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ShengPeng Y, Hong W. RSCMDA: Prediction of Potential miRNA-Disease Associations Based on a Robust Similarity Constraint Learning Method. Interdiscip Sci 2021; 13:559-571. [PMID: 34247324 DOI: 10.1007/s12539-021-00459-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 11/25/2022]
Abstract
With the rapid development of biotechnology and computer technology, increasing studies have shown that the occurrence of many diseases in the human body is closely related to the dysfunction of miRNA, and the relationship between them has become a new research hotspot. Exploring disease-related miRNAs information provides a new perspective for understanding the etiology and pathogenesis of diseases. In this study, we proposed a new method based on similarity constrained learning (RSCMDA) to infer disease-associated miRNAs. Considering the problems of noise and incomplete information in current biological datasets, we designed a new framework RSCMDA, which can learn a new disease similarity network and miRNA similarity network based on the existing biological information, and then update the predicted miRNA-disease associations using robust similarity constraint learning method. Consequently, the AUC scores obtained in the global and local cross-validation of RSCMDA are 0.9465 and 0.8494, respectively, which are superior to the other methods. Besides, the prediction performance of RSCMDA is further confirmed by the case study on lung Neoplasms, because 94% of the top 50 miRNAs predicted by the RSCMDA method are confirmed from the existing biological databases or research results. All the results show that RSCMDA is a reliable and effective framework, which can be used as new technology to explore the relationship between miRNA and disease.
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Affiliation(s)
- Yu ShengPeng
- School of Information Science and Engineering, Shandong Normal University, Jinan, 250358, China
| | - Wang Hong
- School of Information Science and Engineering, Shandong Normal University, Jinan, 250358, China.
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Jin J, Guang M, Ogbuehi AC, Li S, Zhang K, Ma Y, Acharya A, Guo B, Peng Z, Liu X, Deng Y, Fang Z, Zhu X, Hua S, Li C, Haak R, Ziebolz D, Schmalz G, Liu L, Xu B, Huang X. Shared Molecular Mechanisms between Alzheimer's Disease and Periodontitis Revealed by Transcriptomic Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6633563. [PMID: 33869630 PMCID: PMC8032519 DOI: 10.1155/2021/6633563] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/20/2021] [Accepted: 03/09/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To investigate the genetic crosstalk mechanisms that link periodontitis and Alzheimer's disease (AD). BACKGROUND Periodontitis, a common oral infectious disease, is associated with Alzheimer's disease (AD) and considered a putative contributory factor to its progression. However, a comprehensive investigation of potential shared genetic mechanisms between these diseases has not yet been reported. METHODS Gene expression datasets related to periodontitis were downloaded from the Gene Expression Omnibus (GEO) database, and differential expression analysis was performed to identify differentially expressed genes (DEGs). Genes associated with AD were downloaded from the DisGeNET database. Overlapping genes among the DEGs in periodontitis and the AD-related genes were defined as crosstalk genes between periodontitis and AD. The Boruta algorithm was applied to perform feature selection from these crosstalk genes, and representative crosstalk genes were thus obtained. In addition, a support vector machine (SVM) model was constructed by using the scikit-learn algorithm in Python. Next, the crosstalk gene-TF network and crosstalk gene-DEP (differentially expressed pathway) network were each constructed. As a final step, shared genes among the crosstalk genes and periodontitis-related genes in DisGeNET were identified and denoted as the core crosstalk genes. RESULTS Four datasets (GSE23586, GSE16134, GSE10334, and GSE79705) pertaining to periodontitis were included in the analysis. A total of 48 representative crosstalk genes were identified by using the Boruta algorithm. Three TFs (FOS, MEF2C, and USF2) and several pathways (i.e., JAK-STAT, MAPK, NF-kappa B, and natural killer cell-mediated cytotoxicity) were identified as regulators of these crosstalk genes. Among these 48 crosstalk genes and the chronic periodontitis-related genes in DisGeNET, C4A, C4B, CXCL12, FCGR3A, IL1B, and MMP3 were shared and identified as the most pivotal candidate links between periodontitis and AD. CONCLUSIONS Exploration of available transcriptomic datasets revealed C4A, C4B, CXCL12, FCGR3A, IL1B, and MMP3 as the top candidate molecular linkage genes between periodontitis and AD.
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Affiliation(s)
- Jieqi Jin
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Mengkai Guang
- Department of Stomatology, China-Japan Friendship Hospital, Beijing 100029, China
| | | | - Simin Li
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, Leipzig 04103, Germany
| | - Kai Zhang
- Department of Stomatology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Yihong Ma
- Department of Neurology, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Aneesha Acharya
- Dr. D Y Patil Dental College and Hospital, Dr D Y Patil Vidyapeeth, Pimpri, Pune, India
| | - Bihan Guo
- Faculty of Electrical Engineering, Information Technology, and Physics, University Braunschweig, Hans-Sommer-Str. 66, Braunschweig 38106, Germany
| | - Zongwu Peng
- Faculty of Electrical Engineering, Information Technology, and Physics, University Braunschweig, Hans-Sommer-Str. 66, Braunschweig 38106, Germany
| | - Xiangqiong Liu
- Laboratory of Molecular Cell Biology, Beijing Tibetan Hospital, China Tibetology Research Center, 218 Anwaixiaoguanbeili Street, Chaoyang, Beijing 100029, China
| | - Yupei Deng
- Laboratory of Molecular Cell Biology, Beijing Tibetan Hospital, China Tibetology Research Center, 218 Anwaixiaoguanbeili Street, Chaoyang, Beijing 100029, China
| | - Zhaobi Fang
- Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Xiongjie Zhu
- Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Shiting Hua
- Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Cong Li
- Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Rainer Haak
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, Leipzig 04103, Germany
| | - Dirk Ziebolz
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, Leipzig 04103, Germany
| | - Gerhard Schmalz
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, Leipzig 04103, Germany
| | - Lei Liu
- Department of Neurology, Shandong Provincial Third Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 10091 Shandong Province, China
| | - Baohua Xu
- Department of Stomatology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Xiaofeng Huang
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
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Identification of the Potential Biomarkers Involved in the Human Oral Mucosal Wound Healing: A Bioinformatic Study. BIOMED RESEARCH INTERNATIONAL 2021. [DOI: 10.1155/2021/6695245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Objective. To identify the key genetic and epigenetic mechanisms involved in the wound healing process after injury of the oral mucosa. Materials and Methods. Gene expression profiling datasets pertaining to rapid wound healing of oral mucosa were identified using the Gene Expression Omnibus (GEO) database. Differential gene expression analysis was performed to identify differentially expressed genes (DEGs) during oral mucosal wound healing. Next, functional enrichment analysis was performed to identify the biological processes (BPs) and signaling pathways relevant to these DEGs. A protein-protein interaction (PPI) network was constructed to identify hub DEGs. Interaction networks were constructed for both miRNA-target DEGs and DEGs-transcription factors. A DEGs-chemical compound interaction network and a miRNA-small molecular interaction network were also constructed. Results. DEGs were found significantly enriched in several signaling pathways including arachidonic acid metabolism, cell cycle, p53, and ECM-receptor interaction. Hub genes, GABARAPL1, GABARAPL2, HDAC5, MAP1LC3A, AURKA, and PLK1, were identified via PPI network analysis. Two miRNAs, miR-34a-5p and miR-335-5p, were identified as pivotal players in the miRNA-target DEGs network. Four transcription factors FOS, PLAU, BCL6, and RORA were found to play key roles in the TFs-DEGs interaction network. Several chemical compounds including Valproic acid, Doxorubicin, Nickel, and tretinoin and small molecular drugs including atorvastatin, 17β-estradiol, curcumin, and vitamin D3 were noted to influence oral mucosa regeneration by regulating the expression of healing-associated DEGs/miRNAs. Conclusion. Genetic and epigenetic mechanisms and specific drugs were identified as significant molecular mechanisms and entities relevant to oral mucosal healing. These may be valuable potential targets for experimental research.
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Yu MC, Liu JX, Ma XL, Hu B, Fu PY, Sun HX, Tang WG, Yang ZF, Qiu SJ, Zhou J, Fan J, Xu Y. Differential network analysis depicts regulatory mechanisms for hepatocellular carcinoma from diverse backgrounds. Future Oncol 2019; 15:3917-3934. [PMID: 31729887 DOI: 10.2217/fon-2019-0275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To elucidate the integrative combinational gene regulatory network landscape of hepatocellular carcinoma (HCC) molecular carcinogenesis from diverse background. Materials & methods: Modified gene regulatory network analysis was used to prioritize differentially regulated genes and links. Integrative comparisons using bioinformatics methods were applied to identify potential critical molecules and pathways in HCC with different backgrounds. Results: E2F1 with its surrounding regulatory links were identified to play different key roles in the HCC risk factor dysregulation mechanisms. Hsa-mir-19a was identified as showed different effects in the three HCC differential regulation networks, and showed vital regulatory role in HBV-related HCC. Conclusion: We describe in detail the regulatory networks involved in HCC with different backgrounds. E2F1 may serve as a universal target for HCC treatment.
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Affiliation(s)
- Min-Cheng Yu
- Department of Liver Surgery & Transplantation, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis & Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, PR China
| | - Ji-Xiang Liu
- Shanghai Center for Bioinformation Technology & Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai 201203, PR China
| | - Xiao-Lu Ma
- Department of Laboratory Medicine, Shanghai Cancer Center, Fudan University, Shanghai 200032, PR China
| | - Bo Hu
- Department of Liver Surgery & Transplantation, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis & Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, PR China
| | - Pei-Yao Fu
- Department of Liver Surgery & Transplantation, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis & Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, PR China
| | - Hai-Xiang Sun
- Department of Liver Surgery & Transplantation, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis & Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, PR China
| | - Wei-Guo Tang
- Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai 201199, PR China
| | - Zhang-Fu Yang
- Department of Liver Surgery & Transplantation, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis & Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, PR China
| | - Shuang-Jian Qiu
- Department of Liver Surgery & Transplantation, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis & Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, PR China
| | - Jian Zhou
- Department of Liver Surgery & Transplantation, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis & Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, PR China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200032, PR China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, PR China
| | - Jia Fan
- Department of Liver Surgery & Transplantation, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis & Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, PR China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200032, PR China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, PR China
| | - Yang Xu
- Department of Liver Surgery & Transplantation, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis & Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, PR China
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Bo L, Wei B, Wang Z, Kong D, Gao Z, Miao Z. Screening of Critical Genes and MicroRNAs in Blood Samples of Patients with Ruptured Intracranial Aneurysms by Bioinformatic Analysis of Gene Expression Data. Med Sci Monit 2017; 23:4518-4525. [PMID: 28930970 PMCID: PMC5618721 DOI: 10.12659/msm.902953] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background This study aimed to identify more potential genes and miRNAs associated with the pathogenesis of intracranial aneurysms (IAs). Material/Methods The dataset of GSE36791 (accession number) was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened for in the blood samples from patients with ruptured IAs and controls, followed by functional and pathway enrichment analyses. In addition, gene co-expression network was constructed and significant modules were extracted from the network by WGCNA R package. Screening for miRNAs that could regulate DEGs in the modules was performed and an analysis of regulatory relationships was conducted. Results A total of 304 DEGs (167 up-regulated and 137 down-regulated genes) were screened for in blood samples from patients with ruptured IAs compared with those from controls. Functional enrichment analysis showed that the up-regulated genes were mainly associated with immune response and the down-regulated DEGs were mainly concerned with the structure of ribosome and translation. Besides, six functional modules were significantly identified, including four modules enriched by up-regulated genes and two modules enriched by down-regulated genes. Thereinto, the blue, yellow, and turquoise modules of up-regulated genes were all linked with immune response. Additionally, 16 miRNAs were predicted to regulate DEGs in the three modules associated with immune response, such as hsa-miR-1304, hsa-miR-33b, hsa-miR-125b, and hsa-miR-125a-5p. Conclusions Several genes and miRNAs (such as miR-1304, miR-33b, IRS2 and KCNJ2) may take part in the pathogenesis of IAs.
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Affiliation(s)
- Lijuan Bo
- Department of Infections, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Bo Wei
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Zhanfeng Wang
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Daliang Kong
- Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Zheng Gao
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Zhuang Miao
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
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Surveying computational algorithms for identification of miRNA–mRNA regulatory modules. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0208-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Li Q, Li J, Dai W, Li YX, Li YY. Differential regulation analysis reveals dysfunctional regulatory mechanism involving transcription factors and microRNAs in gastric carcinogenesis. Artif Intell Med 2017; 77:12-22. [PMID: 28545608 DOI: 10.1016/j.artmed.2017.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/23/2017] [Accepted: 02/23/2017] [Indexed: 12/12/2022]
Abstract
Gastric cancer (GC) is one of the most incident malignancies in the world. Although lots of featured genes and microRNAs (miRNAs) have been identified to be associated with gastric carcinogenesis, underlying regulatory mechanisms still remain unclear. In order to explore the dysfunctional mechanisms of GC, we developed a novel approach to identify carcinogenesis relevant regulatory relationships, which is characterized by quantifying the difference of regulatory relationships between stages. Firstly, we applied the strategy of differential coexpression analysis (DCEA) to transcriptomic datasets including paired mRNA and miRNA of gastric samples to identify a set of genes/miRNAs related to gastric cancer progression. Based on these genes/miRNAs, we constructed conditional combinatorial gene regulatory networks (cGRNs) involving both transcription factors (TFs) and miRNAs. Enrichment of known cancer genes/miRNAs and predicted prognostic genes/miRNAs was observed in each cGRN. Then we designed a quantitative method to measure differential regulation level of every regulatory relationship between normal and cancer, and the known cancer genes/miRNAs proved to be ranked significantly higher. Meanwhile, we defined differentially regulated link (DRL) by combining differential regulation, differential expression and the regulation contribution of the regulator to the target. By integrating survival analysis and DRL identification, three master regulators TCF7L1, TCF4, and MEIS1 were identified and testable hypotheses of dysfunctional mechanisms underlying gastric carcinogenesis related to them were generated. The fine-tuning effects of miRNAs were also observed. We propose that this differential regulation network analysis framework is feasible to gain insights into dysregulated mechanisms underlying tumorigenesis and other phenotypic changes.
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Affiliation(s)
- Quanxue Li
- School of biotechnology, East China University of Science and Technology, Shanghai, China; Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Junyi Li
- Shanghai Center for Bioinformation Technology, Shanghai, China; Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wentao Dai
- Shanghai Center for Bioinformation Technology, Shanghai, China; Shanghai Industrial Technology Institute, Shanghai, China; Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai, China
| | - Yi-Xue Li
- School of biotechnology, East China University of Science and Technology, Shanghai, China; Shanghai Center for Bioinformation Technology, Shanghai, China; Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Shanghai Industrial Technology Institute, Shanghai, China; Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai, China.
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation Technology, Shanghai, China; Shanghai Industrial Technology Institute, Shanghai, China; Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai, China.
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Vlachos IS, Vergoulis T, Paraskevopoulou MD, Lykokanellos F, Georgakilas G, Georgiou P, Chatzopoulos S, Karagkouni D, Christodoulou F, Dalamagas T, Hatzigeorgiou AG. DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data. Nucleic Acids Res 2016; 44:W128-34. [PMID: 27207881 PMCID: PMC4987956 DOI: 10.1093/nar/gkw455] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/11/2016] [Indexed: 11/20/2022] Open
Abstract
Differential expression analysis (DEA) is one of the main instruments utilized for revealing molecular mechanisms in pathological and physiological conditions. DIANA-mirExTra v2.0 (http://www.microrna.gr/mirextrav2) performs a combined DEA of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded for analysis. Users can combine their data with 350 small-RNA-Seq and 65 RNA-Seq in-house analyzed libraries which are provided by DIANA-mirExTra v2.0. The web server utilizes miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets. More than 450 000 miRNA interactions and 2 000 000 TF binding sites from specific or high-throughput techniques have been incorporated, while accurate miRNA TSS annotation is obtained from microTSS experimental/in silico framework. These comprehensive data sets enable users to perform analyses based solely on experimentally supported information and to uncover central regulators within sequencing data: miRNAs controlling mRNAs and TFs regulating mRNA or miRNA expression. The server also supports predicted miRNA:gene interactions from DIANA-microT-CDS for 4 species (human, mouse, nematode and fruit fly). DIANA-mirExTra v2.0 has an intuitive user interface and is freely available to all users without any login requirement.
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Affiliation(s)
- Ioannis S Vlachos
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 38221 Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece Laboratory for Experimental Surgery and Surgical Research 'N.S. Christeas', Medical School of Athens, University of Athens, Athens 11527, Greece
| | | | - Maria D Paraskevopoulou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 38221 Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece
| | | | - Georgios Georgakilas
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 38221 Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece
| | - Penny Georgiou
- 'Athena' Research and Innovation Center, 11524 Athens, Greece
| | | | - Dimitra Karagkouni
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 38221 Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece
| | | | | | - Artemis G Hatzigeorgiou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 38221 Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece
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Hamed M, Spaniol C, Nazarieh M, Helms V. TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks. Nucleic Acids Res 2015; 43:W283-8. [PMID: 25943543 PMCID: PMC4489273 DOI: 10.1093/nar/gkv418] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/18/2015] [Indexed: 01/27/2023] Open
Abstract
TFmiR is a freely available web server for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease pathogenesis. Since the inner workings of cells rely on the correct functioning of an enormously complex system of activating and repressing interactions that can be perturbed in many ways, TFmiR helps to better elucidate cellular mechanisms at the molecular level from a network perspective. The provided topological and functional analyses promote TFmiR as a reliable systems biology tool for researchers across the life science communities. TFmiR web server is accessible through the following URL: http://service.bioinformatik.uni-saarland.de/tfmir.
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Affiliation(s)
- Mohamed Hamed
- Center for Bioinformatics, Saarland University, 66041 Saarbrucken, Germany
| | - Christian Spaniol
- Center for Bioinformatics, Saarland University, 66041 Saarbrucken, Germany
| | - Maryam Nazarieh
- Center for Bioinformatics, Saarland University, 66041 Saarbrucken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, 66041 Saarbrucken, Germany
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Li L, Lian B, Li C, Li W, Li J, Zhang Y, He X, Li Y, Xie L. Integrative analysis of transcriptional regulatory network and copy number variation in intrahepatic cholangiocarcinoma. PLoS One 2014; 9:e98653. [PMID: 24897108 PMCID: PMC4045758 DOI: 10.1371/journal.pone.0098653] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 05/06/2014] [Indexed: 01/02/2023] Open
Abstract
Background Transcriptional regulatory network (TRN) is used to study conditional regulatory relationships between transcriptional factors and genes. However few studies have tried to integrate genomic variation information such as copy number variation (CNV) with TRN to find causal disturbances in a network. Intrahepatic cholangiocarcinoma (ICC) is the second most common hepatic carcinoma with high malignancy and poor prognosis. Research about ICC is relatively limited comparing to hepatocellular carcinoma, and there are no approved gene therapeutic targets yet. Method We first constructed TRN of ICC (ICC-TRN) using forward-and-reverse combined engineering method, and then integrated copy number variation information with ICC-TRN to select CNV-related modules and constructed CNV-ICC-TRN. We also integrated CNV-ICC-TRN with KEGG signaling pathways to investigate how CNV genes disturb signaling pathways. At last, unsupervised clustering method was applied to classify samples into distinct classes. Result We obtained CNV-ICC-TRN containing 33 modules which were enriched in ICC-related signaling pathways. Integrated analysis of the regulatory network and signaling pathways illustrated that CNV might interrupt signaling through locating on either genomic sites of nodes or regulators of nodes in a signaling pathway. In the end, expression profiles of nodes in CNV-ICC-TRN were used to cluster the ICC patients into two robust groups with distinct biological function features. Conclusion Our work represents a primary effort to construct TRN in ICC, also a primary effort to try to identify key transcriptional modules based on their involvement of genetic variations shown by gene copy number variations (CNV). This kind of approach may bring the traditional studies of TRN based only on expression data one step further to genetic disturbance. Such kind of approach can easily be extended to other disease samples with appropriate data.
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Affiliation(s)
- Ling Li
- School of Life Sciences and Technology, Tongji University, Shanghai, P.R.China
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
| | - Baofeng Lian
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
- School of Life Sciences and Technology, Shanghai Jiaotong University, Shanghai, P.R.China
| | - Chao Li
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
| | - Wei Li
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
| | - Jing Li
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
| | - Yuannv Zhang
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
| | - Xianghuo He
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
| | - Yixue Li
- School of Life Sciences and Technology, Tongji University, Shanghai, P.R.China
- School of Life Sciences and Technology, Shanghai Jiaotong University, Shanghai, P.R.China
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
- * E-mail: (LX); (YL)
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
- * E-mail: (LX); (YL)
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