Cited by 2,681 · see citing works
Comparative assessment of large-scale data sets of protein–protein interactions
von Mering, C., Krause, R., Snel, ., Cornell, M. J., Oliver, S. G., Fields, S., & Peer Bork, B. (2002) · Nature · doi:10.1038/nature750 · Cited by 2,339 · see citing works
Pfam: clans, web tools and services
Finn, R. D. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj149 · Cited by 2,291 · see citing works
Network‐based classification of breast cancer metastasis
Chuang, H., Lee, E., Liu, Y., Lee, D., & Ideker, T. (2007) · Molecular Systems Biology · doi:10.1038/msb4100180 · Cited by 1,431 · see citing works
GoMiner: a resource for biological interpretation of genomic and proteomic data
Zeebèrg, B. R., Feng, W., Wang, G., Wang, M. D., Fojo, A. T., Sunshine, M., Narasimhan, S., Kane, D. W., Reinhold, W. C., Lababidi, S., et al. (2003) · Genome biology · doi:10.1186/gb-2003-4-4-r28 · Cited by 1,198 · see citing works
Kristiansen, T. Z., Navarro, J. D., Amanchy, R., Kristiansen, T. Z., Jonnalagadda, C. K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T. K. B., Gronborg, M., et al. (2003) · Genome Research · doi:10.1101/gr.1680803 · Cited by 1,078 · see citing works
The small world inside large metabolic networks
Wagner, A., & Fell, D. A. (2001) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2001.1711 · Cited by 986 · see citing works
Large‐scale mapping of human protein–protein interactions by mass spectrometry
Ewing, R. M., Chu, P. C., Elisma, F., Li, H., Taylor, P. P., Climie, S. C., McBroom, L. D. B., Robinson, M. D., O'Connor, L., Li, M. M., et al. (2007) · Molecular Systems Biology · doi:10.1038/msb4100134 · Cited by 985 · see citing works
An empirical framework for binary interactome mapping
Venkatesan, K., Rual, J.-F. M., Vázquez, A., Stelzl, U., Lemmens, I. H., Hirozane-Kishikawa, T., Hao, T., Zenkner, M., Xin, X., Goh, K. I., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1280 · Cited by 907 · see citing works
Idiot's Bayes—Not So Stupid After All?
Hand, D. J., & Yu, K. (2001) · International Statistical Review · doi:10.1111/j.1751-5823.2001.tb00465.x · Cited by 886 · see citing works
Pathway-Based Approaches for Analysis of Genomewide Association Studies
Wang, K., Li, M., & Bućan, M. (2007) · The American Journal of Human Genetics · doi:10.1086/522374 · Cited by 858 · see citing works
Knowledge Representation and Reasoning
Lee, N. (2024) · Encyclopedia of Computer Graphics and Games · doi:10.1007/978-3-031-23161-2_300700 · Cited by 819 · see citing works
IntAct--open source resource for molecular interaction data
Kerrien, S., Alam-Faruque, Y., Aranda, B., Bancarz, I., Bridge, A. J., Derow, C., Dimmer, E. C., Feuermann, M., Friedrichsen, A., Huntley, R. P., et al. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl958 · Cited by 800 · see citing works
Coexpression Analysis of Human Genes Across Many Microarray Data Sets
Lee, H. K., Hsu, A. K., Sajdak, J., Qin, J., & Pavlidis, P. (2004) · Genome Research · doi:10.1101/gr.1910904 · Cited by 770 · see citing works
The BioGRID Interaction Database: 2008 update
Breitkreutz, B., Stark, C., Reguly, T., Boucher, L., Breitkreutz, A., Livstone, M. S., Oughtred, R., Lackner, D. H., Bähler, J., Wood, V., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1001 · Cited by 698 · see citing works
Reactome: a knowledge base of biologic pathways and processes
Västrik, I., D’Eustachio, P., Schmidt, E., Geeta, J.-T., Gopinath, G., Croft, D. W., de Bono, B., Gillespie, M. E., Jassal, B., Lewis, S., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-3-r39 · Cited by 656 · see citing works
Self-citationStrohmaier, H. M., Spruck, C., Kaiser, P., Won, K., Sangfelt, O., & Reed, S. I. (2001) · Nature · doi:10.1038/35095076 · Cited by 584 · see citing works
Rowland, B. D., Bernards, R., & Peeper, D. S. (2005) · Nature Cell Biology · doi:10.1038/ncb1314 · Cited by 583 · see citing works
Protein interaction mapping: ADrosophilacase studyPreprint
Formstecher, É., Aresta, S., Collura, V., Hamburger, A., Meil, A., Trehin, A., Reverdy, C., Betin, V. M. S., Maire, S., Brun, C., et al. (2005) · Genome Research · doi:10.1101/gr.2659105 · Cited by 581 · see citing works
Knowledge Representation and Reasoning
(2004) · Elsevier eBooks · doi:10.1016/b978-1-55860-932-7.x5083-3 · Cited by 578 · see citing works
Regulation of T Cell Receptor Signaling by Tyrosine Phosphatase SYP Association with CTLA-4
Marengère, L. E. M., Waterhouse, P., Duncan, G. S., Mittrücker, H.-W., Feng, G.-S., & Mak, T. W. (1996) · Science · doi:10.1126/science.272.5265.1170 · Cited by 551 · see citing works
Signaling of transforming growth factor‐β family members through Smad proteins
Itoh, S., Itoh, F., Goumans, M., & ten Dijke, P. (2000) · European Journal of Biochemistry · doi:10.1046/j.1432-1327.2000.01828.x · Cited by 530 · see citing works
Global topological features of cancer proteins in the human interactome
Jonsson, P. F., & Bates, P. A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl390 · Cited by 490 · see citing works
Inferring cellular networks – a review
Markowetz, F. M., & Spang, R. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-s6-s5 · Cited by 391 · see citing works
Mi, H., Guo, N., Kejariwal, A., & Thomas, P. D. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl869 · Cited by 372 · see citing works
Qi, Y., Bar‐Joseph, Z., & Klein‐Seetharaman, J. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20865 · Cited by 368 · see citing works
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 329 · see citing works
TRED: a transcriptional regulatory element database, new entries and other development
Jiang, C., Xuan, Z., Zhao, F., & Zhang, M. Q. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl1041 · Cited by 329 · see citing works
A phosphoserine‐regulated docking site in the protein kinase RSK2 that recruits and activates PDK1
Frödin, M., Jensen, C. J., Mérienne, K., & Gammeltoft, S. (2000) · The EMBO Journal · doi:10.1093/emboj/19.12.2924 · Cited by 317 · see citing works
Flicek, P., Aken, B. L., Ballester, B., Beal, K. M., Bragin, E., Brent, S., Chen, Y., Clapham, P., Coates, G. M. P., Fairley, S., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp972 · Cited by 291 · see citing works
GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data
Rzhetsky, A., Iossifov, I. H., Koike, T., Krauthammer, M. O., Kra, P., Morris, M., Yu, H. Q., Duboue, P. A., Weng, W., Wilbur, W. J., et al. (2003) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2003.10.001 · Cited by 291 · see citing works
Epidermal growth factor (EGF)-like repeats of human tenascin-C as ligands for EGF receptor
Swindle, C. S., Tran, K. T., Johnson, T. D., Banerjee, P., Mayes, A. M., Griffith, L., & Wells, A. (2001) · The Journal of Cell Biology · doi:10.1083/jcb.200103103 · Cited by 286 · see citing works
Zeebèrg, B. R., Qin, H., Narasimhan, S., Sunshine, M., Cao, H., Kane, D. W., Reimers, M., Stephens, R. M., Bryant, D., Burt, S. K., et al. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-168 · Cited by 279 · see citing works
A map of human cancer signaling
Cui, Q., Ma, Y., Jaramillo, M., Bari, H., Awan, A., Yang, S., Zhang, S. V., Liu, L., Meng, L., O'Connor‐McCourt, M. D., et al. (2007) · Molecular Systems Biology · doi:10.1038/msb4100200 · Cited by 260 · see citing works
van Noort, V., Snel, ., & Huynen, M. A. (2004) · EMBO Reports · doi:10.1038/sj.embor.7400090 · Cited by 256 · see citing works
Choosing negative examples for the prediction of protein-protein interactions
Ben‐Hur, A., & Noble, W. S. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-s1-s2 · Cited by 240 · see citing works
Human Gene Coexpression Landscape: Confident Network Derived from Tissue Transcriptomic Profiles
Prieto, C. A. V., Risueño, A., Fontanillo, C., & Rivas, J. D. L. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003911 · Cited by 239 · see citing works
Ramani, A. K., Bunescu, R., Mooney, R. J., & Marcotte, E. M. (2005) · Genome biology · doi:10.1186/gb-2005-6-5-r40 · Cited by 239 · see citing works
Yoon, J., Blumer, A. C., & Lee, K. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl533 · Cited by 235 · see citing works
A GLI1‐p53 inhibitory loop controls neural stem cell and tumour cell numbers
Stecca, B. A., & Altaba, A. R. I. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.16 · Cited by 233 · see citing works
Dunn, R., Dudbridge, F., & Sanderson, C. M. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-39 · Cited by 204 · see citing works
Phosphorylation of the cell cycle inhibitor p21Cip1/WAF1 by Pim-1 kinase
Wang, Z., Bhattacharya, N., Mixter, P. F., Wei, W., Sedivy, J. M., & Magnuson, N. S. (2002) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/s0167-4889(02)00347-6 · Cited by 197 · see citing works
Predicting co-complexed protein pairs using genomic and proteomic data integration
Zhang, L. V., Wong, S. L., King, O. D., et al. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-38 · Cited by 182 · see citing works
Functional Copy-Number Alterations in Cancer
Taylor, B. S., Barretina, J., Socci, N. D., DeCarolis, P., Ladanyi, M., Meyerson, M., Singer, S., & Sander, C. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003179 · Cited by 170 · see citing works
Plaisier, C. L., Horvath, S., Huertas-Vazquez, A., Cruz-Bautista, I., Herrera, M. F., Tusie-Luna, T., Aguilar-Salinas, C., & Pajukanta, P. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000642 · Cited by 163 · see citing works
Gortzak‐Uzan, L., Ignatchenko, A., Evangelou, A. I., Agochiya, M., Brown, K. A., St.Onge, P., Kireeva, I., Schmitt‐Ulms, G., Brown, T. J., Murphy, J., et al. (2007) · Journal of Proteome Research · doi:10.1021/pr0703223 · Cited by 160 · see citing works
Dumont, N., & Arteaga, C. L. (2000) · Breast Cancer Research · doi:10.1186/bcr44 · Cited by 158 · see citing works
Annexins — Modulators of EGF receptor signalling and trafficking
Grewal, T., & Enrich, C. (2009) · Cellular Signalling · doi:10.1016/j.cellsig.2009.01.031 · Cited by 146 · see citing works
A multidimensional analysis of genes mutated in breast and colorectal cancersPreprint
Lin, J., Gan, C. M., Zhang, X., Jones, S., Sjöblom, T., Wood, L. D., Parsons, D. W., Papadopoulos, N., Kinzler, K. W., Vogelstein, B., et al. (2007) · Genome Research · doi:10.1101/gr.6431107 · Cited by 136 · see citing works
E2F Transcriptional Activation Requires TRRAP and GCN5 Cofactors
Lang, S. E., McMahon, S. B., Cole, M. D., & Hearing, P. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m102067200 · Cited by 131 · see citing works
Donovan, J. C. H., & Slingerland, J. M. (2000) · Breast Cancer Research · doi:10.1186/bcr43 · Cited by 105 · see citing works
Kretzschmar, M. (2000) · Breast Cancer Research · doi:10.1186/bcr42 · Cited by 103 · see citing works
Modulation of DNA Topoisomerase I Activity by p53
Gobert, C., Bracco, L. P., Rossi, F., Olivier, M., Tazi, J., Lavelle, F., Larsen, A. K., & Riou, J. (1996) · Biochemistry · doi:10.1021/bi952327w · Cited by 102 · see citing works
Cooper, M. P., Qu, L., Rohas, L. M., Lin, J. D., Yang, W., Erdjument‐Bromage, H., Tempst, P., & Spiegelman, B. M. (2006) · Genes & Development · doi:10.1101/gad.1483906 · Cited by 100 · see citing works
CREB-binding Protein/p300 Co-activation of Crystallin Gene Expression
Chen, Q., Dowhan, D. H., Liang, D., Moore, D. D., & Overbeek, P. A. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m201821200 · Cited by 88 · see citing works
Transforming growth factor-β and breast cancer: Mammary gland development
Barcellos‐Hoff, M. H., & Ewan, K. (2000) · Breast Cancer Research · doi:10.1186/bcr40 · Cited by 80 · see citing works
CD46 is phosphorylated at tyrosine 354 upon infection of epithelial cells by Neisseria gonorrhoeae
Lee, S. W., Bonnah, R. A., Higashi, D. L., et al. (2002) · The Journal of Cell Biology · doi:10.1083/jcb.200109005 · Cited by 71 · see citing works
Low duplicability and network fragility of cancer genes
Rambaldi, D., Giorgi, F. M., Capuani, F., Ciliberto, A., & Ciccarelli, F. D. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.06.003 · Cited by 66 · see citing works
hGTSE-1 Expression Stimulates Cytoplasmic Localization of p53
Monte, M., Benetti, R., Collavin, L., Marchionni, L., Sal, G. D., & Schneider, C. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m311123200 · Cited by 62 · see citing works
Sodek, K. L., Evangelou, A. I., Ignatchenko, A., Agochiya, M., Brown, T. J., Ringuette, M. J., Jurišica, I., & Kislinger, T. (2008) · Molecular BioSystems · doi:10.1039/b717542f · Cited by 60 · see citing works
Rubinstein, M., Idelman, G., Plymate, S. R., et al. (2004) · Endocrinology · doi:10.1210/en.2004-0173 · Cited by 58 · see citing works
Essential roles of caspases and their upstream regulators in rotenone-induced apoptosis
Lee, J. J., Huang, M., Yang, I.-C., et al. (2008) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2008.03.149 · Cited by 57 · see citing works
Müller, D., Thieke, K., Bürgin, A., et al. (2000) · The EMBO Journal · doi:10.1093/emboj/19.10.2168 · Cited by 52 · see citing works
Epidermal Growth Factor Stimulation of the ACK1/Dbl Pathway in a Cdc42 and Grb2-Dependent Manner
Kato‐Stankiewicz, J., Ueda, S., Kataoka, T., et al. (2001) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.2001.5004 · Cited by 49 · see citing works
Schafmayer, C., Buch, S., Egberts, J. H., et al. (2007) · International Journal of Cancer · doi:10.1002/ijc.22735 · Cited by 48 · see citing works
Wakefield, L. M., Yang, Y.-A., & Dukhanina, O. I. (2000) · Breast Cancer Research · doi:10.1186/bcr41 · Cited by 47 · see citing works
A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations
Vaske, C. J., House, C. D., Luu, T. V., Frank, B. C., Yeang, C., Lee, N. H., & Stuart, J. M. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000274 · Cited by 44 · see citing works
Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases
Cavalieri, D., Castagnini, C., Toti, S., et al. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm333 · Cited by 41 · see citing works
Caohuy, H., & Pollard, H. B. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m202452200 · Cited by 38 · see citing works
Src Family Kinases Directly Regulate JIP1 Module Dynamics and Activation
Nihalani, D., Wong, H. N., Verma, R. K., & Holzman, L. B. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01479-06 · Cited by 30 · see citing works
Comparative Analysis of Protein-Protein Interactions in Cancer-Associated Genes
Guda, P., Chittur, S. V., & Guda, C. (2009) · Genomics Proteomics & Bioinformatics · doi:10.1016/s1672-0229(08)60030-3 · Cited by 28 · see citing works
Mandolesi, G., Gargano, S., Pennuto, M., Illi, B., Molfetta, R., Soucek, L., Mosca, L., Levi, A., Jucker, R., & Nasi, S. (2001) · FEBS Letters · doi:10.1016/s0014-5793(01)03227-6 · Cited by 27 · see citing works
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Comprehensive Characterization of Cancer Driver Genes and Mutations
Bailey, M. H., Tokheim, C., Porta-Pardo, E., Sengupta, S., Bertrand, D., Weerasinghe, A., Colaprico, A., Wendl, M. C., Kim, J., Reardon, B., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.060 · Cited by 2,256 · see citing works
The Reactome pathway knowledgebase
Croft, D., Mundo, A. F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M. R., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1102 · Cited by 1,889 · see citing works
Self-citationThe clonal and mutational evolution spectrum of primary triple-negative breast cancers
Shah, S. P., Roth, A., Goya, R., Oloumi, A., Ha, G., Zhao, Y., Turashvili, G., Ding, J., Tse, K., Haffari, G., et al. (2012) · Nature · doi:10.1038/nature10933 · Cited by 1,967 · see citing works
The BioPAX community standard for pathway data sharing
Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1666 · Cited by 745 · see citing works
Self-citationGeneMANIA Prediction Server 2013 Update
Zuberi, K., Franz, M., Rodriguez, H., Montojo, J., Lopes, C. T., Bader, G. D., & Morris, Q. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt533 · Cited by 396 · see citing works
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes
Huang, J. K., Carlin, D. E., Yu, M. K., Zhang, W., Kreisberg, J. F., Tamayo, P., & Ideker, T. (2018) · Cell Systems · doi:10.1016/j.cels.2018.03.001 · Cited by 289 · see citing works
Morphological, cellular and molecular basis of brain infection in COVID-19 patients
Crunfli, F., Carregari, V. C., Veras, F. P., Vendramini, P. H., Valença, A. G. F., Antunes, A. S. L. M., Brandão-Teles, C., da Silva Zuccoli, G., Reis-de-Oliveira, G., Silva-Costa, L. C., et al. (2020) · doi:10.1101/2020.10.09.20207464 · Cited by 331 · see citing works
Zhu, Y. X., Braggio, E., Shi, C.-X., Kortuem, K. M., Bruins, L. A., Schmidt, J. E., Chang, X.-B., Langlais, P., Luo, M., Jedlowski, P., et al. (2014) · Blood · doi:10.1182/blood-2014-02-557819 · Cited by 213 · see citing works
Macroscopic somatic clonal expansion in morphologically normal human urothelium
Li, R., Du, Y., Chen, Z., Xu, D., Lin, T., Jin, S., Wang, G., Liu, Z., Lu, M., Chen, X., et al. (2020) · Science · doi:10.1126/science.aba7300 · Cited by 206 · see citing works
Single-cell senescence identification reveals senescence heterogeneity, trajectory, and modulators
Tao, W., Yu, Z., & Han, J.-D. J. (2024) · Cell Metabolism · doi:10.1016/j.cmet.2024.03.009 · Cited by 147 · see citing works
Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain
Androvic, P., Kirdajova, D., Tureckova, J., Zucha, D., Rohlova, E., Abaffy, P., Kriska, J., Valny, M., Anderova, M., Kubista, M., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107777 · Cited by 118 · see citing works
Stevens, A., Hanson, D., Whatmore, A., Destenaves, B., Chatelain, P., & Clayton, P. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-547 · Cited by 65 · see citing works
Afroz, S., Giddaluru, J., Vishwakarma, S., Naz, S., Khan, A. A., & Khan, N. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00074 · Cited by 50 · see citing works
Network control principles for identifying personalized driver genes in cancer
Guo, W.-F., Zhang, S.-W., Zeng, T., Akutsu, T., & Chen, L. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbz089 · Cited by 44 · see citing works
- Authors
- Wu, G., Feng, X., & Stein, L.
- Affiliations
- Ontario Institute for Cancer Research (CA)
- Cold Spring Harbor Laboratory (US)
- Corresponding author
- Wu, Guanming
- Venue
- Genome Biology
- Published
- 2010-05-19
- Volume
- 11
- Issue
- 5
- Pages
- R53-R53
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC2898064
- OpenAlex
- W2058539819
- Cited by
- 692
- References
- 90
- Citations by year
- 2026: 10 · 2025: 28 · 2024: 33 · 2023: 41 · 2022: 41 · 2021: 47 · 2020: 48 · 2019: 54 · 2018: 59 · 2017: 60 · 2016: 48 · 2015: 57 · 2014: 63 · 2013: 39 · 2012: 46
- FWCI
- 13.15
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- Funders
- Memorial Sloan-Kettering Cancer Center
- National Institutes of Health
- National Human Genome Research Institute (U41HG003751, P41HG003751)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- protein-protein interaction network, pathway analysis, glioblastoma, network clustering, oncogenes, tumor suppressor, signal transduction, gene ontology annotation, gene co-expression, protein domain interactions, cancer genomics
- MeSH terms
- Glioblastoma, Humans, Neoplasm Proteins, Neoplasms, Protein Binding, ROC Curve, Software, Genome, Human, Gene Expression Regulation, Neoplastic, Cluster Analysis, Internet, Protein Interaction Mapping, Databases, Protein, Genes, Neoplasm, Gene Regulatory Networks
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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.
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