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Zhang F, Zhang Y, Zhu X, Chen X, Lu F, Zhang X. DeepSG2PPI: A Protein-Protein Interaction Prediction Method Based on Deep Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2907-2919. [PMID: 37079417 DOI: 10.1109/tcbb.2023.3268661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Protein-protein interaction (PPI) plays an important role in almost all life activities. Many protein interaction sites have been confirmed by biological experiments, but these PPI site identification methods are time-consuming and expensive. In this study, a deep learning-based PPI prediction method, named DeepSG2PPI, is developed. First, the protein sequence information is retrieved and the local context information of each amino acid residue is calculated. A two-dimensional convolutional neural network (2D-CNN) model is employed to extract features from a two-channel coding structure, in which an attention mechanism is embedded to assign higher weights to key features. Second, the global statistical information of each amino acid residue and the relationship graph between the protein and GO (Gene Ontology) function annotation are built, and the graph embedding vector is constructed to represent the biological features of the protein. Finally, a 2D-CNN model and two 1D-CNN models are combined for PPI prediction. The comparison analysis with existing algorithms shows that the DeepSG2PPI method has better performance. It provides more accurate and effective PPI site prediction, which will be helpful in reducing the cost and failure rate of biological experiments.
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Wessolly M, Mairinger E, Borchert S, Bankfalvi A, Mach P, Schmid KW, Kimmig R, Buderath P, Mairinger FD. CAF-Associated Paracrine Signaling Worsens Outcome and Potentially Contributes to Chemoresistance in Epithelial Ovarian Cancer. Front Oncol 2022; 12:798680. [PMID: 35311102 PMCID: PMC8927667 DOI: 10.3389/fonc.2022.798680] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/07/2022] [Indexed: 01/06/2023] Open
Abstract
Background High-grade serous ovarian cancer (HGSOC) is the predominant and deadliest form of ovarian cancer. Some of its histological subtypes can be distinguished by frequent occurrence of cancer-associated myofibroblasts (CAFs) and desmoplastic stroma reaction (DSR). In this study, we want to explore the relationship between therapy outcome and the activity of CAF-associated signaling pathways in a homogeneous HGSOC patient collective. Furthermore, we want to validate these findings in a general Epithelial ovarian cancer (EOC) cohort. Methods The investigation cohort consists of 24 HGSOC patients. All of them were treated with platinum-based components and clinical follow-up was available. The validation cohort was comprised of 303 patients. Sequencing data (whole transcriptome) and clinical data were extracted from The Cancer Genome Atlas (TCGA). RNA of HGSOC patients was isolated using a Maxwell RSC instrument and the appropriate RNA isolation kit. For digital expression analysis a custom-designed gene panel was employed. All genes were linked to various DSR- and CAF- associated pathways. Expression analysis was performed on the NanoString nCounter platform. Finally, data were explored using the R programming environment (v. 4.0.3). Result In total, 15 CAF-associated genes were associated with patients’ survival. More specifically, 6 genes (MMP13, CGA, EPHA3, PSMD9, PITX2, PHLPP1) were linked to poor therapy outcome. Though a variety of different pathways appeared to be associated with therapy failure, many were related to CAF paracrine signaling, including MAPK, Ras and TGF-β pathways. Similar results were obtained from the validation cohort. Discussion In this study, we could successfully link CAF-associated pathways, as shown by increased Ras, MAPK and PI3K-Akt signaling to therapy failure (chemotherapy) in HGSOC and EOCs in general. As platinum-based chemotherapy has been the state-of-the-art therapy to treat HGSOC for decades, it is necessary to unveil the reasons behind resistance developments and poor outcome. In this work, CAF-associated signaling is shown to compromise therapy response. In the validation cohort, CAF-associated signaling is also associated with therapy failure in general EOC, possibly hinting towards a conserved mechanism. Therefore, it may be helpful to stratify HGSOC patients for CAF activity and consider alternative treatment options.
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Affiliation(s)
- Michael Wessolly
- Institute of Pathology, University Hospital Essen, Essen, Germany
- *Correspondence: Michael Wessolly,
| | - Elena Mairinger
- Institute of Pathology, University Hospital Essen, Essen, Germany
| | - Sabrina Borchert
- Institute of Pathology, University Hospital Essen, Essen, Germany
| | - Agnes Bankfalvi
- Institute of Pathology, University Hospital Essen, Essen, Germany
| | - Pawel Mach
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
| | | | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
| | - Paul Buderath
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
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Mairinger F, Bankfalvi A, Schmid KW, Mairinger E, Mach P, Walter RF, Borchert S, Kasimir-Bauer S, Kimmig R, Buderath P. Digital Immune-Related Gene Expression Signatures In High-Grade Serous Ovarian Carcinoma: Developing Prediction Models For Platinum Response. Cancer Manag Res 2019; 11:9571-9583. [PMID: 31814759 PMCID: PMC6858803 DOI: 10.2147/cmar.s219872] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/28/2019] [Indexed: 12/18/2022] Open
Abstract
Purpose Response to platinum-based therapy is a major prognostic factor in high-grade serous ovarian cancer (HGSOC). While the exact mechanisms of platinum-resistance remain unclear, evidence is accumulating for a connection between the organism’s immune-response and response to platinum. However, predictive tools are missing. This study was performed to examine the putative role of the genetic tumor immune-microenvironment in mediating differential chemotherapy response in HGSOC patients. Patients and methods Expression profiling of 770 immune-related genes was performed in tumor tissues from 23 HGSOC cases. Tumors were screened for prognostic and predictive biomarkers using the NanoString nCounter platform for digital gene expression analysis with the appurtenant PanCancer Immune Profiling panel. As validation cohort, gene expression data (RNA Seq) of 303 patients with epithelial ovarian carcinoma (EOC) were retrieved from the The Cancer Genome Atlas (TCGA) database. Different scoring-systems were computed for prediction of risk-of-resistance to cisplatin, disease-free survival (DFS) and overall survival (OS). Results Validated on the TCGA-dataset, the developed scores identified 11 significantly differentially expressed genes (p <0.01**) associated with platinum response. HSD11B1 was highly significantly associated with lower risk of recurrence and 7 targets were found highly significantly influencing OS time (p <0.01**). Conclusion Our results suggest that response to platinum-based therapy and DFS in ovarian HGSOC is associated with distinct gene-expression patterns related to the tumor immune-system. We generated predictive scoring systems which proved valid when applied to a set of 303 EOC patients.
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Affiliation(s)
- Fabian Mairinger
- Institute for Pathology, University Hospital Essen, Essen, Germany
| | - Agnes Bankfalvi
- Institute for Pathology, University Hospital Essen, Essen, Germany
| | | | - Elena Mairinger
- Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Pawel Mach
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
| | - Robert Fh Walter
- Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sabrina Borchert
- Institute for Pathology, University Hospital Essen, Essen, Germany
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
| | - Paul Buderath
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
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Characterization of human proteins with different subcellular localizations by topological and biological properties. Genomics 2018; 111:1831-1838. [PMID: 30543849 DOI: 10.1016/j.ygeno.2018.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/02/2018] [Accepted: 12/07/2018] [Indexed: 11/20/2022]
Abstract
Knowing the protein localization can provide valuable information resource for elucidating protein function. In recent years, with the advances of human genomics and proteomics, it is possible to characterize human proteins that are located in different subcellular localizations. In this study, we used the topological properties and biological properties to characterize human proteins with six subcellular localizations. Almost all of these properties were found to be significantly different among six protein categories. Network topology analysis indicated that several significant topological properties, including the degree and k-core, were higher for the mitochondrial proteins. Biological property analysis showed that the nuclear proteins appeared to be correlated with important biological function. We hope these findings may provide some important help for comprehensive understanding the biological function of proteins, and prediction of protein subcellular localizations in human.
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Chen W, Yang H, Feng P, Ding H, Lin H. iDNA4mC: identifying DNA N4-methylcytosine sites based on nucleotide chemical properties. Bioinformatics 2018; 33:3518-3523. [PMID: 28961687 DOI: 10.1093/bioinformatics/btx479] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/25/2017] [Indexed: 12/24/2022] Open
Abstract
Motivation DNA N4-methylcytosine (4mC) is an epigenetic modification. The knowledge about the distribution of 4mC is helpful for understanding its biological functions. Although experimental methods have been proposed to detect 4mC sites, they are expensive for performing genome-wide detections. Thus, it is necessary to develop computational methods for predicting 4mC sites. Results In this work, we developed iDNA4mC, the first webserver to identify 4mC sites, in which DNA sequences are encoded with both nucleotide chemical properties and nucleotide frequency. The predictive results of the rigorous jackknife test and cross species test demonstrated that the performance of iDNA4mC is quite promising and holds high potential to become a useful tool for identifying 4mC sites. Availability and implementation The user-friendly web-server, iDNA4mC, is freely accessible at http://lin.uestc.edu.cn/server/iDNA4mC. Contact chenweiimu@gmail.com or hlin@uestc.edu.cn.
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Affiliation(s)
- Wei Chen
- Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063000, China
| | - Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Pengmian Feng
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063000, China
| | - Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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Zhang Q, Wang S, Pan Y, Su D, Lu Q, Zuo Y, Yang L. Characterization of proteins in different subcellular localizations for Escherichia coli K12. Genomics 2018; 111:1134-1141. [PMID: 30026105 DOI: 10.1016/j.ygeno.2018.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/07/2018] [Accepted: 07/11/2018] [Indexed: 10/28/2022]
Abstract
Knowing the comprehensive knowledge about the protein subcellular localization is an important step to understand the function of the proteins. Recent advances in system biology have allowed us to develop more accurate methods for characterizing the proteins at subcellular localization level. In this study, the analysis method was developed to characterize the topological properties and biological properties of the cytoplasmic proteins, inner membrane proteins, outer membrane proteins and periplasmic proteins in Escherichia coli (E. coli). Statistical significant differences were found in all topological properties and biological properties among proteins in different subcellular localizations. In addition, investigation was carried out to analyze the differences in 20 amino acid compositions for four protein categories. We also found that there were significant differences in all of the 20 amino acid compositions. These findings may be helpful for understanding the comprehensive relationship between protein subcellular localization and biological function.
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Affiliation(s)
- Qi Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shiyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yi Pan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Dongqing Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Qianzi Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yongchun Zuo
- The State key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China.
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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Zhu J, Wang J, Ding Y, Liu B, Xiao W. A systems-level approach for investigating organophosphorus pesticide toxicity. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 149:26-35. [PMID: 29149660 DOI: 10.1016/j.ecoenv.2017.10.066] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/28/2017] [Accepted: 10/31/2017] [Indexed: 06/07/2023]
Abstract
The full understanding of the single and joint toxicity of a variety of organophosphorus (OP) pesticides is still unavailable, because of the extreme complex mechanism of action. This study established a systems-level approach based on systems toxicology to investigate OP pesticide toxicity by incorporating ADME/T properties, protein prediction, and network and pathway analysis. The results showed that most OP pesticides are highly toxic according to the ADME/T parameters, and can interact with significant receptor proteins to cooperatively lead to various diseases by the established OP pesticide -protein and protein-disease networks. Furthermore, the studies that multiple OP pesticides potentially act on the same receptor proteins and/or the functionally diverse proteins explained that multiple OP pesticides could mutually enhance toxicological synergy or additive on a molecular/systematic level. To the end, the integrated pathways revealed the mechanism of toxicity of the interaction of OP pesticides and elucidated the pathogenesis induced by OP pesticides. This study demonstrates a systems-level approach for investigating OP pesticide toxicity that can be further applied to risk assessments of various toxins, which is of significant interest to food security and environmental protection.
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Affiliation(s)
- Jingbo Zhu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning 116034, PR China; Institute of Chemistry and Applications of Plant Resources, Dalian Polytechnic University, Dalian, Liaoning 16034, PR China.
| | - Jing Wang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning 116034, PR China; Institute of Chemistry and Applications of Plant Resources, Dalian Polytechnic University, Dalian, Liaoning 16034, PR China; Jiangsu Kanion Pharmaceutical Co. Ltd., Lianyungang, Jiangsu 222000, PR China; State Key Laboratory of Pharmaceutical New-tech for Chinese Medicine, Lianyungang, Jiangsu 222000, PR China
| | - Yan Ding
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning 116034, PR China; Institute of Chemistry and Applications of Plant Resources, Dalian Polytechnic University, Dalian, Liaoning 16034, PR China
| | - Baoyue Liu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning 116034, PR China; Institute of Chemistry and Applications of Plant Resources, Dalian Polytechnic University, Dalian, Liaoning 16034, PR China
| | - Wei Xiao
- Jiangsu Kanion Pharmaceutical Co. Ltd., Lianyungang, Jiangsu 222000, PR China; State Key Laboratory of Pharmaceutical New-tech for Chinese Medicine, Lianyungang, Jiangsu 222000, PR China
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Characterize the relationship between essential and TATA-containing genes for S. cerevisiae by network topologies in the perturbation sensitivity network. Genomics 2016; 108:177-183. [DOI: 10.1016/j.ygeno.2016.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 09/01/2016] [Accepted: 09/01/2016] [Indexed: 01/11/2023]
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9
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Yang L, Wang S, Zhou M, Chen X, Zuo Y, Sun D, Lv Y. Comparative analysis of housekeeping and tissue-selective genes in human based on network topologies and biological properties. Mol Genet Genomics 2016; 291:1227-41. [PMID: 26897376 DOI: 10.1007/s00438-016-1178-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/26/2016] [Indexed: 01/14/2023]
Abstract
Housekeeping genes are genes that are turned on most of the time in almost every tissue to maintain cellular functions. Tissue-selective genes are predominantly expressed in one or a few biologically relevant tissue types. Benefitting from the massive gene expression microarray data obtained over the past decades, the properties of housekeeping and tissue-selective genes can now be investigated on a large-scale manner. In this study, we analyzed the topological properties of housekeeping and tissue-selective genes in the protein-protein interaction (PPI) network. Furthermore, we compared the biological properties and amino acid usage between these two gene groups. The results indicated that there were significant differences in topological properties between housekeeping and tissue-selective genes in the PPI network, and housekeeping genes had higher centrality properties and may play important roles in the complex biological network environment. We also found that there were significant differences in multiple biological properties and many amino acid compositions. The functional genes enrichment and subcellular localizations analysis was also performed to investigate the characterization of housekeeping and tissue-selective genes. The results indicated that the two gene groups showed significant different enrichment in drug targets, disease genes and toxin targets, and located in different subcellular localizations. At last, the discriminations between the properties of two gene groups were measured by the F-score, and expression stage had the most discriminative index in all properties. These findings may elucidate the biological mechanisms for understanding housekeeping and tissue-selective genes and may contribute to better annotate housekeeping and tissue-selective genes in other organisms.
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Affiliation(s)
- Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Shiyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Meng Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xiaowen Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yongchun Zuo
- The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot, 010021, China
| | - Dianjun Sun
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, China.
| | - Yingli Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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Yang L, Hao D, Lv Y, Zuo Y, Jiang W. Genome-wide characterization of essential, toxicity-modulating and no-phenotype genes in S. cerevisiae. Gene 2015; 559:1-8. [PMID: 25576218 DOI: 10.1016/j.gene.2015.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 12/25/2014] [Accepted: 01/04/2015] [Indexed: 11/30/2022]
Abstract
Based on the requirements for an organism's viability, genes can be classified into essential genes and non-essential genes. Non-essential genes can be further classified into toxicity-modulating genes and no-phenotype genes based on the fitness phenotype of yeast cells when the gene is deleted under DNA-damaging conditions. In this study, graph theoretical approaches were used to characterize essential, toxicity-modulating and no-phenotype genes for S. cerevisiae in the physical interaction (PI) network and the perturbation sensitivity (PS) network. We also gained previously published biological datasets to gain a more complete understanding of the differences and relationships between essential, toxicity-modulating genes and no-phenotype genes. The analysis results indicate that toxicity-modulating genes have similar properties as essential genes, and toxicity-modulating genes might represent a middle ground between essential genes and no-phenotype genes, suggesting that cells initiate highly coordinated responses to damage that are similar to those needed for vital cellular functions. These findings may elucidate the mechanisms for understanding toxicity-modulating processes relevant to certain diseases.
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Affiliation(s)
- Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Dapeng Hao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Yingli Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Yongchun Zuo
- The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot 010021, PR China.
| | - Wei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
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Yang L, Hao D, Wang J, Xing X, Lv Y, Zuo Y, Jiang W. Characterization of proteins in S. cerevisiae with subcellular localizations. MOLECULAR BIOSYSTEMS 2015; 11:1360-9. [DOI: 10.1039/c5mb00124b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Acquiring comprehensive knowledge of protein in various subcellular localizations is one of the fundamental goals in cell biology and proteomics.
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Affiliation(s)
- Lei Yang
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- PR China
| | - Dapeng Hao
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- PR China
| | - Jizhe Wang
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- PR China
| | - Xudong Xing
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- PR China
| | - Yingli Lv
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- PR China
| | - Yongchun Zuo
- The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education
- College of Life Sciences
- Inner Mongolia University
- Hohhot 010021
- PR China
| | - Wei Jiang
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- PR China
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12
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Yang L, Wang J, Lv Y, Hao D, Zuo Y, Li X, Jiang W. Characterization of TATA-containing genes and TATA-less genes in S. cerevisiae by network topologies and biological properties. Genomics 2014; 104:562-71. [DOI: 10.1016/j.ygeno.2014.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 10/01/2014] [Accepted: 10/04/2014] [Indexed: 01/11/2023]
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Analysis and identification of essential genes in humans using topological properties and biological information. Gene 2014; 551:138-51. [DOI: 10.1016/j.gene.2014.08.046] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 08/25/2014] [Indexed: 12/19/2022]
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System analysis of LWDH related genes based on text mining in biological networks. BIOMED RESEARCH INTERNATIONAL 2014; 2014:484926. [PMID: 25243143 PMCID: PMC4163428 DOI: 10.1155/2014/484926] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 01/06/2023]
Abstract
Liuwei-dihuang (LWDH) is widely used in traditional Chinese medicine (TCM), but its molecular mechanism about gene interactions is unclear. LWDH genes were extracted from the existing literatures based on text mining technology. To simulate the complex molecular interactions that occur in the whole body, protein-protein interaction networks (PPINs) were constructed and the topological properties of LWDH genes were analyzed. LWDH genes have higher centrality properties and may play important roles in the complex biological network environment. It was also found that the distances within LWDH genes are smaller than expected, which means that the communication of LWDH genes during the biological process is rapid and effectual. At last, a comprehensive network of LWDH genes, including the related drugs and regulatory pathways at both the transcriptional and posttranscriptional levels, was constructed and analyzed. The biological network analysis strategy used in this study may be helpful for the understanding of molecular mechanism of TCM.
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15
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Human proteins characterization with subcellular localizations. J Theor Biol 2014; 358:61-73. [PMID: 24862400 DOI: 10.1016/j.jtbi.2014.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 05/04/2014] [Accepted: 05/05/2014] [Indexed: 11/20/2022]
Abstract
Proteins are responsible for performing the vast majority of cellular functions which are critical to a cell's survival. The knowledge of the subcellular localization of proteins can provide valuable information about their molecular functions. Therefore, one of the fundamental goals in cell biology and proteomics is to analyze the subcellular localizations and functions of these proteins. Recent large-scale human genomics and proteomics studies have made it possible to characterize human proteins at a subcellular localization level. In this study, according to the annotation in Swiss-Prot, 8842 human proteins were classified into seven subcellular localizations. Human proteins in the seven subcellular localizations were compared by using topological properties, biological properties, codon usage indices, mRNA expression levels, protein complexity and physicochemical properties. All these properties were found to be significantly different in the seven categories. In addition, based on these properties and pseudo-amino acid compositions, a machine learning classifier was built for the prediction of protein subcellular localization. The study presented here was an attempt to address the aforementioned properties for comparing human proteins of different subcellular localizations. We hope our findings presented in this study may provide important help for the prediction of protein subcellular localization and for understanding the general function of human proteins in cells.
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Yang L, Wang J, Wang H, Lv Y, Zuo Y, Jiang W. Characterization of essential genes by topological properties in the perturbation sensitivity network. Biochem Biophys Res Commun 2014; 448:473-9. [PMID: 24802397 DOI: 10.1016/j.bbrc.2014.04.136] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 04/25/2014] [Indexed: 11/29/2022]
Abstract
Genes that are indispensable for survival are called essential genes. In recent years, the analysis of essential genes has become extremely important for understanding the way a cell functions. With the advent of large-scale gene expression profiling technologies, it is now possible to profile transcriptional changes in the entire genome of Saccharomyces cerevisiae. Notwithstanding the accumulation of gene expression profiling in recent years, only a few studies have used these data to construct the network for S. cerevisiae. In this paper, based on the transcriptional profiling of the S. cerevisiae genome in hundreds of different gene disruptions, the perturbation sensitivity (PS) network is constructed. A scale-free topology with node degree following a power-law distribution is shown in the PS network. Twelve topological properties are used to investigate the characteristics of essential and non-essential genes in the PS network. Most of the properties are found to be statistically discriminative between essential and non-essential genes. In addition, the F-score is used to estimate the essentiality of each property, and the core number demonstrates the highest F-score among all properties.
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Affiliation(s)
- Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Jizhe Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Huiping Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Yingli Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Yongchun Zuo
- The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot 010021, PR China.
| | - Wei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
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