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Karatzas E, Baltoumas FA, Aplakidou E, Kontou PI, Stathopoulos P, Stefanis L, Bagos PG, Pavlopoulos GA. Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources. Bioinformatics 2023; 39:btad490. [PMID: 37540207 PMCID: PMC10423032 DOI: 10.1093/bioinformatics/btad490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/31/2023] [Accepted: 08/03/2023] [Indexed: 08/05/2023] Open
Abstract
Functional enrichment is the process of identifying implicated functional terms from a given input list of genes or proteins. In this article, we present Flame (v2.0), a web tool which offers a combinatorial approach through merging and visualizing results from widely used functional enrichment applications while also allowing various flexible input options. In this version, Flame utilizes the aGOtool, g: Profiler, WebGestalt, and Enrichr pipelines and presents their outputs separately or in combination following a visual analytics approach. For intuitive representations and easier interpretation, it uses interactive plots such as parameterizable networks, heatmaps, barcharts, and scatter plots. Users can also: (i) handle multiple protein/gene lists and analyse union and intersection sets simultaneously through interactive UpSet plots, (ii) automatically extract genes and proteins from free text through text-mining and Named Entity Recognition (NER) techniques, (iii) upload single nucleotide polymorphisms (SNPs) and extract their relative genes, or (iv) analyse multiple lists of differentially expressed proteins/genes after selecting them interactively from a parameterizable volcano plot. Compared to the previous version of 197 supported organisms, Flame (v2.0) currently allows enrichment for 14 436 organisms. AVAILABILITY AND IMPLEMENTATION Web Application: http://flame.pavlopouloslab.info. Code: https://github.com/PavlopoulosLab/Flame. Docker: https://hub.docker.com/r/pavlopouloslab/flame.
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Affiliation(s)
- Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari (Athens), 16672, Greece
| | - Fotis A Baltoumas
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari (Athens), 16672, Greece
| | - Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari (Athens), 16672, Greece
| | - Panagiota I Kontou
- Department of Mathematics, University of Thessaly, Lamia, 35100, Greece
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, 35131, Greece
| | - Panos Stathopoulos
- 1st Department of Neurology, Eginition Hospital, Athens, 11528, Greece
- School of Medicine, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | - Leonidas Stefanis
- 1st Department of Neurology, Eginition Hospital, Athens, 11528, Greece
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, 35131, Greece
| | - Georgios A Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari (Athens), 16672, Greece
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
- Hellenic Army Academy, Vari, 16673, Greece
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Papaefthimiou M, Kontou PI, Bagos PG, Braliou GG. Antioxidant Activity of Leaf Extracts from Stevia rebaudiana Bertoni Exerts Attenuating Effect on Diseased Experimental Rats: A Systematic Review and Meta-Analysis. Nutrients 2023; 15:3325. [PMID: 37571265 PMCID: PMC10420666 DOI: 10.3390/nu15153325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Stevia (Stevia rebaudiana Bertoni) is an aromatic plant known for its high sweetening power ascribed to its glycosides. Stevia also contains several bioactive compounds showing antioxidant, antiproliferative, antimicrobial, and anti-inflammatory activities. Since inflammation and oxidative stress play critical roles in the pathogenesis of many diseases, stevia emerges as a promising natural product that could support human health. In this study we set out to investigate the way stevia affects oxidative stress markers (e.g., SOD, CAT, GPx, GSH, MDA) in diseased rats administered stevia leaf extracts or glycosides. To this end, we performed an inclusive literature search, following PRISMA guidelines, and recruited multivariate meta-analysis and meta-regression to synthesize all available data on experimental animal models encountering (a) healthy, (b) diseased, and (c) stevia-treated diseased rats. From the 184 articles initially retrieved, 24 satisfied the eligibility criteria, containing 104 studies. Our results demonstrate that regardless of the assay employed, stevia leaf extracts restored all oxidative stress markers to a higher extent compared to pure glycosides. Meta-regression analysis revealed that results from SOD, CAT, GSH, and TAC assays are not statistically significantly different (p = 0.184) and can be combined in meta-analysis. Organic extracts from stevia leaves showed more robust antioxidant properties compared to aqueous or hydroalcoholic ones. The restoration of oxidative markers ranged from 65% to 85% and was exhibited in all tested tissues. Rats with diabetes mellitus were found to have the highest restorative response to stevia leaf extract administration. Our results suggest that stevia leaf extract can act protectively against various diseases through its antioxidant properties. However, which of each of the multitude of stevia compounds contribute to this effect, and to what extent, awaits further investigation.
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Affiliation(s)
- Maria Papaefthimiou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35 131 Lamia, Greece; (M.P.); (P.G.B.)
| | | | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35 131 Lamia, Greece; (M.P.); (P.G.B.)
| | - Georgia G. Braliou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35 131 Lamia, Greece; (M.P.); (P.G.B.)
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Özbek M, Toy HI, Takan I, Asfa S, Arshinchi Bonab R, Karakülah G, Kontou PI, Geronikolou SA, Pavlopoulou A. A Counterintuitive Neutrophil-Mediated Pattern in COVID-19 Patients Revealed through Transcriptomics Analysis. Viruses 2022; 15:104. [PMID: 36680144 PMCID: PMC9866184 DOI: 10.3390/v15010104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/25/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023] Open
Abstract
The COVID-19 pandemic has persisted for almost three years. However, the mechanisms linked to the SARS-CoV-2 effect on tissues and disease severity have not been fully elucidated. Since the onset of the pandemic, a plethora of high-throughput data related to the host transcriptional response to SARS-CoV-2 infections has been generated. To this end, the aim of this study was to assess the effect of SARS-CoV-2 infections on circulating and organ tissue immune responses. We profited from the publicly accessible gene expression data of the blood and soft tissues by employing an integrated computational methodology, including bioinformatics, machine learning, and natural language processing in the relevant transcriptomics data. COVID-19 pathophysiology and severity have mainly been associated with macrophage-elicited responses and a characteristic "cytokine storm". Our counterintuitive findings suggested that the COVID-19 pathogenesis could also be mediated through neutrophil abundance and an exacerbated suppression of the immune system, leading eventually to uncontrolled viral dissemination and host cytotoxicity. The findings of this study elucidated new physiological functions of neutrophils, as well as tentative pathways to be explored in asymptomatic-, ethnicity- and locality-, or staging-associated studies.
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Affiliation(s)
- Melih Özbek
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | - Halil Ibrahim Toy
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | - Işil Takan
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | - Seyedehsadaf Asfa
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | - Reza Arshinchi Bonab
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | | | - Styliani A. Geronikolou
- Clinical, Translational and Experimental Surgery Research Centre, Biomedical Research Foundation Academy of Athens, 11527 Athens, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, UNESCO on Adolescent Health Care, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, 11527 Athens, Greece
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
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Papathanassiou M, Tamposis I, Exarchou-Kouveli KK, Kontou PI, de Paz AT, Mitrakas L, Samara M, Bagos PG, Tzortzis V, Vlachostergios PJ. Immune-based treatment re-challenge in renal cell carcinoma: A systematic review and meta-analysis. Front Oncol 2022; 12:996553. [DOI: 10.3389/fonc.2022.996553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022] Open
Abstract
IntroductionThe use of immune checkpoint inhibitors (ICIs) as a front-line treatment for metastatic renal cell carcinoma (RCC) has significantly improved patient’ outcome. However, little is known about the efficacy or lack thereof of immunotherapy after prior use of anti-PD1/PD-L1 or/and anti-CTLA monoclonal antibodies.MethodsElectronic databases, including PubMed, EMBASE, Medline, Web of Science, and Cochrane Library, were comprehensively searched from inception to July 2022. Objective response rates (ORR), progression-free survival (PFS), and ≥ grade 3 adverse events (AEs) were assessed in the meta-analysis, along with corresponding 95% confidence intervals (CIs) and publication bias.ResultsTen studies which contained a total of 500 patients were included. The pooled ORR was 19% (95% CI: 10, 31), and PFS was 5.6 months (95% CI: 4.1, 7.8). There were ≥ grade 3 AEs noted in 25% of patients (95% CI: 14, 37).ConclusionThis meta-analysis on different second-line ICI-containing therapies in ICI-pretreated mRCC patients supports a modest efficacy and tolerable toxicity.
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Charitou T, Kontou PI, Tamposis IA, Pavlopoulos GA, Braliou GG, Bagos PG. Drug genetic associations with COVID-19 manifestations: a data mining and network biology approach. Pharmacogenomics J 2022; 22:294-302. [PMID: 36171417 PMCID: PMC9517961 DOI: 10.1038/s41397-022-00289-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 07/16/2022] [Accepted: 09/08/2022] [Indexed: 01/08/2023]
Abstract
Available drugs have been used as an urgent attempt through clinical trials to minimize severe cases of hospitalizations with Coronavirus disease (COVID-19), however, there are limited data on common pharmacogenomics affecting concomitant medications response in patients with comorbidities. To identify the genomic determinants that influence COVID-19 susceptibility, we use a computational, statistical, and network biology approach to analyze relationships of ineffective concomitant medication with an adverse effect on patients. We statistically construct a pharmacogenetic/biomarker network with significant drug-gene interactions originating from gene-disease associations. Investigation of the predicted pharmacogenes encompassing the gene-disease-gene pharmacogenomics (PGx) network suggests that these genes could play a significant role in COVID-19 clinical manifestation due to their association with autoimmune, metabolic, neurological, cardiovascular, and degenerative disorders, some of which have been reported to be crucial comorbidities in a COVID-19 patient.
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Tamposis IA, Manios GA, Charitou T, Vennou KE, Kontou PI, Bagos PG. MAGE: An Open-Source Tool for Meta-Analysis of Gene Expression Studies. Biology 2022; 11:biology11060895. [PMID: 35741417 PMCID: PMC9220151 DOI: 10.3390/biology11060895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022]
Abstract
MAGE (Meta-Analysis of Gene Expression) is a Python open-source software package designed to perform meta-analysis and functional enrichment analysis of gene expression data. We incorporate standard methods for the meta-analysis of gene expression studies, bootstrap standard errors, corrections for multiple testing, and meta-analysis of multiple outcomes. Importantly, the MAGE toolkit includes additional features for the conversion of probes to gene identifiers, and for conducting functional enrichment analysis, with annotated results, of statistically significant enriched terms in several formats. Along with the tool itself, a web-based infrastructure was also developed to support the features of this package.
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Affiliation(s)
- Ioannis A. Tamposis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.A.T.); (G.A.M.); (T.C.); (K.E.V.)
| | - Georgios A. Manios
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.A.T.); (G.A.M.); (T.C.); (K.E.V.)
| | - Theodosia Charitou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.A.T.); (G.A.M.); (T.C.); (K.E.V.)
| | - Konstantina E. Vennou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.A.T.); (G.A.M.); (T.C.); (K.E.V.)
| | | | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.A.T.); (G.A.M.); (T.C.); (K.E.V.)
- Correspondence:
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Lianou DT, Skoulakis A, Michael CK, Katsarou EI, Chatzopoulos DC, Solomakos N, Tsilipounidaki K, Florou Z, Cripps PJ, Katsafadou AI, Vasileiou NGC, Dimoveli KS, Bourganou MV, Liagka DV, Papatsiros VG, Kontou PI, Mavrogianni VS, Caroprese M, Petinaki E, Fthenakis GC. Isolation of Listeria ivanovii from Bulk-Tank Milk of Sheep and Goat Farms-From Clinical Work to Bioinformatics Studies: Prevalence, Association with Milk Quality, Antibiotic Susceptibility, Predictors, Whole Genome Sequence and Phylogenetic Relationships. Biology (Basel) 2022; 11:biology11060871. [PMID: 35741392 PMCID: PMC9220212 DOI: 10.3390/biology11060871] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/04/2022] [Accepted: 06/05/2022] [Indexed: 02/03/2023]
Abstract
Simple Summary An extensive countrywide study in Greece revealed that isolation of the zoonotic pathogens Listeria monocytogenes and Listeria ivanovii from the milk produced in sheep or goat farms was infrequent: 1.2% of farms sampled. The presence of pigs on the farms, low average relative humidity in the environment and a high number of animals on the farms were found to be associated with the isolations. Detailed assessment of the L. ivanovii strains, for which there is a paucity of information worldwide, revealed that the isolated strains belonged to the L. ivanovii subsp. ivanovii branch. All strains of the branch appeared to be very similar, with the distance between them being small, which suggests that global spread of this clonal branch is a recent evolutionary event or that the branch is characterized by a slow evolutionary rate. Abstract A cross-sectional study was performed in 325 sheep and 119 goat dairy farms in Greece. Samples of bulk-tank milk were examined by standard microbiological techniques for Listeria spp. Listeria monocytogenes was isolated from one (0.3%) and Listeria ivanovii from three (0.9%) sheep farms. No associations between the isolation of L. monocytogenes or L. ivanovii and milk quality were found. No resistance to antibiotics was identified. Three variables emerged as significant predictors of isolation of the organism: the presence of pigs, low average relative humidity and a high number of ewes on the farm. The three L. ivanovii isolates were assessed in silico for identification of plasmids, prophages, antibiotic resistance genes, virulence factors, CRISPRs and CAS genes. Phylogenetic analysis using the core genome revealed that the three strains belonged to the L. ivanovii subsp. ivanovii branch and were especially close to the PAM 55 strain. All strains of the branch appeared to be very similar, with the distance between them being small.
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Affiliation(s)
- Daphne T. Lianou
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (C.K.M.); (E.I.K.); (N.S.); (P.J.C.); (K.S.D.); (V.G.P.); (V.S.M.)
| | | | - Charalambia K. Michael
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (C.K.M.); (E.I.K.); (N.S.); (P.J.C.); (K.S.D.); (V.G.P.); (V.S.M.)
| | - Eleni I. Katsarou
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (C.K.M.); (E.I.K.); (N.S.); (P.J.C.); (K.S.D.); (V.G.P.); (V.S.M.)
| | - Dimitris C. Chatzopoulos
- Faculty of Public and One Health, University of Thessaly, 43100 Karditsa, Greece; (D.C.C.); (A.I.K.); (M.V.B.)
| | - Nikolaos Solomakos
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (C.K.M.); (E.I.K.); (N.S.); (P.J.C.); (K.S.D.); (V.G.P.); (V.S.M.)
| | | | - Zoe Florou
- University Hospital of Larissa, 41110 Larissa, Greece; (K.T.); (Z.F.); (E.P.)
| | - Peter J. Cripps
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (C.K.M.); (E.I.K.); (N.S.); (P.J.C.); (K.S.D.); (V.G.P.); (V.S.M.)
| | - Angeliki I. Katsafadou
- Faculty of Public and One Health, University of Thessaly, 43100 Karditsa, Greece; (D.C.C.); (A.I.K.); (M.V.B.)
| | - Natalia G. C. Vasileiou
- Faculty of Animal Science, University of Thessaly, 41110 Larissa, Greece; (N.G.C.V.); (D.V.L.)
| | - Konstantina S. Dimoveli
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (C.K.M.); (E.I.K.); (N.S.); (P.J.C.); (K.S.D.); (V.G.P.); (V.S.M.)
| | - Maria V. Bourganou
- Faculty of Public and One Health, University of Thessaly, 43100 Karditsa, Greece; (D.C.C.); (A.I.K.); (M.V.B.)
| | - Dimitra V. Liagka
- Faculty of Animal Science, University of Thessaly, 41110 Larissa, Greece; (N.G.C.V.); (D.V.L.)
| | - Vasileios G. Papatsiros
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (C.K.M.); (E.I.K.); (N.S.); (P.J.C.); (K.S.D.); (V.G.P.); (V.S.M.)
| | | | - Vasia S. Mavrogianni
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (C.K.M.); (E.I.K.); (N.S.); (P.J.C.); (K.S.D.); (V.G.P.); (V.S.M.)
| | - Mariangela Caroprese
- Department of Agriculture, Food, Natural Resources and Engineering (DAFNE), University of Foggia, 71122 Foggia, Italy;
| | - Efthymia Petinaki
- University Hospital of Larissa, 41110 Larissa, Greece; (K.T.); (Z.F.); (E.P.)
| | - George C. Fthenakis
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (C.K.M.); (E.I.K.); (N.S.); (P.J.C.); (K.S.D.); (V.G.P.); (V.S.M.)
- Correspondence:
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Tapari A, Braliou GG, Papaefthimiou M, Mavriki H, Kontou PI, Nikolopoulos GK, Bagos PG. Performance of Antigen Detection Tests for SARS-CoV-2: A Systematic Review and Meta-Analysis. Diagnostics (Basel) 2022; 12:1388. [PMID: 35741198 PMCID: PMC9221910 DOI: 10.3390/diagnostics12061388] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) initiated global health care challenges such as the necessity for new diagnostic tests. Diagnosis by real-time PCR remains the gold-standard method, yet economical and technical issues prohibit its use in points of care (POC) or for repetitive tests in populations. A lot of effort has been exerted in developing, using, and validating antigen-based tests (ATs). Since individual studies focus on few methodological aspects of ATs, a comparison of different tests is needed. Herein, we perform a systematic review and meta-analysis of data from articles in PubMed, medRxiv and bioRxiv. The bivariate method for meta-analysis of diagnostic tests pooling sensitivities and specificities was used. Most of the AT types for SARS-CoV-2 were lateral flow immunoassays (LFIA), fluorescence immunoassays (FIA), and chemiluminescence enzyme immunoassays (CLEIA). We identified 235 articles containing data from 220,049 individuals. All ATs using nasopharyngeal samples show better performance than those with throat saliva (72% compared to 40%). Moreover, the rapid methods LFIA and FIA show about 10% lower sensitivity compared to the laboratory-based CLEIA method (72% compared to 82%). In addition, rapid ATs show higher sensitivity in symptomatic patients compared to asymptomatic patients, suggesting that viral load is a crucial parameter for ATs performed in POCs. Finally, all methods perform with very high specificity, reaching around 99%. LFIA tests, though with moderate sensitivity, appear as the most attractive method for use in POCs and for performing seroprevalence studies.
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Affiliation(s)
- Anastasia Tapari
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (A.T.); (G.G.B.); (M.P.); (H.M.); (P.I.K.)
| | - Georgia G. Braliou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (A.T.); (G.G.B.); (M.P.); (H.M.); (P.I.K.)
| | - Maria Papaefthimiou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (A.T.); (G.G.B.); (M.P.); (H.M.); (P.I.K.)
| | - Helen Mavriki
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (A.T.); (G.G.B.); (M.P.); (H.M.); (P.I.K.)
| | - Panagiota I. Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (A.T.); (G.G.B.); (M.P.); (H.M.); (P.I.K.)
| | | | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (A.T.); (G.G.B.); (M.P.); (H.M.); (P.I.K.)
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Tamposis IA, Sarantopoulou D, Theodoropoulou MC, Stasi EA, Kontou PI, Tsirigos KD, Bagos PG. Hidden neural networks for transmembrane protein topology prediction. Comput Struct Biotechnol J 2021; 19:6090-6097. [PMID: 34849210 PMCID: PMC8606341 DOI: 10.1016/j.csbj.2021.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 11/21/2022] Open
Abstract
Hidden Markov Models (HMMs) are amongst the most successful methods for predicting protein features in biological sequence analysis. However, there are biological problems where the Markovian assumption is not sufficient since the sequence context can provide useful information for prediction purposes. Several extensions of HMMs have appeared in the literature in order to overcome their limitations. We apply here a hybrid method that combines HMMs and Neural Networks (NNs), termed Hidden Neural Networks (HNNs), for biological sequence analysis in a straightforward manner. In this framework, the traditional HMM probability parameters are replaced by NN outputs. As a case study, we focus on the topology prediction of for alpha-helical and beta-barrel membrane proteins. The HNNs show performance gains compared to standard HMMs and the respective predictors outperform the top-scoring methods in the field. The implementation of HNNs can be found in the package JUCHMME, downloadable from http://www.compgen.org/tools/juchmme, https://github.com/pbagos/juchmme. The updated PRED-TMBB2 and HMM-TM prediction servers can be accessed at www.compgen.org.
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Key Words
- CHMM, Class Hidden Markov Models
- CML, Conditional Maximum Likelihood
- EM, Expectation-Maximization
- HMM, Hidden Markov Models
- HNN, Hidden Neural Networks
- Hidden Markov Models
- Hidden Neural Networks
- JUCHMME, Java Utility for Class Hidden Markov Models and Extensions
- MCC, Matthews Correlation Coefficient
- ML, Maximum Likelihood
- MSA, Multiple Sequence Alignment
- Membrane proteins
- NN, Neural Networks
- Neural Networks
- Protein structure prediction
- SOV, segment overlap
- Sequence analysis
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Affiliation(s)
- Ioannis A. Tamposis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35100 Lamia, Greece
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Present address: National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | | | - Evangelia A. Stasi
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35100 Lamia, Greece
| | - Panagiota I. Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35100 Lamia, Greece
| | | | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35100 Lamia, Greece
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Yılmaz H, Toy HI, Marquardt S, Karakülah G, Küçük C, Kontou PI, Logotheti S, Pavlopoulou A. In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia. Int J Mol Sci 2021; 22:ijms22179601. [PMID: 34502522 PMCID: PMC8431757 DOI: 10.3390/ijms22179601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022] Open
Abstract
Acute myeloid leukemia (AML), the most common type of acute leukemia in adults, is mainly asymptomatic at early stages and progresses/recurs rapidly and frequently. These attributes necessitate the identification of biomarkers for timely diagnosis and accurate prognosis. In this study, differential gene expression analysis was performed on large-scale transcriptomics data of AML patients versus corresponding normal tissue. Weighted gene co-expression network analysis was conducted to construct networks of co-expressed genes, and detect gene modules. Finally, hub genes were identified from selected modules by applying network-based methods. This robust and integrative bioinformatics approach revealed a set of twenty-four genes, mainly related to cell cycle and immune response, the diagnostic significance of which was subsequently compared against two independent gene expression datasets. Furthermore, based on a recent notion suggesting that molecular characteristics of a few, unusual patients with exceptionally favorable survival can provide insights for improving the outcome of individuals with more typical disease trajectories, we defined groups of long-term survivors in AML patient cohorts and compared their transcriptomes versus the general population to infer favorable prognostic signatures. These findings could have potential applications in the clinical setting, in particular, in diagnosis and prognosis of AML.
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Affiliation(s)
- Hande Yılmaz
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany;
| | - Halil Ibrahim Toy
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
| | - Stephan Marquardt
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany;
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
| | - Can Küçük
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
| | - Panagiota I. Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece;
| | - Stella Logotheti
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany;
- Correspondence: (S.L.); (A.P.)
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
- Correspondence: (S.L.); (A.P.)
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11
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Karatzas E, Gkonta M, Hotova J, Baltoumas FA, Kontou PI, Bobotsis CJ, Bagos PG, Pavlopoulos GA. VICTOR: A visual analytics web application for comparing cluster sets. Comput Biol Med 2021; 135:104557. [PMID: 34139436 DOI: 10.1016/j.compbiomed.2021.104557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 01/21/2023]
Abstract
Clustering is the process of grouping different data objects based on similar properties. Clustering has applications in various case studies from several fields such as graph theory, image analysis, pattern recognition, statistics and others. Nowadays, there are numerous algorithms and tools able to generate clustering results. However, different algorithms or parameterizations may produce quite dissimilar cluster sets. In this way, the user is often forced to manually filter and compare these results in order to decide which of them generate the ideal clusters. To automate this process, in this study, we present VICTOR, the first fully interactive and dependency-free visual analytics web application which allows the visual comparison of the results of various clustering algorithms. VICTOR can handle multiple cluster set results simultaneously and compare them using ten different metrics. Clustering results can be filtered and compared to each other with the use of data tables or interactive heatmaps, bar plots, correlation networks, sankey and circos plots. We demonstrate VICTOR's functionality using three examples. In the first case, we compare five different network clustering algorithms on a Yeast protein-protein interaction dataset whereas in the second example, we test four different parameters of the MCL clustering algorithm on the same dataset. Finally, as a third example, we compare four different meta-analyses with hierarchically clustered differentially expressed genes found to be involved in myocardial infarction. VICTOR is available at http://victor.pavlopouloslab.info or http://bib.fleming.gr:3838/VICTOR.
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Affiliation(s)
- Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece.
| | - Maria Gkonta
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece; Department of Biology, University of Athens, Greece
| | - Joana Hotova
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece; Department of Biology, University of Athens, Greece
| | - Fotis A Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Panagiota I Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | | | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
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12
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Toy HI, Karakülah G, Kontou PI, Alotaibi H, Georgakilas AG, Pavlopoulou A. Investigating Molecular Determinants of Cancer Cell Resistance to Ionizing Radiation Through an Integrative Bioinformatics Approach. Front Cell Dev Biol 2021; 9:620248. [PMID: 33898418 PMCID: PMC8058375 DOI: 10.3389/fcell.2021.620248] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Eradication of cancer cells through exposure to high doses of ionizing radiation (IR) is a widely used therapeutic strategy in the clinical setting. However, in many cases, cancer cells can develop remarkable resistance to radiation. Radioresistance represents a prominent obstacle in the effective treatment of cancer. Therefore, elucidation of the molecular mechanisms and pathways related to radioresistance in cancer cells is of paramount importance. In the present study, an integrative bioinformatics approach was applied to three publicly available RNA sequencing and microarray transcriptome datasets of human cancer cells of different tissue origins treated with ionizing radiation. These data were investigated in order to identify genes with a significantly altered expression between radioresistant and corresponding radiosensitive cancer cells. Through rigorous statistical and biological analyses, 36 genes were identified as potential biomarkers of radioresistance. These genes, which are primarily implicated in DNA damage repair, oxidative stress, cell pro-survival, and apoptotic pathways, could serve as potential diagnostic/prognostic markers cancer cell resistance to radiation treatment, as well as for therapy outcome and cancer patient survival. In addition, our findings could be potentially utilized in the laboratory and clinical setting for enhancing cancer cell susceptibility to radiation therapy protocols.
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Affiliation(s)
- Halil Ibrahim Toy
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Panagiota I Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Hani Alotaibi
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Alexandros G Georgakilas
- DNA Damage Laboratory, Department of Physics, School of Applied Mathematical and Physical Sciences, Zografou, National Technical University of Athens, Athens, Greece
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
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13
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Katsarou EI, Chatzopoulos DC, Giannoulis T, Ioannidi KS, Katsafadou AI, Kontou PI, Lianou DT, Mamuris Z, Mavrogianni VS, Michael CK, Papadopoulos E, Petinaki E, Sarrou S, Vasileiou NGC, Fthenakis GC. MLST-Based Analysis and Antimicrobial Resistance of Staphylococcus epidermidis from Cases of Sheep Mastitis in Greece. Biology (Basel) 2021; 10:biology10030170. [PMID: 33668332 PMCID: PMC7996216 DOI: 10.3390/biology10030170] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 12/17/2022]
Abstract
Staphylococcus epidermidis is an important causal agent of ovine mastitis. A literature search indicated a lack of systematic studies of causal agents of the infection by using multi-locus sequence typing (MLST). The objectives were to analyse MLST-based data and evaluate the antimicrobial resistance of S. epidermidis isolates from ovine mastitis in Greece. The database included 1593 isolates from 46 countries: 1215 of human, 195 of environmental and 134 of animal origin, distributed into 949 sequence types (STs) and cumulatively with 450 alleles therein. Among mastitis isolates, bovine isolates were distributed into 36 different STs and ovine ones into 15 STs. The 33 isolates from ovine mastitis in Greece were in 15 different STs, 6 of these (ST677, ST678, ST700, ST 709, ST710, ST711) assigned for the first time; in addition, 5 alleles (65 for arcC, 59 for aroE, 56 and 57 for gtr and 48 for tpiA) were identified for the first time. The spanning tree of these isolates included 15 nodes and 14 edges (i.e., branches). Among these isolates, 19 showed resistance to antimicrobial agents (tetracycline, penicillin, fucidic adic, erythromycin, clindamycin, cefoxitin). Resistance-related genes (tetK, tetT, msrA, tetM, tetS, ermC, mecA) were detected. There was no association between STs and resistance to antimicrobial agents. Isolates with antimicrobial resistance were recovered more often from flocks where hand-milking was practised.
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Affiliation(s)
- Eleni I. Katsarou
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (E.I.K.); (D.C.C.); (K.S.I.); (A.I.K.); (D.T.L.); (V.S.M.); (C.K.M.)
| | - Dimitris C. Chatzopoulos
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (E.I.K.); (D.C.C.); (K.S.I.); (A.I.K.); (D.T.L.); (V.S.M.); (C.K.M.)
| | - Themis Giannoulis
- Faculty of Animal Science, University of Thessaly, 41110 Larissa, Greece; (T.G.); (N.G.C.V.)
| | - Katerina S. Ioannidi
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (E.I.K.); (D.C.C.); (K.S.I.); (A.I.K.); (D.T.L.); (V.S.M.); (C.K.M.)
| | - Angeliki I. Katsafadou
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (E.I.K.); (D.C.C.); (K.S.I.); (A.I.K.); (D.T.L.); (V.S.M.); (C.K.M.)
| | - Panagiota I. Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece;
| | - Daphne T. Lianou
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (E.I.K.); (D.C.C.); (K.S.I.); (A.I.K.); (D.T.L.); (V.S.M.); (C.K.M.)
| | - Zissis Mamuris
- Faculty of Biochemistry and Biotechnology, University of Thessaly, 41110 Larissa, Greece;
| | - Vasia S. Mavrogianni
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (E.I.K.); (D.C.C.); (K.S.I.); (A.I.K.); (D.T.L.); (V.S.M.); (C.K.M.)
| | - Charalambia K. Michael
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (E.I.K.); (D.C.C.); (K.S.I.); (A.I.K.); (D.T.L.); (V.S.M.); (C.K.M.)
| | - Elias Papadopoulos
- Laboratory of Parasitology and Parasitic Diseases, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Efthymia Petinaki
- University Hospital of Larissa, 41110 Larissa, Greece; (E.P.); (S.S.)
| | - Styliani Sarrou
- University Hospital of Larissa, 41110 Larissa, Greece; (E.P.); (S.S.)
| | - Natalia G. C. Vasileiou
- Faculty of Animal Science, University of Thessaly, 41110 Larissa, Greece; (T.G.); (N.G.C.V.)
| | - George C. Fthenakis
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (E.I.K.); (D.C.C.); (K.S.I.); (A.I.K.); (D.T.L.); (V.S.M.); (C.K.M.)
- Correspondence:
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14
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Kapoula GV, Kontou PI, Bagos PG. Diagnostic Performance of Biomarkers Urinary KIM-1 and YKL-40 for Early Diabetic Nephropathy, in Patients with Type 2 Diabetes: A Systematic Review and Meta-Analysis. Diagnostics (Basel) 2020; 10:diagnostics10110909. [PMID: 33171707 PMCID: PMC7695026 DOI: 10.3390/diagnostics10110909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/14/2023] Open
Abstract
There is a lack of prediction markers for early diabetic nephropathy (DN) in patients with type 2 diabetes mellitus (T2DM). The aim of this systematic review and meta-analysis was to evaluate the performance of two promising biomarkers, urinary kidney injury molecule 1 (uKIM-1) and Chitinase-3-like protein 1 (YKL-40) in the diagnosis of early diabetic nephropathy in type 2 diabetic patients. A comprehensive search was performed on PubMed by two reviewers until May 2020. For each study, a 2 × 2 contingency table was formulated. Sensitivity, specificity, and other estimates of accuracy were calculated using the bivariate random effects model. The hierarchical summary receiver operating characteristic curve hsROC) was used to pool data and evaluate the area under curve (AUC). The sources of heterogeneity were explored by sensitivity analysis. Publication bias was assessed using Deek’s test. The meta-analysis enrolled 14 studies involving 598 healthy individuals, 765 T2DM patients with normoalbuminuria, 549 T2DM patients with microalbuminuria, and 551 T2DM patients with macroalbuminuria, in total for both biomarkers. The AUC of uKIM-1 and YKL-40 for T2DM patients with normoalbuminuria, was 0.85 (95%CI; 0.82–0.88) and 0.91 (95%CI; 0.88–0.93), respectively. The results of this meta-analysis suggest that both uKIM-1 and YKL-40 can be considered as valuable biomarkers for the early detection of DN in T2DM patients with the latter showing slightly better performance than the former.
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Affiliation(s)
- Georgia V. Kapoula
- Department of Biochemistry, General Hospital of Lamia, End of Papasiopoulou, 35100 Lamia, Greece;
- Department of Computer Science and Biomedical Informatics, School of Science, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece;
| | - Panagiota I. Kontou
- Department of Computer Science and Biomedical Informatics, School of Science, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece;
- Department of Mathematics and Engineering Sciences, Informatics LAB, Hellenic Military Academy, 16673 Athens, Greece
| | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, School of Science, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece;
- Correspondence: ; Tel.: +30-2231066914; Fax: +30-2231066915
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15
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Tamposis IA, Tsirigos KD, Theodoropoulou MC, Kontou PI, Tsaousis GN, Sarantopoulou D, Litou ZI, Bagos PG. JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis. Bioinformatics 2020; 35:5309-5312. [PMID: 31250907 DOI: 10.1093/bioinformatics/btz533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/04/2019] [Accepted: 06/25/2019] [Indexed: 11/14/2022] Open
Abstract
SUMMARY JUCHMME is an open-source software package designed to fit arbitrary custom Hidden Markov Models (HMMs) with a discrete alphabet of symbols. We incorporate a large collection of standard algorithms for HMMs as well as a number of extensions and evaluate the software on various biological problems. Importantly, the JUCHMME toolkit includes several additional features that allow for easy building and evaluation of custom HMMs, which could be a useful resource for the research community. AVAILABILITY AND IMPLEMENTATION http://www.compgen.org/tools/juchmme, https://github.com/pbagos/juchmme. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ioannis A Tamposis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Konstantinos D Tsirigos
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Panagiota I Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | | | - Dimitra Sarantopoulou
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Zoi I Litou
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
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16
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Tamposis IA, Tsirigos KD, Theodoropoulou MC, Kontou PI, Bagos PG. Semi-supervised learning of Hidden Markov Models for biological sequence analysis. Bioinformatics 2020; 35:2208-2215. [PMID: 30445435 DOI: 10.1093/bioinformatics/bty910] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/29/2018] [Accepted: 11/09/2018] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Hidden Markov Models (HMMs) are probabilistic models widely used in applications in computational sequence analysis. HMMs are basically unsupervised models. However, in the most important applications, they are trained in a supervised manner. Training examples accompanied by labels corresponding to different classes are given as input and the set of parameters that maximize the joint probability of sequences and labels is estimated. A main problem with this approach is that, in the majority of the cases, labels are hard to find and thus the amount of training data is limited. On the other hand, there are plenty of unclassified (unlabeled) sequences deposited in the public databases that could potentially contribute to the training procedure. This approach is called semi-supervised learning and could be very helpful in many applications. RESULTS We propose here, a method for semi-supervised learning of HMMs that can incorporate labeled, unlabeled and partially labeled data in a straightforward manner. The algorithm is based on a variant of the Expectation-Maximization (EM) algorithm, where the missing labels of the unlabeled or partially labeled data are considered as the missing data. We apply the algorithm to several biological problems, namely, for the prediction of transmembrane protein topology for alpha-helical and beta-barrel membrane proteins and for the prediction of archaeal signal peptides. The results are very promising, since the algorithms presented here can significantly improve the prediction performance of even the top-scoring classifiers. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ioannis A Tamposis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Konstantinos D Tsirigos
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Panagiota I Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
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17
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Kontou PI, Braliou GG, Dimou NL, Nikolopoulos G, Bagos PG. Antibody Tests in Detecting SARS-CoV-2 Infection: A Meta-Analysis. Diagnostics (Basel) 2020; 10:E319. [PMID: 32438677 PMCID: PMC7278002 DOI: 10.3390/diagnostics10050319] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 01/03/2023] Open
Abstract
The emergence of Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 made imperative the need for diagnostic tests that can identify the infection. Although Nucleic Acid Test (NAT) is considered to be the gold standard, serological tests based on antibodies could be very helpful. However, individual studies are usually inconclusive, thus, a comparison of different tests is needed. We performed a systematic review and meta-analysis in PubMed, medRxiv and bioRxiv. We used the bivariate method for meta-analysis of diagnostic tests pooling sensitivities and specificities. We evaluated IgM and IgG tests based on Enzyme-linked immunosorbent assay (ELISA), Chemiluminescence Enzyme Immunoassays (CLIA), Fluorescence Immunoassays (FIA), and the Lateral Flow Immunoassays (LFIA). We identified 38 studies containing data from 7848 individuals. Tests using the S antigen are more sensitive than N antigen-based tests. IgG tests perform better compared to IgM ones and show better sensitivity when the samples were taken longer after the onset of symptoms. Moreover, a combined IgG/IgM test seems to be a better choice in terms of sensitivity than measuring either antibody alone. All methods yield high specificity with some of them (ELISA and LFIA) reaching levels around 99%. ELISA- and CLIA-based methods perform better in terms of sensitivity (90%-94%) followed by LFIA and FIA with sensitivities ranging from 80% to 89%. ELISA tests could be a safer choice at this stage of the pandemic. LFIA tests are more attractive for large seroprevalence studies but show lower sensitivity, and this should be taken into account when designing and performing seroprevalence studies.
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Affiliation(s)
- Panagiota I. Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35131 Lamia, Greece; (P.I.K.); (G.G.B.)
| | - Georgia G. Braliou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35131 Lamia, Greece; (P.I.K.); (G.G.B.)
| | - Niki L. Dimou
- International Agency for Research on Cancer, 69372 Lyon, France;
| | | | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35131 Lamia, Greece; (P.I.K.); (G.G.B.)
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18
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Vennou KE, Piovani D, Kontou PI, Bonovas S, Bagos PG. Methods for multiple outcome meta-analysis of gene-expression data. MethodsX 2020; 7:100834. [PMID: 32195147 PMCID: PMC7078352 DOI: 10.1016/j.mex.2020.100834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 02/16/2020] [Indexed: 11/24/2022] Open
Abstract
Meta-analysis is a valuable tool for the synthesis of evidence across a wide range study types including high-throughput experiments such as genome-wide association studies (GWAS) and gene expression studies. There are situations though, in which we have multiple outcomes or multiple treatments, in which the multivariate meta-analysis framework which performs a joint modeling of the different quantities of interest may offer important advantages, such as increasing statistical power and allowing performing global tests. In this work we adapted the multivariate meta-analysis method and applied it in gene expression data. With this method we can test for pleiotropic effects, that is, for genes that influence both outcomes or discover genes that have a change in expression not detectable in the univariate method. We tested this method on data regarding inflammatory bowel disease (IBD), with its two main forms, Crohn’s disease (CD) and Ulcerative colitis (UC), sharing many clinical manifestations, but differing in the location and extent of inflammation and in complications. The Stata code is given in the Appendix and it is available at: www.compgen.org/tools/multivariate-microarrays.Multivariate meta-analysis method for gene expression data. Discover genes with pleiotropic effects. Differentially Expressed Genes (DEGs) identification in complex traits.
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Affiliation(s)
- Konstantina E Vennou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia 35131, Greece
| | - Daniele Piovani
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IBD Center, Humanitas Clinical and Research Center - IRCCS, Milan, Italy
| | - Panagiota I Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia 35131, Greece
| | - Stefanos Bonovas
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IBD Center, Humanitas Clinical and Research Center - IRCCS, Milan, Italy
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia 35131, Greece
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19
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Vennou KE, Piovani D, Kontou PI, Bonovas S, Bagos PG. Multiple outcome meta-analysis of gene-expression data in inflammatory bowel disease. Genomics 2020; 112:1761-1767. [DOI: 10.1016/j.ygeno.2019.09.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 01/02/2023]
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Braliou GG, Kontou PI, Boleti H, Bagos PG. Susceptibility to leishmaniasis is affected by host SLC11A1 gene polymorphisms: a systematic review and meta-analysis. Parasitol Res 2019; 118:2329-2342. [PMID: 31230160 DOI: 10.1007/s00436-019-06374-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/07/2019] [Indexed: 12/31/2022]
Abstract
Leishmaniases are cutaneous, mucocutaneous, and visceral diseases affecting humans and domesticated animals mostly in the tropical and subtropical areas of the planet. Host genetics have been widely investigated for their role in developing various infectious diseases. The SLC11A1 gene has been reported to play a role in neutrophil function and is associated with susceptibility to infectious and inflammatory diseases such as tuberculosis or rheumatoid arthritis. In the present meta-analysis, we investigate the genetic association of SLC11A1 polymorphisms with susceptibility to leishmaniasis. Genotypes and other risk-related data were collected from 13 case-control and family-based studies (after literature search). Conventional random-effects meta-analysis was performed using STATA 13. To pool case-control and family-based data, the weighted Stouffer's method was also applied. Eight polymorphisms were investigated: rs2276631, rs3731865, rs3731864, rs17221959, rs201565523, rs2279015, rs17235409, and rs17235416. We found that rs17235409 (D543N) and rs17235416 (1729 + 55del4) are significantly associated with a risk for cutaneous leishmaniasis (CL), whereas rs17221959, rs2279015, and rs17235409 are associated with visceral leishmaniasis (VL). Our results suggest that polymorphisms in SLC11A1 affect susceptibility to CL and VL. These findings open new pathways in understanding macrophage response to Leishmania infection and the genetic factors predisposing to symptomatic CL or VL that can lead to the usage of predictive biomarkers in populations at risk.
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Affiliation(s)
- Georgia G Braliou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4, Papasiopoulou str., 35131, Lamia, Greece.
| | - Panagiota I Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4, Papasiopoulou str., 35131, Lamia, Greece
| | - Haralabia Boleti
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4, Papasiopoulou str., 35131, Lamia, Greece.
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Kapoula GV, Kontou PI, Bagos PG. Diagnostic Accuracy of Neutrophil Gelatinase-Associated Lipocalin for Predicting Early Diabetic Nephropathy in Patients with Type 1 and Type 2 Diabetes Mellitus: A Systematic Review and Meta-analysis. J Appl Lab Med 2019; 4:78-94. [PMID: 31639710 DOI: 10.1373/jalm.2018.028530] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/04/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Currently, there is a lack of prediction markers for diabetic nephropathy (DN) in patients with type 1 and type 2 diabetes mellitus (T1DM/T2DM). The aim of this systematic review and meta-analysis was to evaluate the value of a promising biomarker, neutrophil gelatinase-associated lipocalin (NGAL), in both serum and urine for the diagnosis of early DN in T1DM and T2DM patients with different stages of albuminuria. METHODS A comprehensive search was performed on PubMed by 2 reviewers until September 2018. Studies in which (a) the degree of DN was determined according to the urinary albumin/creatinine ratio and (b) NGAL was measured in healthy individuals and in diabetes patients with DN were included in the meta-analysis. For each study, a 2 × 2 contingency table was formulated. Sensitivity, specificity, and other estimates of accuracy were calculated using a bivariate random effects model. The hierarchical summary ROC method was used to pool data and to evaluate the area under the curve (AUC). The sources of heterogeneity were explored by subgroup analysis. Publication bias was assessed using the Deeks test. RESULTS The meta-analysis enrolled 22 studies involving 683 healthy individuals and 3249 patients with diabetes, of which 488 were T1DM and 2761 were T2DM patients. Overall, pooled sensitivity and specificity among the different settings analyzed ranged from 0.42 (95% CI, 0.22-0.66) to 1.00 (95% CI, 0.99-1.00) and 0.72 (95% CI, 0.62-0.80) to 0.98 (95% CI, 0.50-1.00) in T2DM patients, respectively. For T1DM patients, the corresponding estimates were 0.71 (95% CI, 0.59-0.81) to 0.89 (95% CI, 0.64-0.97) and 0.72 (95% CI, 0.62-0.80) to 0.79 (95% CI, 0.67-0.87). The AUC of NGAL for T2DM patients ranged from 0.69 (95% CI, 0.65-0.73) to 1.00 (95% CI, 0.99-1.00) in the different settings. CONCLUSION The results of this meta-analysis suggest that NGAL in both serum and urine can be considered a valuable biomarker for early detection of DN in diabetes patients.
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Affiliation(s)
- Georgia V Kapoula
- Department of Computer Science and Biomedical Informatics, School of Science, University of Thessaly, Lamia, Greece
| | - Panagiota I Kontou
- Department of Computer Science and Biomedical Informatics, School of Science, University of Thessaly, Lamia, Greece
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, School of Science, University of Thessaly, Lamia, Greece.
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Ligda G, Ploubidis D, Foteli S, Kontou PI, Nikolaou C, Tentolouris N. Quality of life in subjects with type 2 diabetes mellitus with diabetic retinopathy: A case-control study. Diabetes Metab Syndr 2019; 13:947-952. [PMID: 31336549 DOI: 10.1016/j.dsx.2018.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 12/19/2018] [Indexed: 01/07/2023]
Abstract
AIMS Diabetic retinopathy (DR) as a common complication of Type 2 Diabetes Mellitus (T2DM) affecting negatively quality of life (QoL). Assessing of QoL in patients with DR is a prerequisite for the evaluation of their needs and for understanding the perception of the patients themselves about their health status and how the disease affects their lives. Additionally, QoL indicators detect individual psychosocial problems that may impact therapeutic response. MATERIALS AND METHODS A total of 70 subjects with T2DM and DR as well as 70 T2DM individuals without DR were included. For the evaluation of QoL we used (a) WHO QoL - BREF for the estimation of QoL, (b) Life Satisfaction Scale for the estimation of satisfaction from life, and (c) the special recording document for demographic, socioeconomic, and clinical data. At the same time, blood was collected for the measurement of glucose control and renal function. DR was diagnosed by dilated fundoscopy. RESULTS Patients with DR had significantly worse scores in all scales of QoL and Life Satisfaction in comparison with those without DR. We found significant impact of the severity of DR in many domains of the QoL and Life Satisfaction. Multivariate logistic regression analysis demonstrated that DR was associated with worse QoL and Life Satisfaction scores as well as lower income, while no significant associations were found with education level, family, insurance and employment status as well as type of residence. CONCLUSION DR affects QoL and Life Satisfaction and is associated with lower income.
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Affiliation(s)
- Georgia Ligda
- Department of Psychiatry, Sismanoglio General Hospital, Athens, Greece.
| | - Dimitrios Ploubidis
- First Psychiatric Department, Medical School, National and Kapodistrian University of Athens, Greece, Athens
| | - Stefania Foteli
- Evangelismos, General Hospital, Department of Psychiatry, Athens, Greece
| | - Panagiota I Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Greece
| | - Chrysoula Nikolaou
- Department of Medical Biopathology - Psychoimmunology, Eginition Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolaos Tentolouris
- First Department of Propaedeutic Internal Medicine, Medical School, National and Kapodistrian University of Athens, Laiko General Hospital, Athens, Greece
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Pavlopoulos GA, Kontou PI, Pavlopoulou A, Bouyioukos C, Markou E, Bagos PG. Bipartite graphs in systems biology and medicine: a survey of methods and applications. Gigascience 2018; 7:1-31. [PMID: 29648623 PMCID: PMC6333914 DOI: 10.1093/gigascience/giy014] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 02/13/2018] [Indexed: 11/14/2022] Open
Abstract
The latest advances in high-throughput techniques during the past decade allowed the systems biology field to expand significantly. Today, the focus of biologists has shifted from the study of individual biological components to the study of complex biological systems and their dynamics at a larger scale. Through the discovery of novel bioentity relationships, researchers reveal new information about biological functions and processes. Graphs are widely used to represent bioentities such as proteins, genes, small molecules, ligands, and others such as nodes and their connections as edges within a network. In this review, special focus is given to the usability of bipartite graphs and their impact on the field of network biology and medicine. Furthermore, their topological properties and how these can be applied to certain biological case studies are discussed. Finally, available methodologies and software are presented, and useful insights on how bipartite graphs can shape the path toward the solution of challenging biological problems are provided.
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Affiliation(s)
- Georgios A Pavlopoulos
- Lawrence Berkeley Labs, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Panagiota I Kontou
- University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2-4, Lamia, 35100, Greece
| | - Athanasia Pavlopoulou
- Izmir International Biomedicine and Genome Institute (iBG-Izmir), Dokuz Eylül University, 35340, Turkey
| | - Costas Bouyioukos
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, France
| | - Evripides Markou
- University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2-4, Lamia, 35100, Greece
| | - Pantelis G Bagos
- University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2-4, Lamia, 35100, Greece
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Abstract
Microarray approaches are widely used high-throughput techniques to assess simultaneously the expression of thousands of genes under certain conditions and study the effects of certain treatments, diseases, and developmental stages. The traditional way to perform such experiments is to design oligonucleotide hybridization probes that correspond to specific genes and then measure the expression of the genes in order to determine which of them are up- or down-regulated compared to a condition that is used as a control. Hitherto, individual experiments cannot capture the bigger picture of how a biological system works and, therefore, data integration from multiple experimental studies and external data repositories is necessary to understand the function of genes and their expression patterns under certain conditions. Therefore, the development of methods for handling, integrating, comparing, interpreting and visualizing microarray data is necessary. The selection of an appropriate method for analysing microarray datasets is not an easy task. In this chapter, we provide an overview of the various methods developed for microarray data analysis, as well as suggestions for choosing the appropriate method for microarray meta-analysis.
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Affiliation(s)
- Panagiota I Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Athanasia Pavlopoulou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece.,International Biomedicine and Genome Institute (iBG-Izmir), Dokuz Eylul University, Izmir, 35340, Turkey
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece.
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Kapoula GV, Kontou PI, Bagos PG. The impact of pneumatic tube system on routine laboratory parameters: a systematic review and meta-analysis. ACTA ACUST UNITED AC 2017; 55:1834-1844. [DOI: 10.1515/cclm-2017-0008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/27/2017] [Indexed: 11/15/2022]
Abstract
AbstractBackground:Pneumatic tube system (PTS) is a widely used method of transporting blood samples in hospitals. The aim of this study was to evaluate the effects of the PTS transport in certain routine laboratory parameters as it has been implicated with hemolysis.Methods:A systematic review and a meta-analysis were conducted. PubMed and Scopus databases were searched (up until November 2016) to identify prospective studies evaluating the impact of PTS transport in hematological, biochemical and coagulation measurements. The random-effects model was used in the meta-analysis utilizing the mean difference (MD). Heterogeneity was quantitatively assessed using the Cohran’sResults:From a total of 282 studies identified by the searching procedure, 24 were finally included in the meta-analysis. The meta-analysis yielded statistically significant results for potassium (K) [MD=0.04 mmol/L; 95% confidence interval (CI)=0.015–0.065; p=0.002], lactate dehydrogenase (LDH) (MD=10.343 U/L; 95% CI=6.132–14.554; p<10Conclusions:This meta-analysis suggests that PTS may be associated with alterations in K, LDH and AST measurements. Although these findings may not have any significant clinical effect on laboratory results, it is wise that each hospital validates their PTS.
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Kontou PI, Pavlopoulou A, Dimou NL, Pavlopoulos GA, Bagos PG. Network analysis of genes and their association with diseases. Gene 2016; 590:68-78. [PMID: 27265032 DOI: 10.1016/j.gene.2016.05.044] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 05/20/2016] [Accepted: 05/30/2016] [Indexed: 12/21/2022]
Abstract
A plethora of network-based approaches within the Systems Biology universe have been applied, to date, to investigate the underlying molecular mechanisms of various human diseases. In the present study, we perform a bipartite, topological and clustering graph analysis in order to gain a better understanding of the relationships between human genetic diseases and the relationships between the genes that are implicated in them. For this purpose, disease-disease and gene-gene networks were constructed from combined gene-disease association networks. The latter, were created by collecting and integrating data from three diverse resources, each one with different content covering from rare monogenic disorders to common complex diseases. This data pluralism enabled us to uncover important associations between diseases with unrelated phenotypic manifestations but with common genetic origin. For our analysis, the topological attributes and the functional implications of the individual networks were taken into account and are shortly discussed. We believe that some observations of this study could advance our understanding regarding the etiology of a disease with distinct pathological manifestations, and simultaneously provide the springboard for the development of preventive and therapeutic strategies and its underlying genetic mechanisms.
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Affiliation(s)
- Panagiota I Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Greece
| | - Athanasia Pavlopoulou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Greece
| | - Niki L Dimou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Greece
| | - Georgios A Pavlopoulos
- Lawrence Berkeley Lab, Joint Genome Institute, United States Department of Energy, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Greece.
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