The DOI matches its Crossref record; 103 of the 104 references it cites were found in a registry or an index.
Protein networks in disease
Open accessAbstract
During a decade of proof-of-principle analysis in model organisms, protein networks have been used to further the study of molecular evolution, to gain insight into the robustness of cells to perturbation, and for assignment of new protein functions. Following these analyses, and with the recent rise of protein interaction measurements in mammals, protein networks are increasingly serving as tools to unravel the molecular basis of disease. We review promising applications of protein networks to disease in four major areas: identifying new disease genes; the study of their network properties; identifying disease-related subnetworks; and network-based disease classification. Applications in infectious disease, personalized medicine, and pharmacology are also forthcoming as the available protein network information improves in quality and coverage.
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
“Human disease genes tend to interact with each other with higher network connectivity than non-disease genes [71].”
From An integrated analysis of genes and functional pathways for aggression in human and rodent models (2019) · cites this paper as [71]
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
Network biology: understanding the cell's functional organization
Barabási, A.-L., & Oltvai, Z. N. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1272 · Cited by 7,903
Network motifs: simple building blocks of complex networks.
Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D., & Alon, U. (2002) · Science · doi:10.1126/science.298.5594.824 · Cited by 7,368
Lethality and centrality in protein networks
Jeong, H., Mason, S., Barabási, A., & Oltvai, Z. (2001) · Nature · doi:10.1038/35075138 · Cited by 5,327
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706
The Gene Ontology (GO) database and informatics resource
Gene Ontology Consortium (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh036 · Cited by 4,596
From molecular to modular cell biology.
Hartwell, L. H., Hopfield, J. J., Leibler, S., & Murray, A. W. (1999) · Nature · doi:10.1038/35011540 · Cited by 3,632
A comprehensive two-hybrid analysis to explore the yeast protein interactome
Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566
Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
Hamosh, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki033 · Cited by 3,443
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
A census of human cancer genes
Futreal, P. A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., & Stratton, M. R. (2004) · Nature Reviews Cancer · doi:10.1038/nrc1299 · Cited by 3,184
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A., et al. (2006) · Nature · doi:10.1038/nature04670 · Cited by 2,964
STRING: a database of predicted functional associations between proteins
von Mering, C. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg034 · Cited by 2,942
Towards a proteome-scale map of the human protein–protein interaction network
Rual, J.-F. M., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., et al. (2005) · Nature · doi:10.1038/nature04209 · Cited by 2,904
An Introduction to Systems Biology: Design Principles of Biological Circuits
Alon, U. (2006) · doi:10.1201/9781420011432 · Cited by 2,825
Ghrelin: Structure and Function
Kojima, M., & Kangawa, K. (2005) · Physiological Reviews · doi:10.1152/physrev.00012.2004 · Cited by 2,810
Proteome survey reveals modularity of the yeast cell machinery
Gavin, A., Aloy, P., Grandi, P., Krause, R., Böesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., et al. (2006) · Nature · doi:10.1038/nature04532 · Cited by 2,570
Functional Discovery via a Compendium of Expression Profiles
Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R. B., Armour, C. D., Bennett, H. A., Coffey, E. M., Dai, H. A., He, Y. D., et al. (2000) · Cell · doi:10.1016/s0092-8674(00)00015-5 · Cited by 2,534
A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome
Stelzl, U., Worm, U., Lalowski, M. M., Haenig, C., Brembeck, F. H., Goehler, H., Strödicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.029 · Cited by 2,433
Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants
Tong, A. H. Y., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D., Pagé, N., Robinson, M., Raghibizadeh, S., Hogue, C. W. V., Bussey, H., et al. (2001) · Science · doi:10.1126/science.1065810 · Cited by 2,138
Transcriptional regulatory code of a eukaryotic genome
Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., MacIsaac, K. D., Danford, T., Hannett, N. M., Tagne, J., Reynolds, D. B., Yoo, J. Y., et al. (2004) · Nature · doi:10.1038/nature02800 · Cited by 2,135
Global Mapping of the Yeast Genetic Interaction Network
Tong, A. H. Y., Lesage, G., Bader, G. D., Ding, H., Xu, H., Xin, X., Young, J., Berriz, G. F., Brost, R. L., Chang, M., et al. (2004) · Science · doi:10.1126/science.1091317 · Cited by 2,089
Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network
Ideker, T., Thorsson, V., Ranish, J. A., Christmas, R., Buhler, J., Eng, J. K., Bumgarner, R., Goodlett, D. R., Aebersold, R., & Hood, L. (2001) · Science · doi:10.1126/science.292.5518.929 · Cited by 2,050
Self-citationStructure and function of the feed-forward loop network motif
Mangan, S., & Alon, U. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2133841100 · Cited by 1,827
Yıldırım, M. A., Goh, K.-I., Cusick, M. E., Barabási, A.-Ĺ., & Vidal, M. (2007) · Nature Biotechnology · doi:10.1038/nbt1338 · Cited by 1,744
BIND--The Biomolecular Interaction Network Database
Bader, G. D. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.242 · Cited by 1,560
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
Self-citationA network-based analysis of systemic inflammation in humans
Program, I. A. H. R. T. I. L. S. C. R., Calvano, S. E., Xiao, W., Richards, D. R., Felciano, R. M., Baker, H. V., Cho, R. J., Chen, R. O., Brownstein, B. H., Cobb, J. P., et al. (2005) · Nature · doi:10.1038/nature03985 · Cited by 1,429
A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data
Jansen, R., Yu, H., Greenbaum, D. S., Kluger, Y., Krogan, N. J., Chung, S., Emili, A., Snyder, M. P., Greenblatt, J. F., & Gerstein, M. (2003) · Science · doi:10.1126/science.1087361 · Cited by 1,254
Discovering regulatory and signalling circuits in molecular interaction networks
Ideker, T., Ozier, O., Schwikowski, B., & Siegel, A. F. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s233 · Cited by 1,197
Self-citationThe protein–protein interaction map of Helicobacter pylori
Rain, J., Selig, L., Reuse, H. D., Battaglia, V., Reverdy, C., Simon, S., Lenzen, G., Petel, F., Wojcik, J., Schächter, V., et al. (2001) · Nature · doi:10.1038/35051615 · Cited by 1,160
Population genomics of human gene expression
Stranger, B. E., Nica, A. C., Forrest, M. S., Dimas, A. S., Bird, C., Beazley, C., Ingle, C., Dunning, M., Flicek, P., Koller, D., et al. (2007) · Nature Genetics · doi:10.1038/ng2142 · Cited by 1,153
BIND: the Biomolecular Interaction Network Database
Bader, G. D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg056 · Cited by 1,122
The 1.2-Megabase Genome Sequence of Mimivirus
Raoult, D., Audic, S., Robert, C., Abergel, C., Renesto, P., Ogata, H., Scola, B. L., Suzan, M., & Claverie, J. (2004) · Science · doi:10.1126/science.1101485 · Cited by 1,045
MINT: the Molecular INTeraction database
Chatr‐aryamontri, A., Ceol, A. G. M., Montecchi‐Palazzi, L., Nardelli, G., Schneider, M. V., Castagnoli, L., & Cesareni, G. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl950 · Cited by 1,027
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
Global analysis of protein phosphorylation in yeast
Ptacek, J., Devgan, G., Michaud, G. A., Zhu, H., Zhu, X., Fasolo, J., Guo, H., Jona, G., Breitkreutz, A., Sopko, R., et al. (2005) · Nature · doi:10.1038/nature04187 · Cited by 984
A human phenome-interactome network of protein complexes implicated in genetic disorders
Lage, K., Karlberg, E., Størling, Z. M., Olason, P., Pedersen, A., Rigina, O., Hinsby, A., Tümer, Z., Pociot, F., Tommerup, N., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1295 · Cited by 973
A genome-wide association study of global gene expression
Dixon, A. L., Liang, L., Moffatt, M. F., Chen, W., Heath, S. C., Wong, K., Taylor, J. C., Burnett, E. C., Gut, I. G., Farrall, M., et al. (2007) · Nature Genetics · doi:10.1038/ng2109 · Cited by 946
Evaluation of clustering algorithms for protein-protein interaction networks
Brohée, S., & van Helden, J. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-488 · Cited by 903
Schuldiner, M., Collins, S. R., Thompson, N. J., Denic, V., Bhamidipati, A., Punna, T., Ihmels, J., Andrews, B., Boone, C., Greenblatt, J. F., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.031 · Cited by 870
Collins, S. R., Miller, K. M., Maas, N. L., Roguev, A., Fillingham, J., Chu, C. S., Schuldiner, M., Gebbia, M., Recht, J., Shales, M., et al. (2007) · Nature · doi:10.1038/nature05649 · Cited by 869
The Protein Network of HIV Budding
von Schwedler, U. K., Stuchell‐Brereton, M. D., Müller, B., Ward, D. M., Chung, H.-Y., Morita, E., Wang, H. E., Davis, T., He, G.-P., Cimbora, D. M., et al. (2003) · Cell · doi:10.1016/s0092-8674(03)00714-1 · Cited by 835
Lim, J., Hao, T., Shaw, C., Patel, A. J., Szabó, G., Rual, J.-F., Fisk, C. J., Li, N., Smolyar, A., Hill, D. E., et al. (2006) · Cell · doi:10.1016/j.cell.2006.03.032 · Cited by 789
Global protein function prediction from protein-protein interaction networks
Vázquez, A., Flammini, A., Maritan, A., & Vespignani, A. (2003) · Nature Biotechnology · doi:10.1038/nbt825 · Cited by 693
Berger, M. F., Philippakis, A., Qureshi, A. M., He, F. S., Estep, P. W., & Bulyk, M. L. (2006) · Nature Biotechnology · doi:10.1038/nbt1246 · Cited by 685
A Probabilistic Functional Network of Yeast Genes
Lee, I., Date, S. V., Adai, A. T., & Marcotte, E. M. (2004) · Science · doi:10.1126/science.1099511 · Cited by 684
Parsons, A. B., Brost, R. L., Ding, H., Li, Z., Zhang, C., Sheikh, B., Brown, G. W., Kane, P. M., Hughes, T. R., & Boone, C. M. (2003) · Nature Biotechnology · doi:10.1038/nbt919 · Cited by 651
Network modeling links breast cancer susceptibility and centrosome dysfunction
Pujana, M. Á., Han, J.-D. J., Starita, L. M., Purrington, K. S., Tewari, M., Ahn, J. S., Rennert, G., Moreno, V. R., Kirchhoff, T., Gold, B., et al. (2007) · Nature Genetics · doi:10.1038/ng.2007.2 · Cited by 616
Functional and topological characterization of protein interaction networks
Yook, S., Oltvai, Z. N., & Barabási, A.-Ĺ. (2004) · PROTEOMICS · doi:10.1002/pmic.200300636 · Cited by 613
The landscape of genetic complexity across 5,700 gene expression traits in yeast
Brem, R. B., & Kruglyak, L. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408709102 · Cited by 603
Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae
Ge, H., Liu, Z., Church, G. M., & Vidal, M. (2001) · Nature Genetics · doi:10.1038/ng776 · Cited by 575
Predicting disease genes using protein–protein interactions
Oti, M., Snel, ., Huynen, M. A., & Brunner, H. G. (2006) · Journal of Medical Genetics · doi:10.1136/jmg.2006.041376 · Cited by 571
Modeling cellular machinery through biological network comparison
Sharan, R., & Ideker, T. (2006) · Nature Biotechnology · doi:10.1038/nbt1196 · Cited by 557
Self-citationA DNA Integrity Network in the Yeast Saccharomyces cerevisiae
Pan, X., Ye, P., Yuan, D., Wang, X., Bader, J. S., & Boeke, J. D. (2006) · Cell · doi:10.1016/j.cell.2005.12.036 · Cited by 540
A protein interaction network of the malaria parasite Plasmodium falciparum
LaCount, D. J., Vignali, M., Chettier, R., Phansalkar, A. R., Bell, R. N., Hesselberth, J. R., Schoenfeld, L. W., Ota, I. M., Sahasrabudhe, S. R., Kurschner, C., et al. (2005) · Nature · doi:10.1038/nature04104 · Cited by 524
Exploring the Mode-of-Action of Bioactive Compounds by Chemical-Genetic Profiling in Yeast
Parsons, A. B., López, A., Givoni, I. E., Williams, D. E., Gray, C. A., Porter, J., Chua, G., Sopko, R., Brost, R. L., Ho, C.-H., et al. (2006) · Cell · doi:10.1016/j.cell.2006.06.040 · Cited by 512
Pivotal role of oligomerization in expanded polyglutamine neurodegenerative disorders
Sánchez, I., Mahlke, C., & Yuan, J. (2003) · Nature · doi:10.1038/nature01301 · Cited by 504
Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes
Göring, H. H. H., Curran, J. E., Johnson, M. P., Dyer, T. D., Charlesworth, J., Cole, S. A., Jowett, J. B. M., Abraham, L. J., Rainwater, D. L., Comuzzie, A. G., et al. (2007) · Nature Genetics · doi:10.1038/ng2119 · Cited by 503
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 498
Matthews, L. R., Vaglio, P., Reboul, J., Ge, H., Davis, B. P., Garrels, J. I., Vincent, S., & Vidal, M. (2001) · Genome Research · doi:10.1101/gr.205301 · Cited by 482
Franke, L., Bakel, H. V., Fokkens, L., de Jong, E. D., Egmont-Petersen, M., & Wijmenga, C. (2006) · The American Journal of Human Genetics · doi:10.1086/504300 · Cited by 476
Gaining confidence in high-throughput protein interaction networks
Bader, J. S., Chaudhuri, A., Rothberg, J. M., & Chant, J. (2003) · Nature Biotechnology · doi:10.1038/nbt924 · Cited by 466
Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight
Ghazalpour, A., Doss, S., Zhang, B., Wang, S., Plaisier, C., Castellanos, R., Brozell, A., Schadt, E. E., Drake, T. A., Lusis, A. J., et al. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020130 · Cited by 462
Microarray Analysis and Tumor Classification
Quackenbush, J. F. (2006) · New England Journal of Medicine · doi:10.1056/nejmra042342 · Cited by 459
Sotiriou, C. P., & Piccart, M. J. (2007) · Nature reviews. Cancer · doi:10.1038/nrc2173 · Cited by 456
Goehler, H., Lalowski, M., Stelzl, U., Waelter, S., Stroedicke, M., Worm, U., Droege, A., Lindenberg, K. S., Knoblich, M., Haenig, C., et al. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.09.016 · Cited by 453
Gandhi, T. K. B., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Nagaraju, S., Periaswamy, B., et al. (2006) · Nature Genetics · doi:10.1038/ng1747 · Cited by 442
Genetic reconstruction of a functional transcriptional regulatory network
Hu, Z., Killion, P. J., & Iyer, V. R. (2007) · Nature Genetics · doi:10.1038/ng2012 · Cited by 416
The modular nature of genetic diseases
Oti, M., & Brunner, H. G. (2006) · Clinical Genetics · doi:10.1111/j.1399-0004.2006.00708.x · Cited by 411
Herpesviral Protein Networks and Their Interaction with the Human Proteome
Uetz, P., Dong, Y., Zeretzke, C., Atzler, C., Baiker, A. E., Berger, B., Rajagopala, S. V., Roupelieva, M., Rose, D., Fossum, E., et al. (2005) · Science · doi:10.1126/science.1116804 · Cited by 408
Wachi, S., Yoneda, K. Y., & Wu, R. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti688 · Cited by 406
Epstein–Barr virus and virus human protein interaction maps
Calderwood, M. A., Venkatesan, K., Xing, L., Chase, M. R., Vazquez, A., Holthaus, A. M., Ewence, A. E., Li, N., Hirozane-Kishikawa, T., Hill, D. E., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0702332104 · Cited by 388
Predicting protein function from protein/protein interaction data: a probabilistic approach
Letovsky, S. I., & Kasif, S. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg1026 · Cited by 375
Co-clustering of biological networks and gene expression data
Hanisch, D., Zien, A., Zimmer, R., & Lengauer, T. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s145 · Cited by 317
Genome-wide analysis of vaccinia virus protein–protein interactions
McCraith, S. M., Holtzman, T., Moss, B., & Fields, S. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.080078197 · Cited by 289
A Systems Approach to Mapping DNA Damage Response Pathways
Workman, C. T., Mak, H. C., McCuine, S., Tagne, J., Agarwal, M., Ozier, O. W., Begley, T. J., Samson, L. D., & Ideker, T. (2006) · Science · doi:10.1126/science.1122088 · Cited by 272
Self-citationEfficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks
Scott, J., Ideker, T. E., Karp, R. M., & Sharan, R. (2006) · Journal of Computational Biology · doi:10.1089/cmb.2006.13.133 · Cited by 270
Self-citationA proteome-wide protein interaction map for Campylobacter jejuni
Parrish, J. R., Yu, J., Liu, G., Hines, J. A., Chan, J. E., Mangiola, B. A., Zhang, H., Pacifico, S., Fotouhi, F. A., DiRita, V. J., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-7-r130 · Cited by 243
Self-citationRamani, A. K., Bunescu, R., Mooney, R. J., & Marcotte, E. M. (2005) · Genome biology · doi:10.1186/gb-2005-6-5-r40 · Cited by 239
An evaluation of human protein-protein interaction data in the public domain
Mathivanan, S., Periaswamy, B., Gandhi, T., Kandasamy, K., Suresh, S., Mohmood, R., Ramachandra, Y., & Pandey, A. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-s5-s19 · Cited by 231
Automated modelling of signal transduction networks
Steffen, M. A., Petti, A. A., Aach, J., D’haeseleer, P., & Church, G. M. (2002) · BMC Bioinformatics · doi:10.1186/1471-2105-3-34 · Cited by 226
Protein interactions and disease: computational approaches to uncover the etiology of diseases
Kann, M. G. (2007) · Briefings in Bioinformatics · doi:10.1093/bib/bbm031 · Cited by 202
Systematic identification of functional orthologs based on protein network comparisonPreprint
Bandyopadhyay, S., Sharan, R., & Ideker, T. (2006) · Genome Research · doi:10.1101/gr.4526006 · Cited by 191
Self-citationWhere Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps
Huang, H., Jedynak, B. M., & Bader, J. S. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030214 · Cited by 182
Yeang, C., Ideker, T., & Jaakkola, T. (2004) · Journal of Computational Biology · doi:10.1089/1066527041410382 · Cited by 164
Self-citationA genomic approach of the hepatitis C virus generates a protein interaction map
Flajolet, M., Rotondo, G., Daviet, L., Bergametti, F., Inchauspé, G., Tiollais, P., Transy, C., & Legrain, P. (2000) · Gene · doi:10.1016/s0378-1119(99)00511-9 · Cited by 164
The Plasmodium protein network diverges from those of other eukaryotes
Suthram, S., Sittler, T., & Ideker, T. (2005) · Nature · doi:10.1038/nature04135 · Cited by 134
Self-citationIdentification of Key Processes Underlying Cancer Phenotypes Using Biologic Pathway Analysis
Efroni, S., Schaefer, C. F., & Buetow, K. H. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000425 · Cited by 132
eQED: an efficient method for interpreting eQTL associations using protein networks
Suthram, S., Beyer, A., Karp, R. M., Eldar, Y. C., & Ideker, T. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.4 · Cited by 130
Self-citationSaid, M. R., Begley, T. J., Oppenheim, A. V., Lauffenburger, D. A., & Samson, L. D. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0405996101 · Cited by 122
Analysis of gene expression data with pathway scores.
Zien, A., Küffner, R., Zimmer, R., & Lengauer, T. (2000) · PubMed · Cited by 120
Ma, X., Lee, H., Wang, L., & Sun, F. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl569 · Cited by 114
SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments
Ourfali, O., Shlomi, T., Ideker, T., Ruppin, E., & Sharan, R. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm170 · Cited by 110
Self-citationContext-sensitive data integration and prediction of biological networks
Myers, C. L., & Troyanskaya, O. G. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm332 · Cited by 108
Diffusion Kernel-Based Logistic Regression Models for Protein Function Prediction
Lee, H., Tu, Z., Deng, M., Sun, F., & Chen, T. (2006) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2006.10.40 · Cited by 104
An integrative approach for causal gene identification and gene regulatory pathway inference
Tu, Z., Wang, L., Arbeitman, M. N., Chen, T., & Sun, F. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl234 · Cited by 94
Validation and refinement of gene-regulatory pathways on a network of physical interactions
Yeang, C., Mak, H. C., McCuine, S., Workman, C. T., Jaakkola, T., & Ideker, T. (2005) · Genome biology · doi:10.1186/gb-2005-6-7-r62 · Cited by 84
Self-citationA systems‐level approach to mapping the telomere length maintenance gene circuitry
Shachar, R., Ungar, L., Kupiec, M., Ruppin, E., & Sharan, R. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.13 · Cited by 54
Self-citationCharacterizing disease states from topological properties of transcriptional regulatory networks
Tuck, D. P., Kluger, H. M., & Kluger, Y. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-236 · Cited by 42
Detecting remotely related proteins by their interactions and sequence similarity
Espadaler, J., Aragüés, R., Eswar, N., Martı́-Renom, M. A., Querol, E., Avilés, F. X., Šali, A., & Oliva, B. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0500831102 · Cited by 37
Predicting protein functions with message passing algorithms
Leone, M., & Pagnani, A. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth491 · Cited by 33
Werther, M. (2008) · Advances in biochemical engineering, biotechnology · doi:10.1007/978-3-540-68820-4 · Cited by 26
Dove, A. (1999) · Nature Biotechnology · doi:10.1038/6104 · Cited by 10
Cited by
Sorted by citations
Network medicine: a network-based approach to human disease
Barabási, A.-L., Gulbahce, N., & Loscalzo, J. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2918 · Cited by 5,034
Biological and Chemical Approaches to Diseases of Proteostasis Deficiency
Powers, E. T., Morimoto, R. I., Dillin, A., Kelly, J. W., & Balch, W. E. (2009) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.052308.114844 · Cited by 1,149
ConsensusPathDB: toward a more complete picture of cell biology
Kamburov, A., Pentchev, K., Galicka, H., Wierling, C., Lehrach, H., & Herwig, R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1156 · Cited by 671
Prioritizing candidate disease genes by network-based boosting of genome-wide association dataPreprint
Lee, I., Singh-Blom, U. M., Wang, P. I., Shim, J. E., & Marcotte, E. M. (2011) · Genome Research · doi:10.1101/gr.118992.110 · Cited by 690
Network propagation: a universal amplifier of genetic associations
Cowen, L., Ideker, T., Raphael, B. J., & Sharan, R. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.38 · Cited by 669
Self-citation
Metadata
- Authors
- Ideker, T., & Sharan, R.
- Affiliations
- University of California San Diego (US)
- Tel Aviv University (IL)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2008-04
- Volume
- 18
- Issue
- 4
- Pages
- 644-652
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC3863981
- OpenAlex
- W2100025044
- Cited by
- 817
- References
- 104
- Citations by year
- 2026: 7 · 2025: 16 · 2024: 21 · 2023: 30 · 2022: 15 · 2021: 33 · 2020: 50 · 2019: 46 · 2018: 40 · 2017: 42 · 2016: 43 · 2015: 64 · 2014: 61 · 2013: 81 · 2012: 77
- Type
- posted content
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- public-domain
- Locations
- Genome Research (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Israel Science Foundation
- National Institutes of Health
- National Institute of General Medical Sciences (GM 070743, R01GM070743)
- National Institute of Environmental Health Sciences (ES14811, R01ES014811)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Health Sciences › Medicine › Health Informatics › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- protein-protein interaction network, disease-associated genes, network characteristics, molecular basis of disease, protein function prediction, molecular evolution, infectious diseases, personalized medicine
- MeSH terms
- Disease, Fungal Proteins, Humans, Huntington Disease, Phenotype, Yeasts, Gene Expression Regulation, Neoplastic, Case-Control Studies, Genetic Predisposition to Disease, Protein Interaction Mapping, Genetic Diseases, Inborn, Gene Regulatory Networks
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
