Biological process linkage networks
Open accessAbstract
BACKGROUND: The traditional approach to studying complex biological networks is based on the identification of interactions between internal components of signaling or metabolic pathways. By comparison, little is known about interactions between higher order biological systems, such as biological pathways and processes. We propose a methodology for gleaning patterns of interactions between biological processes by analyzing protein-protein interactions, transcriptional co-expression and genetic interactions. At the heart of the methodology are the concept of Linked Processes and the resultant network of biological processes, the Process Linkage Network (PLN). RESULTS: We construct, catalogue, and analyze different types of PLNs derived from different data sources and different species. When applied to the Gene Ontology, many of the resulting links connect processes that are distant from each other in the hierarchy, even though the connection makes eminent sense biologically. Some others, however, carry an element of surprise and may reflect mechanisms that are unique to the organism under investigation. In this aspect our method complements the link structure between processes inherent in the Gene Ontology, which by its very nature is species-independent. As a practical application of the linkage of processes we demonstrate that it can be effectively used in protein function prediction, having the power to increase both the coverage and the accuracy of predictions, when carefully integrated into prediction methods. CONCLUSIONS: Our approach constitutes a promising new direction towards understanding the higher levels of organization of the cell as a system which should help current efforts to re-engineer ontologies and improve our ability to predict which proteins are involved in specific biological processes.
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
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?
Developing a multiscale representation requires analyzing communities in biological networks at more than one scale, defining and identifying communities at each scale, and tracing containment to infer a hierarchical map.
“Developing a multiscale representation requires analyzing communities in biological networks at more than one scale. Communities (clusters of highly interconnected nodes) are first defined and identified at each of multiple scales; subsequently, communities that are contained within other communities, in whole or in part, can be traced to infer a hierarchical map (Figure 2) (Dotan-Cohen et al., 20”
From Mapping the multiscale structure of biological systems (2021) · cites this paper as Dotan-Cohen et al., 2009
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Lethality and centrality in protein networks
Jeong, H., Mason, S., Barabási, A., & Oltvai, Z. (2001) · Nature · doi:10.1038/35075138 · Cited by 5,327 · see citing works
Spellman, P. T., Sherlock, G. J., Zhang, M. Q., Iyer, V. R., Anders, K. R., Eisen, M. B., Brown, P. O., Botstein, D., & Futcher, B. (1998) · Molecular Biology of the Cell · doi:10.1091/mbc.9.12.3273 · Cited by 4,724 · see citing works
The Gene Ontology (GO) database and informatics resource
Gene Ontology Consortium (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh036 · Cited by 4,533 · see citing works
BioGRID: a general repository for interaction datasets
Stark, C. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj109 · Cited by 3,960 · see citing works
An Information-Theoretic Definition of Similarity
Lin, D. (1998) · Cited by 3,803 · see citing works
Classes of small-world networks
Amaral, L. A. N., Scala, A., Barthélémy, M., & Stanley, H. E. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.200327197 · Cited by 3,051 · see citing works
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 2,544 · see citing works
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 · see citing works
A Protein Interaction Map of Drosophila melanogaster
Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y. L., Ooi, C., Godwin, B., Vitols, E., et al. (2003) · Science · doi:10.1126/science.1090289 · Cited by 2,266 · see citing works
A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules
Stuart, J. M., Segal, E., Koller, D., & Kim, S. K. (2003) · Science · doi:10.1126/science.1087447 · Cited by 2,235 · see citing works
Xénarios, I. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.303 · Cited by 1,746 · see citing works
Segal, E., Shapira, M., Regev, A., Pe’er, D., Botstein, D., Koller, D., & Friedman, N. (2003) · Nature Genetics · doi:10.1038/ng1165 · Cited by 1,686 · see citing works
A network of protein–protein interactions in yeast
Schwikowski, B., Uetz, P. H., & Fields, S. (2000) · Nature Biotechnology · doi:10.1038/82360 · Cited by 1,371 · see citing works
A combined algorithm for genome-wide prediction of protein function
Marcotte, E. M., Pellegrini, M. A., Thompson, M. J., Yeates, T. O., & Eisenberg, D. S. (1999) · Nature · doi:10.1038/47048 · Cited by 901 · see citing works
Lord, P., Stevens, R., Brass, A., & Goble, C. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg153 · Cited by 839 · see citing works
Conserved patterns of protein interaction in multiple species
Sharan, R., Suthram, S., Kelley, R., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R. M., & Ideker, T. E. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409522102 · Cited by 788 · see citing works
Finley, D. J., Bartel, B., & Varshavsky, A. J. (1989) · Nature · doi:10.1038/338394a0 · Cited by 720 · see citing works
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 · see citing works
Tong, A. H. Y., Drees, B., Nardelli, G., Bader, G. D., Brannetti, B., Castagnoli, L., Evangelista, M., Ferracuti, S., Nelson, B., Paoluzi, S., et al. (2002) · Science · doi:10.1126/science.1064987 · Cited by 692 · see citing works
A new measure for functional similarity of gene products based on Gene Ontology
Schlicker, A., Domingues, F. S., Rahnenführer, J., & Lengauer, T. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-302 · Cited by 692 · see citing works
Butte, A. J., Tamayo, P., Slonim, D. K., Golub, T. R., & Kohane, I. S. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.220392197 · Cited by 604 · see citing works
Online Predicted Human Interaction Database
Brown, K. R., & Jurišica, I. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti273 · Cited by 601 · 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
Modular epistasis in yeast metabolism
Segrè, D., DeLuna, A., Church, G. M., & Kishony, R. (2005) · Nature Genetics · doi:10.1038/ng1489 · Cited by 575 · see citing works
Ünal, E., Arbel‐Eden, A., Sattler, U., Shroff, R., Lichten, M., Haber, J. E., & Koshland, D. E. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.11.027 · Cited by 568 · see citing works
Systematic interpretation of genetic interactions using protein networks
Kelley, R., & Ideker, T. (2005) · Nature Biotechnology · doi:10.1038/nbt1096 · Cited by 437 · see citing works
Dynamic Complex Formation During the Yeast Cell Cycle
de Lichtenberg, U., Jensen, L. J., Brunak, S., & Peer Bork, B. (2005) · Science · doi:10.1126/science.1105103 · Cited by 405 · see citing works
Assessment of prediction accuracy of protein function from protein–protein interaction data
Hishigaki, H., Nakai, K., Ono, T., Tanigami, A., & Takagi, T. (2001) · Yeast · doi:10.1002/yea.706 · Cited by 362 · see citing works
Wu, L. F., Hughes, T. R., Davierwala, A. P., Robinson, M. D., Stoughton, R. B., & Altschuler, S. J. (2002) · Nature Genetics · doi:10.1038/ng906 · Cited by 349 · see citing works
Protein interaction networks from yeast to human
Bork, P., Jensen, L. J., von Mering, C., Ramani, A. K., Lee, I., & Marcotte, E. M. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.05.003 · Cited by 344 · see citing works
Whole-genome annotation by using evidence integration in functional-linkage networks
Karaöz, U., Murali, T. M., Letovsky, S., Zheng, Y., Ding, C., Cantor, C. R., & Kasif, S. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307326101 · Cited by 315 · see citing works
Self-citationCombining 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 · see citing works
Assessing semantic similarity measures for the characterization of human regulatory pathways
Guo, X., Liu, R., Shriver, C. D., et al. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl042 · Cited by 180 · see citing works
Modular organization of protein interaction networks
Luo, F., Yang, Y., Chen, C., Chang, R. L., Zhou, J. Z., & Scheuermann, R. H. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl562 · Cited by 167 · see citing works
Larochelle, M., Drouin, S., Robert, F., & Turcotte, B. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.02450-05 · Cited by 144 · see citing works
Function prediction and protein networks
Huynen, M. A., Snel, ., von Mering, C., & Peer Bork, B. (2003) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(03)00009-7 · Cited by 141 · see citing works
Lubovac-Pilav, Z., Gamalielsson, J., & Olsson, B. E. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21071 · Cited by 101 · see citing works
Potential Roles for Ubiquitin and the Proteasome during Ribosome Biogenesis
Stavreva, D. A., Kawasaki, M., Dundr, M., Koberna, K., Müller, W. G., Tsujimura-Takahashi, T., Komatsu, W., Hayano, T., Isobe, T., Raška, I., et al. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.02227-05 · Cited by 96 · see citing works
Comparing classical pathways and modern networks: towards the development of an edge ontology
Lu, L. J., Sboner, A., Huang, Y. J., Lu, H. X., Gianoulis, T. A., Yip, K. Y.-L., Kim, P. M., Montelione, G. T., & Gerstein, M. (2007) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2007.06.003 · Cited by 59 · see citing works
Probabilistic Discovery of Overlapping Cellular Processes and Their Regulation
Battle, A. J., Segal, E., & Koller, D. (2005) · Journal of Computational Biology · doi:10.1089/cmb.2005.12.909 · Cited by 37 · see citing works
The Cretaceous Flora of North America
Dawson, J. W. (1884) · Nature · doi:10.1038/030631b0 · Cited by 8 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
A gene ontology inferred from molecular networks
Dutkowski, J., Kramer, M., Surma, M. A., Balakrishnan, R., Cherry, J. M., Krogan, N. J., & Ideker, T. (2013) · Nature Biotechnology · doi:10.1038/nbt.2463 · Cited by 184 · see citing works
Mapping the multiscale structure of biological systems
Schaffer, L. V., & Ideker, T. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.012 · Cited by 75 · see citing works
- Authors
- Dotan-Cohen, D., Letovsky, S., Melkman, A. A., & Kasif, S.
- Affiliations
- Ben-Gurion University of the Negev (IL)
- Boston University (US)
- Corresponding author
- Dotan-Cohen, Dikla
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2009-04-23
- Volume
- 4
- Issue
- 4
- Pages
- e5313
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC2669181
- OpenAlex
- W2003031595
- Cited by
- 38
- References
- 41
- Citations by year
- 2025: 2 · 2021: 2 · 2019: 2 · 2018: 1 · 2017: 3 · 2016: 1 · 2015: 6 · 2014: 5 · 2013: 4 · 2012: 5
- FWCI
- 1.61
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- OpenBU (Boston University) (submittedVersion)
- Funders
- National Science Foundation
- National Institutes of Health (5r01hg003367-03, LM008748)
- National Human Genome Research Institute (R01 HG003367, R01 HG003367-01A1, R33HG002850, HG003367)
- U.S. National Library of Medicine (U54LM008748)
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- protein-protein interaction, genetic interactions, Gene Ontology, protein function prediction
- MeSH terms
- Algorithms, Biological Phenomena, Proteins, Saccharomyces cerevisiae, Computational Biology, Protein Interaction Mapping, Databases, Protein, 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
