The DOI matches its Crossref record; 52 of the 52 references it cites were found in a registry or an index.
Systematic Discovery of Human Gene Function and Principles of Modular Organization through Phylogenetic Profiling
Abstract
Functional links between genes can be predicted using phylogenetic profiling, by correlating the appearance and loss of homologs in subsets of species. However, effective genome-wide phylogenetic profiling has been hindered by the large fraction of human genes related to each other through historical duplication events. Here, we overcame this challenge by automatically profiling over 30,000 groups of homologous human genes (orthogroups) representing the entire protein-coding genome across 177 eukaryotic species (hOP profiles). By generating a full pairwise orthogroup phylogenetic co-occurrence matrix, we derive unbiased genome-wide predictions of functional modules (hOP modules). Our approach predicts functions for hundreds of poorly characterized genes. The results suggest evolutionary constraints that lead components of protein complexes and metabolic pathways to co-evolve while genes in signaling and transcriptional networks do not. As a proof of principle, we validated two subsets of candidates experimentally for their predicted link to the actin-nucleating WASH complex and cilia/basal body function.
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“The CCC complex comprises twelve components, the coiled coil domain-containing proteins CCDC22 and CCDC93 and ten COMMD (copper metabolism MURR1 [Mouse U2af1-rs1 region 1) domain) family members COMMD1-COMMD10.2,16,17,18,19”
From Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome (2023) · cites this paper as [18]
Experimental — accuracy not yet measuredIn the citing paper
“It comprises two sub-assemblies: Retriever composed of VPS35L, VPS26C, and VPS29; and the CCC complex which contains twelve subunits: COMMD1-COMMD10 and the coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93.”
From Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome (2023) · cites this paper as [18]
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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1094 · Cited by 4,398
The Spliceosome: Design Principles of a Dynamic RNP Machine
Wahl, M. C., Will, C. L., & Lührmann, R. (2009) · Cell · doi:10.1016/j.cell.2009.02.009 · Cited by 2,665
Evolution by gene duplication: An update
Zhang, J. (2003) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(03)00033-8 · Cited by 2,201
Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter
Baughman, J. M., Perocchi, F., Girgis, H. S., Plovanich, M., Belcher-Timme, C. A., Sancak, Y., Bao, X. R., Strittmatter, L., Goldberger, O., Bogorad, R. L., et al. (2011) · Nature · doi:10.1038/nature10234 · Cited by 1,906
Computer Control of Microscopes Using µManager
Edelstein, A., Amodaj, N., Hoover, K., Vale, R. D., & Stuurman, N. (2010) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb1420s92 · Cited by 1,678
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D., & Yeates, T. O. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.8.4285 · Cited by 1,585
Turning a hobby into a job: How duplicated genes find new functions
Conant, G. C., & Wolfe, K. H. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2482 · Cited by 1,281
A nucleator arms race: cellular control of actin assembly
Campellone, K. G., & Welch, M. D. (2010) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2867 · Cited by 928
Berg, J. S., Powell, B. C., & Cheney, R. E. (2001) · Molecular Biology of the Cell · doi:10.1091/mbc.12.4.780 · Cited by 770
Cited by
Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome
Healy, M. D., McNally, K. E., Butkovič, R., Chilton, M., Kato, K., Sacharz, J., McConville, C., Moody, E. R. R., Shaw, S., Planelles-Herrero, V. J., et al. (2023) · Cell · doi:10.1016/j.cell.2023.04.003 · Cited by 91
Structural insights into the architecture and membrane interactions of the conserved COMMD proteins
Healy, M. D., Hospenthal, M. K., Hall, R. J., Chandra, M., Chilton, M., Tillu, V., Chen, K.-E., Celligoi, D. J., McDonald, F. J., Cullen, P. J., et al. (2018) · eLife · doi:10.7554/elife.35898 · Cited by 50
Structure and interactions of the endogenous human Commander complex
Laulumaa, S., Kumpula, E.-P., Huiskonen, J. T., & Varjosalo, M. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01246-1 · Cited by 46
Nagy, L. G., Merényi, Z., Hegedüs, B., & Bálint, B. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkz1241 · Cited by 43
Sailem, H. Z., Rittscher, J., & Pelkmans, L. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199083 · Cited by 16
Nishimura, Y., Omae, K., Tominaga, K., & Iwasaki, W. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaf182 · Cited by 1
Endosomal protein DENND10 promotes developmental competence of neurite extension
Li, A., Zhang, J., Ma, C., Qi, L., Hu, Q., Li, Q., Fang, Y., Song, J., Liu, Y., & Zhang, Y. (2025) · iScience · doi:10.1016/j.isci.2025.112385
Metadata
- Authors
- Dey, G., Jaimovich, A., Collins, S. R., Seki, A., & Meyer, T.
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2015-02
- Volume
- 10
- Issue
- 6
- Pages
- 993-1006
- ISSN
- 2211-1247
- PMC
- PMC5016211
- Cited by
- 77
- References
- 52
- Language
- en
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- creativecommons.org/licenses/by-nc-nd/3.0/ (vor)
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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.
