The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
A Map of the Interactome Network of the Metazoan C. elegans
Open accessAbstract
To initiate studies on how protein-protein interaction (or “interactome”) networks relate to multicellular functions, we have mapped a large fraction of the Caenorhabditis elegans interactome network. Starting with a subset of metazoan-specific proteins, more than 4000 interactions were identified from high-throughput, yeast two-hybrid (HT=Y2H) screens. Independent coaffinity purification assays experimentally validated the overall quality of this Y2H data set. Together with already described Y2H interactions and interologs predicted in silico , the current version of the Worm Interactome (WI5) map contains ∼5500 interactions. Topological and biological features of this interactome network, as well as its integration with phenome and transcriptome data sets, lead to numerous biological hypotheses.
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.
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
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
Cited by
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
BioGRID: a general repository for interaction datasets
Stark, C. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj109 · Cited by 3,960
The economy of brain network organization
Bullmore, E., & Sporns, O. (2012) · Nature Reviews Neuroscience · doi:10.1038/nrn3214 · Cited by 3,284
Organization, development and function of complex brain networks
SPORNS, O., CHIALVO, D., KAISER, M., & HILGETAG, C. (2004) · Trends in Cognitive Sciences · doi:10.1016/j.tics.2004.07.008 · Cited by 2,055
Interactome Networks and Human Disease
Vidal, M., Cusick, M. E., & Barabási, A.-L. (2011) · Cell · doi:10.1016/j.cell.2011.02.016 · Cited by 1,771
Self-citationProtein Analysis by Shotgun/Bottom-up Proteomics
Zhang, Y., Fonslow, B. R., Shan, B., Baek, M.-C., & Yates, J. R. (2013) · Chemical Reviews · doi:10.1021/cr3003533 · Cited by 1,491
High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
Yu, H., Braun, P., Yıldırım, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., et al. (2008) · Science · doi:10.1126/science.1158684 · Cited by 1,392
Self-citationFlexible nets: The roles of intrinsic disorder in protein interaction networks
Dunker, A. K., Cortese, M. S., Romero, P., Iakoucheva, L. M., & Uversky, V. N. (2005) · The FEBS Journal · doi:10.1111/j.1742-4658.2005.04948.x · Cited by 1,122
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
Self-citationCell Fates as High-Dimensional Attractor States of a Complex Gene Regulatory Network
Huang, S., Eichler, G., Bar-Yam, Y., & Ingber, D. E. (2005) · Physical Review Letters · doi:10.1103/physrevlett.94.128701 · Cited by 775
Comparative Genomics of Centrality and Essentiality in Three Eukaryotic Protein-Interaction Networks
Hahn, M. W., & Kern, A. D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi072 · Cited by 656
ConsensusPathDB--a database for integrating human functional interaction networks
Kamburov, A., Wierling, C., Lehrach, H., & Herwig, R. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn698 · Cited by 565
A Protein Complex Network of Drosophila melanogaster
Guruharsha, K. G., Rual, J.-F., Zhai, B., Mintseris, J., Vaidya, P., Vaidya, N., Beekman, C., Wong, C., Rhee, D. Y., Cenaj, O., et al. (2011) · Cell · doi:10.1016/j.cell.2011.08.047 · Cited by 616
Self-citationPanorama of ancient metazoan macromolecular complexes
Wan, C., Borgeson, B., Phanse, S., Tu, F., Drew, K., Clark, G., Xiong, X., Kagan, O., Kwan, J., Bezginov, A., et al. (2015) · Nature · doi:10.1038/nature14877 · Cited by 546
Protein interaction mapping: A Drosophila case study
Formstecher, E., Aresta, S., Collura, V., Hamburger, A., Meil, A., Trehin, A., Reverdy, C., Betin, V., Maire, S., Brun, C., et al. (2005) · Genome Research · doi:10.1101/gr.2659105 · Cited by 542
Systematic interpretation of genetic interactions using protein networks
Kelley, R., & Ideker, T. (2005) · Nature Biotechnology · doi:10.1038/nbt1096 · Cited by 437
Analysis of the Human Endogenous Coregulator Complexome
Malovannaya, A., Lanz, R. B., Jung, S. Y., Bulynko, Y., Le, N. T., Chan, D. W., Ding, C., Shi, Y., Yucer, N., Krenciute, G., et al. (2011) · Cell · doi:10.1016/j.cell.2011.05.006 · Cited by 432
Hepatitis C virus infection protein network
de Chassey, B., Navratil, V, Tafforeau, L., Hiet, M. S., Aublin‐Gex, A., Agaugué, S., Meiffren, G., Pradezynski, F., Faria, B. F., Chantier, T., et al. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.66 · Cited by 384
Self-citationBiological control through regulated transcriptional coactivators
Spiegelman, B. M., & Heinrich, R. (2004) · Cell · doi:10.1016/j.cell.2004.09.037 · Cited by 377
Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks
Neduva, V., Linding, R., Su-Angrand, I., Stark, A., Masi, F. D., Gibson, T. J., Lewis, J., Serrano, L., & Russell, R. B. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030405 · Cited by 359
Disorder and Sequence Repeats in Hub Proteins and Their Implications for Network Evolution
Dosztányi, Z., Chen, J., Dunker, A. K., Simon, I., & Tompa, P. (2006) · Journal of Proteome Research · doi:10.1021/pr060171o · Cited by 341
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B.-J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., et al. (2006) · Journal of Biology · doi:10.1186/jbiol36 · Cited by 326
Lee, I., Lehner, B., Crombie, C., Wong, W., Fraser, A. G., & Marcotte, E. M. (2008) · Nature Genetics · doi:10.1038/ng.2007.70 · Cited by 281
Self-citationHypothesis-based RNAi screening identifies neuroprotective genes in a Parkinson's disease model
Hamamichi, S., Rivas, R. N., Knight, A. L., Cao, S., Caldwell, K. A., & Caldwell, G. A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0711018105 · Cited by 268
Combining biological networks to predict genetic interactions
Wong, S. L., Zhang, L. V., Tong, A. H. Y., Li, Z., Goldberg, D. S., King, O. D., Lesage, G., Vidal, M., Andrews, B., Bussey, H., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0406614101 · Cited by 245
Self-citationMyD88-5 links mitochondria, microtubules, and JNK3 in neurons and regulates neuronal survival
Kim, Y., Zhou, P., Qian, L., Chuang, J.-Z., Lee, J., Li, C., Iadecola, C., Nathan, C., & Ding, A. (2007) · The Journal of Experimental Medicine · doi:10.1084/jem.20070868 · Cited by 234
Jia, D., Gomez, T. S., Metlagel, Z., Umetani, J., Otwinowski, Z., Rosen, M. K., & Billadeau, D. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0913293107 · Cited by 232
Protein interactome reveals converging molecular pathways among autism disorders
Sakai, Y., Shaw, C. A., Dawson, B. C., Dugas, D. V., Al-Mohtaseb, Z., Hill, D. E., & Zoghbi, H. Y. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3002166 · Cited by 226
Self-citationChiang, W.-C., Ching, T.-T., Lee, H. C., Mousigian, C., & Hsu, A.-L. (2012) · Cell · doi:10.1016/j.cell.2011.12.019 · Cited by 219
Integrating physical and genetic maps: from genomes to interaction networks
Beyer, A., Bandyopadhyay, S., & Ideker, T. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2144 · Cited by 207
Where 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
Geometric De-noising of Protein-Protein Interaction Networks
Kuchaiev, O., Rašajski, M., Higham, D. J., & Pržulj, N. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000454 · Cited by 180
A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system
van Wijk, S. J. L., de Vries, S. J., Kemmeren, P., Huang, A., Boelens, R., Bonvin, A. M. J. J., & Timmers, H. T. M. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.55 · Cited by 164
Binding properties and evolution of homodimers in protein-protein interaction networks
Ispolatov, I. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki678 · Cited by 169
The Arabidopsis genome: A foundation for plant research
Bevan, M., & Walsh, S. (2005) · Genome Research · doi:10.1101/gr.3723405 · Cited by 153
Robotic cloning and protein production platform of the northeast structural genomics consortium
Acton, T. B., Gunsalus, K. C., Xiao, R., Ma, L. C., Aramini, J., Baran, M. C., Chiang, Y.-W., Climent, T., Cooper, B., Denissova, N. G., et al. (2005) · Methods in Enzymology · doi:10.1016/s0076-6879(05)94008-1 · Cited by 129
Self-citationReactome pathway analysis to enrich biological discovery in proteomics data sets
Haw, R., Hermjakob, H., D'Eustachio, P., & Stein, L. (2011) · PROTEOMICS · doi:10.1002/pmic.201100066 · Cited by 117
Intraflagellar transport complex structure and cargo interactions
Bhogaraju, S., Engel, B. D., & Lorentzen, E. (2013) · Cilia · doi:10.1186/2046-2530-2-10 · Cited by 111
A map of human protein interactions derived from co‐expression of human mRNAs and their orthologs
Ramani, A. K., Li, Z., Hart, G. T., Carlson, M. W., Boutz, D. R., & Marcotte, E. M. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.19 · Cited by 78
Hsing, M., Byler, K. G., & Cherkasov, A. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-80 · Cited by 66
New benchmark metrics for protein‐protein docking methods
Gao, M., & Skolnick, J. (2011) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22987 · Cited by 42
A modified TurboID approach identifies tissue-specific centriolar components in C. elegans
Holzer, E., Rumpf-Kienzl, C., Falk, S., & Dammermann, A. (2022) · PLOS Genetics · doi:10.1371/journal.pgen.1010150 · Cited by 37
Gingras, A.-C., & Raught, B. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.03.065 · Cited by 34
The Inner Nuclear Membrane Protein Nemp1 Is a New Type of RanGTP-Binding Protein in Eukaryotes
Shibano, T., Mamada, H., Hakuno, F., Takahashi, S.-I., & Taira, M. (2015) · PLOS ONE · doi:10.1371/journal.pone.0127271 · Cited by 27
Early Systems Biology and Prebiotic Networks
Shenhav, B., Solomon, A., Lancet, D., & Kafri, R. (2005) · Lecture Notes in Computer Science · doi:10.1007/978-3-540-32126-2_2 · Cited by 13
Medwig-Kinney, T. N., Kinney, B. A., Martinez, M. A. Q., Yee, C., Sirota, S. S., Mullarkey, A. A., Somineni, N., Hippler, J., Zhang, W., Shen, K., et al. (2023) · doi:10.7554/elife.84355.2
Self-citation
Metadata
- Authors
- Li, S., Armstrong, C. M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P.-O., Han, J.-D. J., Chesneau, A., Hao, T., Goldberg, D. S., Li, N., Martinez, M., Rual, J.-F., Lamesch, P., Xu, L., Tewari, M., Wong, S. L., Zhang, L. V., Berriz, G. F., Jacotot, L., Vaglio, P., Reboul, J., Hirozane-Kishikawa, T., Li, Q., Gabel, H. W., Elewa, A., Baumgartner, B., Rose, D. J., Yu, H., Bosak, S., Sequerra, R., Fraser, A., Mango, S. E., Saxton, W. M., Strome, S., van den Heuvel, S., Piano, F., Vandenhaute, J., Sardet, C., Gerstein, M., Doucette-Stamm, L., Gunsalus, K. C., Harper, J. W., Cusick, M. E., Roth, F. P., Hill, D. E., & Vidal, M.
- Venue
- Science
- Published
- 2004-01-23
- Volume
- 303
- Issue
- 5657
- Pages
- 540-543
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2113019448
- Cited by
- 1,628
- References
- 1
- FWCI
- 64.95
- Type
- journal article
- Language
- en
- Open access
- green
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
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
