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Matsui Y, Abe Y, Uno K, Miyano S. RoDiCE: robust differential protein co-expression analysis for cancer complexome. Bioinformatics 2022; 38:1269-1276. [PMID: 34529752 DOI: 10.1093/bioinformatics/btab612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 08/09/2021] [Accepted: 08/23/2021] [Indexed: 01/05/2023] Open
Abstract
MOTIVATION The full spectrum of abnormalities in cancer-associated protein complexes remains largely unknown. Comparing the co-expression structure of each protein complex between tumor and healthy cells may provide insights regarding cancer-specific protein dysfunction. However, the technical limitations of mass spectrometry-based proteomics, including contamination with biological protein variants, causes noise that leads to non-negligible over- (or under-) estimating co-expression. RESULTS We propose a robust algorithm for identifying protein complex aberrations in cancer based on differential protein co-expression testing. Our method based on a copula is sufficient for improving identification accuracy with noisy data compared to conventional linear correlation-based approaches. As an application, we use large-scale proteomic data from renal cancer to show that important protein complexes, regulatory signaling pathways and drug targets can be identified. The proposed approach surpasses traditional linear correlations to provide insights into higher-order differential co-expression structures. AVAILABILITY AND IMPLEMENTATION https://github.com/ymatts/RoDiCE. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yusuke Matsui
- Biomedical and Health Informatics Unit, Department of Integrated Health Science, Nagoya University Graduate School of Medicine, 461-8673 Nagoya, Aichi, Japan.,Institute for Glyco-core Research (iGCORE), Nagoya University, 461-8673 Nagoya, Aichi, Japan
| | - Yuichi Abe
- Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, 464-0021 Nagoya, Aichi, Japan
| | - Kohei Uno
- Biomedical and Health Informatics Unit, Department of Integrated Health Science, Nagoya University Graduate School of Medicine, 461-8673 Nagoya, Aichi, Japan
| | - Satoru Miyano
- Department of Integrated Data Science, M&D Data Science Center, Tokyo Medical and Dental University, 113-8510 Tokyo, Japan
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Will T, Helms V. Differential analysis of combinatorial protein complexes with CompleXChange. BMC Bioinformatics 2019; 20:300. [PMID: 31159772 PMCID: PMC6547514 DOI: 10.1186/s12859-019-2852-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 04/26/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although a considerable number of proteins operate as multiprotein complexes and not on their own, organism-wide studies so far are only able to quantify individual proteins or protein-coding genes in a condition-specific manner for a sizeable number of samples, but not their assemblies. Consequently, there exist large amounts of transcriptomic data and an increasing amount of data on proteome abundance, but quantitative knowledge on complexomes is missing. This deficiency impedes the applicability of the powerful tool of differential analysis in the realm of macromolecular complexes. Here, we present a pipeline for differential analysis of protein complexes based on predicted or manually assigned complexes and inferred complex abundances, which can be easily applied on a whole-genome scale. RESULTS We observed for simulated data that results obtained by our complex abundance estimation algorithm were in better agreement with the ground truth and physicochemically more reasonable compared to previous efforts that used linear programming while running in a fraction of the time. The practical usability of the method was assessed in the context of transcription factor complexes in human monocyte and lymphoblastoid samples. We demonstrated that our new method is robust against false-positive detection and reports deregulated complexomes that can only be partially explained by differential analysis of individual protein-coding genes. Furthermore we showed that deregulated complexes identified by the tool potentially harbor significant yet unused information content. CONCLUSIONS CompleXChange allows to analyze deregulation of the protein complexome on a whole-genome scale by integrating a plethora of input data that is already available. A platform-independent Java binary, a user guide with example data and the source code are freely available at https://sourceforge.net/projects/complexchange/ .
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Affiliation(s)
- Thorsten Will
- Center for Bioinformatics, Saarland University, Campus E2.1, Saarbrücken, 66123, Germany.,Graduate School of Computer Science, Saarland University, Campus E1.3, Saarbrücken, 66123, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Campus E2.1, Saarbrücken, 66123, Germany.
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3
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Galanos P, Pappas G, Polyzos A, Kotsinas A, Svolaki I, Giakoumakis NN, Glytsou C, Pateras IS, Swain U, Souliotis VL, Georgakilas AG, Geacintov N, Scorrano L, Lukas C, Lukas J, Livneh Z, Lygerou Z, Chowdhury D, Sørensen CS, Bartek J, Gorgoulis VG. Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability. Genome Biol 2018; 19:37. [PMID: 29548335 PMCID: PMC5857109 DOI: 10.1186/s13059-018-1401-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/30/2018] [Indexed: 02/07/2023] Open
Abstract
Background Genomic instability promotes evolution and heterogeneity of tumors. Unraveling its mechanistic basis is essential for the design of appropriate therapeutic strategies. In a previous study, we reported an unexpected oncogenic property of p21WAF1/Cip1, showing that its chronic expression in a p53-deficient environment causes genomic instability by deregulation of the replication licensing machinery. Results We now demonstrate that p21WAF1/Cip1 can further fuel genomic instability by suppressing the repair capacity of low- and high-fidelity pathways that deal with nucleotide abnormalities. Consequently, fewer single nucleotide substitutions (SNSs) occur, while formation of highly deleterious DNA double-strand breaks (DSBs) is enhanced, crafting a characteristic mutational signature landscape. Guided by the mutational signatures formed, we find that the DSBs are repaired by Rad52-dependent break-induced replication (BIR) and single-strand annealing (SSA) repair pathways. Conversely, the error-free synthesis-dependent strand annealing (SDSA) repair route is deficient. Surprisingly, Rad52 is activated transcriptionally in an E2F1-dependent manner, rather than post-translationally as is common for DNA repair factor activation. Conclusions Our results signify the importance of mutational signatures as guides to disclose the repair history leading to genomic instability. We unveil how chronic p21WAF1/Cip1 expression rewires the repair process and identifies Rad52 as a source of genomic instability and a candidate therapeutic target. Electronic supplementary material The online version of this article (10.1186/s13059-018-1401-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Panagiotis Galanos
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece.,Danish Cancer Society Research Centre, Strandboulevarden 49, DK-2100, Copenhagen, Denmark
| | - George Pappas
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece.,Danish Cancer Society Research Centre, Strandboulevarden 49, DK-2100, Copenhagen, Denmark
| | - Alexander Polyzos
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str, GR-11527, Athens, Greece
| | - Athanassios Kotsinas
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece
| | - Ioanna Svolaki
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece
| | | | | | - Ioannis S Pateras
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece
| | - Umakanta Swain
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Vassilis L Souliotis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave, GR-11635, Athens, Greece
| | - Alexandros G Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), 15780, Zografou, Athens, Greece
| | | | - Luca Scorrano
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Claudia Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jiri Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zvi Livneh
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Zoi Lygerou
- Laboratory of Biology, School of Medicine, University of Patras, 26505, Patras, Rio, Greece
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.,Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA
| | - Claus Storgaard Sørensen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Copenhagen, Denmark
| | - Jiri Bartek
- Danish Cancer Society Research Centre, Strandboulevarden 49, DK-2100, Copenhagen, Denmark. .,Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77, Stockholm, Sweden.
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece. .,Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str, GR-11527, Athens, Greece. .,Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Wilmslow Road, Manchester, M20 4QL, UK.
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Jalili M, Gebhardt T, Wolkenhauer O, Salehzadeh-Yazdi A. Unveiling network-based functional features through integration of gene expression into protein networks. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2349-2359. [PMID: 29466699 DOI: 10.1016/j.bbadis.2018.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 02/02/2023]
Abstract
Decoding health and disease phenotypes is one of the fundamental objectives in biomedicine. Whereas high-throughput omics approaches are available, it is evident that any single omics approach might not be adequate to capture the complexity of phenotypes. Therefore, integrated multi-omics approaches have been used to unravel genotype-phenotype relationships such as global regulatory mechanisms and complex metabolic networks in different eukaryotic organisms. Some of the progress and challenges associated with integrated omics studies have been reviewed previously in comprehensive studies. In this work, we highlight and review the progress, challenges and advantages associated with emerging approaches, integrating gene expression and protein-protein interaction networks to unravel network-based functional features. This includes identifying disease related genes, gene prioritization, clustering protein interactions, developing the modules, extract active subnetworks and static protein complexes or dynamic/temporal protein complexes. We also discuss how these approaches contribute to our understanding of the biology of complex traits and diseases. This article is part of a Special Issue entitled: Cardiac adaptations to obesity, diabetes and insulin resistance, edited by Professors Jan F.C. Glatz, Jason R.B. Dyck and Christine Des Rosiers.
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Affiliation(s)
- Mahdi Jalili
- Hematology, Oncology and SCT Research Center, Tehran University of Medical Sciences, Tehran, Iran; Hematologic Malignancies Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Tom Gebhardt
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
| | - Ali Salehzadeh-Yazdi
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany.
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Srihari S, Yong CH, Patil A, Wong L. Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes. FEBS Lett 2015; 589:2590-602. [PMID: 25913176 DOI: 10.1016/j.febslet.2015.04.026] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/14/2015] [Accepted: 04/14/2015] [Indexed: 12/30/2022]
Abstract
Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand the functional organisation of cells. In this review, we discuss the key contributions of computational methods developed till date (approximately between 2003 and 2015) for identifying complexes from the network of interacting proteins (PPI network). We evaluate in depth the performance of these methods on PPI datasets from yeast, and highlight their limitations and challenges, in particular at detecting sparse and small or sub-complexes and discerning overlapping complexes. We describe methods for integrating diverse information including expression profiles and 3D structures of proteins with PPI networks to understand the dynamics of complex formation, for instance, of time-based assembly of complex subunits and formation of fuzzy complexes from intrinsically disordered proteins. Finally, we discuss methods for identifying dysfunctional complexes in human diseases, an application that is proving invaluable to understand disease mechanisms and to discover novel therapeutic targets. We hope this review aptly commemorates a decade of research on computational prediction of complexes and constitutes a valuable reference for further advancements in this exciting area.
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Affiliation(s)
- Sriganesh Srihari
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4067, Australia.
| | - Chern Han Yong
- Department of Computer Science, National University of Singapore, Singapore 117417, Singapore
| | - Ashwini Patil
- Human Genome Centre, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Limsoon Wong
- Department of Computer Science, National University of Singapore, Singapore 117417, Singapore
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Ranganathan S, Tan TW, Schönbach C. InCoB2014: Systems Biology update from the Asia-Pacific. Introduction. BMC SYSTEMS BIOLOGY 2014; 8 Suppl 4:I1. [PMID: 25521591 PMCID: PMC4290681 DOI: 10.1186/1752-0509-8-s4-i1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Selected papers from the 13th International Conference on Bioinformatics (InCoB2014), July 31-2 August, 2014 in Sydney, Australia have been compiled in this supplement. These range from network analysis and gene regulatory networks to systems level biological analysis, providing the 2014 update to InCoB's computational systems biology research.
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Affiliation(s)
- Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599
| | - Christian Schönbach
- Department of Biology, School of Science and Technology, Nazarbayev University, Astana 010000, Republic of Kazakhstan
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
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