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New adaptive lasso approaches for variable selection in automated pharmacovigilance signal detection. BMC Med Res Methodol 2021; 21:271. [PMID: 34852782 PMCID: PMC8638444 DOI: 10.1186/s12874-021-01450-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/26/2021] [Indexed: 12/05/2022] Open
Abstract
Background Adverse effects of drugs are often identified after market introduction. Post-marketing pharmacovigilance aims to detect them as early as possible and relies on spontaneous reporting systems collecting suspicious cases. Signal detection tools have been developed to mine these large databases and counts of reports are analysed with disproportionality methods. To address disproportionality method biases, recent methods apply to individual observations taking into account all exposures for the same patient. In particular, the logistic lasso provides an efficient variable selection framework, yet the choice of the regularization parameter is a challenging issue and the lasso variable selection may give inconsistent results. Methods We propose a new signal detection methodology based on the adaptive lasso. We derived two new adaptive weights from (i) a lasso regression using the Bayesian Information Criterion (BIC), and (ii) the class-imbalanced subsampling lasso (CISL), an extension of stability selection. The BIC is used in the adaptive lasso stage for variable selection. We performed an extensive simulation study and an application to real data, where we compared our methods to the existing adaptive lasso, and recent detection approaches based on lasso regression or propensity scores in high dimension. For both studies, we evaluate the methods in terms of false discoveries and sensitivity. Results In the simulations and the application, both proposed adaptive weights show equivalent or better performances than the other competitors, with an advantage for the CISL-based adaptive weights. CISL and lasso regression using BIC are solid alternatives. Conclusion Our proposed adaptive lasso is an appealing methodology for signal detection in pharmacovigilance. Although we cannot rely on test theory, our approaches show a low and stable False Discovery Rate in all simulation settings. All methods evaluated in this work are implemented in the adapt4pv R package. Supplementary Information The online version contains supplementary material available at (10.1186/s12874-021-01450-3).
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Rauner M, Foessl I, Formosa MM, Kague E, Prijatelj V, Lopez NA, Banerjee B, Bergen D, Busse B, Calado Â, Douni E, Gabet Y, Giralt NG, Grinberg D, Lovsin NM, Solan XN, Ostanek B, Pavlos NJ, Rivadeneira F, Soldatovic I, van de Peppel J, van der Eerden B, van Hul W, Balcells S, Marc J, Reppe S, Søe K, Karasik D. Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques. Front Endocrinol (Lausanne) 2021; 12:731217. [PMID: 34938269 PMCID: PMC8686830 DOI: 10.3389/fendo.2021.731217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022] Open
Abstract
The availability of large human datasets for genome-wide association studies (GWAS) and the advancement of sequencing technologies have boosted the identification of genetic variants in complex and rare diseases in the skeletal field. Yet, interpreting results from human association studies remains a challenge. To bridge the gap between genetic association and causality, a systematic functional investigation is necessary. Multiple unknowns exist for putative causal genes, including cellular localization of the molecular function. Intermediate traits ("endophenotypes"), e.g. molecular quantitative trait loci (molQTLs), are needed to identify mechanisms of underlying associations. Furthermore, index variants often reside in non-coding regions of the genome, therefore challenging for interpretation. Knowledge of non-coding variance (e.g. ncRNAs), repetitive sequences, and regulatory interactions between enhancers and their target genes is central for understanding causal genes in skeletal conditions. Animal models with deep skeletal phenotyping and cell culture models have already facilitated fine mapping of some association signals, elucidated gene mechanisms, and revealed disease-relevant biology. However, to accelerate research towards bridging the current gap between association and causality in skeletal diseases, alternative in vivo platforms need to be used and developed in parallel with the current -omics and traditional in vivo resources. Therefore, we argue that as a field we need to establish resource-sharing standards to collectively address complex research questions. These standards will promote data integration from various -omics technologies and functional dissection of human complex traits. In this mission statement, we review the current available resources and as a group propose a consensus to facilitate resource sharing using existing and future resources. Such coordination efforts will maximize the acquisition of knowledge from different approaches and thus reduce redundancy and duplication of resources. These measures will help to understand the pathogenesis of osteoporosis and other skeletal diseases towards defining new and more efficient therapeutic targets.
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Affiliation(s)
- Martina Rauner
- Department of Medicine III, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
- University Hospital Carl Gustav Carus, Dresden, Germany
| | - Ines Foessl
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Endocrine Lab Platform, Medical University of Graz, Graz, Austria
| | - Melissa M. Formosa
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Erika Kague
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Vid Prijatelj
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- The Generation R Study, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Nerea Alonso Lopez
- Rheumatology and Bone Disease Unit, CGEM, Institute of Genetics and Cancer (IGC), Edinburgh, United Kingdom
| | - Bodhisattwa Banerjee
- Musculoskeletal Genetics Laboratory, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Dylan Bergen
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Björn Busse
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ângelo Calado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
| | - Eleni Douni
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
- Institute for Bioinnovation, B.S.R.C. “Alexander Fleming”, Vari, Greece
| | - Yankel Gabet
- Department of Anatomy & Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Natalia García Giralt
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Nika M. Lovsin
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Xavier Nogues Solan
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - Barbara Ostanek
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Nathan J. Pavlos
- Bone Biology & Disease Laboratory, School of Biomedical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | | | - Ivan Soldatovic
- Institute of Medical Statistics and Informatic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jeroen van de Peppel
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Bram van der Eerden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Wim van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Janja Marc
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Sjur Reppe
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Kent Søe
- Clinical Cell Biology, Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Ramat Gan, Israel
- Marcus Research Institute, Hebrew SeniorLife, Boston, MA, United States
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3
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Lingjærde C, Lien TG, Borgan Ø, Bergholtz H, Glad IK. Tailored graphical lasso for data integration in gene network reconstruction. BMC Bioinformatics 2021; 22:498. [PMID: 34654363 PMCID: PMC8518261 DOI: 10.1186/s12859-021-04413-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 09/30/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Identifying gene interactions is a topic of great importance in genomics, and approaches based on network models provide a powerful tool for studying these. Assuming a Gaussian graphical model, a gene association network may be estimated from multiomic data based on the non-zero entries of the inverse covariance matrix. Inferring such biological networks is challenging because of the high dimensionality of the problem, making traditional estimators unsuitable. The graphical lasso is constructed for the estimation of sparse inverse covariance matrices in such situations, using [Formula: see text]-penalization on the matrix entries. The weighted graphical lasso is an extension in which prior biological information from other sources is integrated into the model. There are however issues with this approach, as it naïvely forces the prior information into the network estimation, even if it is misleading or does not agree with the data at hand. Further, if an associated network based on other data is used as the prior, the method often fails to utilize the information effectively. RESULTS We propose a novel graphical lasso approach, the tailored graphical lasso, that aims to handle prior information of unknown accuracy more effectively. We provide an R package implementing the method, tailoredGlasso. Applying the method to both simulated and real multiomic data sets, we find that it outperforms the unweighted and weighted graphical lasso in terms of all performance measures we consider. In fact, the graphical lasso and weighted graphical lasso can be considered special cases of the tailored graphical lasso, and a parameter determined by the data measures the usefulness of the prior information. We also find that among a larger set of methods, the tailored graphical is the most suitable for network inference from high-dimensional data with prior information of unknown accuracy. With our method, mRNA data are demonstrated to provide highly useful prior information for protein-protein interaction networks. CONCLUSIONS The method we introduce utilizes useful prior information more effectively without involving any risk of loss of accuracy should the prior information be misleading.
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Affiliation(s)
- Camilla Lingjærde
- MRC Biostatistics Unit, University of Cambridge, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK.
| | - Tonje G Lien
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Ullernchausseen 70, 0310, Oslo, Norway
| | - Ørnulf Borgan
- Department of Mathematics, University of Oslo, PO Box 1053 Blindern, 0316, Oslo, Norway
| | - Helga Bergholtz
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Ullernchausseen 70, 0310, Oslo, Norway
| | - Ingrid K Glad
- Department of Mathematics, University of Oslo, PO Box 1053 Blindern, 0316, Oslo, Norway
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Levy JJ, Chen Y, Azizgolshani N, Petersen CL, Titus AJ, Moen EL, Vaickus LJ, Salas LA, Christensen BC. MethylSPWNet and MethylCapsNet: Biologically Motivated Organization of DNAm Neural Networks, Inspired by Capsule Networks. NPJ Syst Biol Appl 2021; 7:33. [PMID: 34417465 PMCID: PMC8379254 DOI: 10.1038/s41540-021-00193-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
DNA methylation (DNAm) alterations have been heavily implicated in carcinogenesis and the pathophysiology of diseases through upstream regulation of gene expression. DNAm deep-learning approaches are able to capture features associated with aging, cell type, and disease progression, but lack incorporation of prior biological knowledge. Here, we present modular, user-friendly deep-learning methodology and software, MethylCapsNet and MethylSPWNet, that group CpGs into biologically relevant capsules-such as gene promoter context, CpG island relationship, or user-defined groupings-and relate them to diagnostic and prognostic outcomes. We demonstrate these models' utility on 3,897 individuals in the classification of central nervous system (CNS) tumors. MethylCapsNet and MethylSPWNet provide an opportunity to increase DNAm deep-learning analyses' interpretability by enabling a flexible organization of DNAm data into biologically relevant capsules.
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Affiliation(s)
- Joshua J Levy
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Emerging Diagnostic and Investigative Technologies, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA.
| | - Youdinghuan Chen
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Curtis L Petersen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- The Dartmouth Institute for Health Policy and Clinical Practice, Lebanon, NH, USA
| | - Alexander J Titus
- Department of Life Sciences, University of New Hampshire, Manchester, NH, USA
| | - Erika L Moen
- The Dartmouth Institute for Health Policy and Clinical Practice, Lebanon, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Louis J Vaickus
- Emerging Diagnostic and Investigative Technologies, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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5
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Gautvik KM, Günther CC, Prijatelj V, Medina-Gomez C, Shevroja E, Rad LH, Yazdani M, Lindalen E, Valland H, Gautvik VT, Olstad OK, Holden M, Rivadeneira F, Utheim TP, Reppe S. Distinct Subsets of Noncoding RNAs Are Strongly Associated With BMD and Fracture, Studied in Weight-Bearing and Non-Weight-Bearing Human Bone. J Bone Miner Res 2020; 35:1065-1076. [PMID: 32017184 DOI: 10.1002/jbmr.3974] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 01/22/2020] [Accepted: 01/26/2020] [Indexed: 12/14/2022]
Abstract
We investigated mechanisms resulting in low bone mineral density (BMD) and susceptibility to fracture by comparing noncoding RNAs (ncRNAs) in biopsies of non-weight-bearing (NWB) iliac (n = 84) and weight bearing (WB) femoral (n = 18) postmenopausal bone across BMDs varying from normal (T-score > -1.0) to osteoporotic (T-score ≤ -2.5). Global bone ncRNA concentrations were determined by PCR and microchip analyses. Association with BMD or fracture, adjusted by age and body mass index, were calculated using linear and logistic regression and least absolute shrinkage and selection operator (Lasso) analysis. At 10% false discovery rate (FDR), 75 iliac bone ncRNAs and 94 femoral bone ncRNAs were associated with total hip BMD. Eight of the ncRNAs were common for the two sites, but five of them (miR-484, miR-328-3p, miR-27a-5p, miR-28-3p, and miR-409-3p) correlated positively to BMD in femoral bone, but negatively in iliac bone. Of predicted pathways recognized in bone metabolism, ECM-receptor interaction and proteoglycans in cancer emerged at both sites, whereas fatty acid metabolism and focal adhesion were only identified in iliac bone. Lasso analysis and cross-validations identified sets of nine bone ncRNAs correlating strongly with adjusted total hip BMD in both femoral and iliac bone. Twenty-eight iliac ncRNAs were associated with risk of fracture (FDR < 0.1). The small nucleolar RNAs, RNU44 and RNU48, have a function in stabilization of ribosomal RNAs (rRNAs), and their association with fracture and BMD suggest that aberrant processing of rRNAs may be involved in development of osteoporosis. Cis-eQTL (expressed quantitative trait loci) analysis of the iliac bone biopsies identified two loci associated with microRNAs (miRNAs), one previously identified in a heel-BMD genomewide association study (GWAS). In this comprehensive investigation of the skeletal genetic background in postmenopausal women, we identified functional bone ncRNAs associated to fracture and BMD, representing distinct subsets in WB and NWB skeletal sites. © 2020 The Authors. Journal of Bone and Mineral Research published by American Society for Bone and Mineral Research.
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Affiliation(s)
- Kaare M Gautvik
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway.,Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | | | - Vid Prijatelj
- Department of Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.,Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Enisa Shevroja
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Leila Heidary Rad
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Mazyar Yazdani
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Einar Lindalen
- Orthopaedic Department, Lovisenberg Diaconal Hospital, Oslo, Norway
| | - Haldor Valland
- Department of Surgery, Diakonhjemmet Hospital, Oslo, Norway
| | - Vigdis T Gautvik
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
| | - Ole K Olstad
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | | | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Tor P Utheim
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Oslo, Norway.,Department of Ophthalmology, Stavanger University Hospital, Oslo, Norway.,Department of Ophthalmology, Sørlandet Hospital, Arendal, Norway
| | - Sjur Reppe
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway.,Department of Molecular Medicine, University of Oslo, Oslo, Norway.,Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Oslo, Norway
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6
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Morais-Rodrigues F, Silv Erio-Machado R, Kato RB, Rodrigues DLN, Valdez-Baez J, Fonseca V, San EJ, Gomes LGR, Dos Santos RG, Vinicius Canário Viana M, da Cruz Ferraz Dutra J, Teixeira Dornelles Parise M, Parise D, Campos FF, de Souza SJ, Ortega JM, Barh D, Ghosh P, Azevedo VAC, Dos Santos MA. Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression. Gene 2019; 726:144168. [PMID: 31759986 DOI: 10.1016/j.gene.2019.144168] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/21/2019] [Accepted: 10/11/2019] [Indexed: 01/02/2023]
Abstract
Methods based around statistics and linear algebra have been increasingly used in attempts to address emerging questions in microarray literature. Microarray technology is a long-used tool in the global analysis of gene expression, allowing for the simultaneous investigation of hundreds or thousands of genes in a sample. It is characterized by a low sample size and a large feature number created a non-square matrix, and by the incomplete rank, that can generate countless more solution in classifiers. To avoid the problem of the 'curse of dimensionality' many authors have performed feature selection or reduced the size of data matrix. In this work, we introduce a new logistic regression-based model to classify breast cancer tumor samples based on microarray expression data, including all features of gene expression and without reducing the microarray data matrix. If the user still deems it necessary to perform feature reduction, it can be done after the application of the methodology, still maintaining a good classification. This methodology allowed the correct classification of breast cancer sample data sets from Gene Expression Omnibus (GEO) data series GSE65194, GSE20711, and GSE25055, which contain the microarray data of said breast cancer samples. Classification had a minimum performance of 80% (sensitivity and specificity), and explored all possible data combinations, including breast cancer subtypes. This methodology highlighted genes not yet studied in breast cancer, some of which have been observed in Gene Regulatory Networks (GRNs). In this work we examine the patterns and features of a GRN composed of transcription factors (TFs) in MCF-7 breast cancer cell lines, providing valuable information regarding breast cancer. In particular, some genes whose αi ∗ associated parameter values revealed extreme positive and negative values, and, as such, can be identified as breast cancer prediction genes. We indicate that the PKN2, MKL1, MED23, CUL5 and GLI genes demonstrate a tumor suppressor profile, and that the MTR, ITGA2B, TELO2, MRPL9, MTTL1, WIPI1, KLHL20, PI4KB, FOLR1 and SHC1 genes demonstrate an oncogenic profile. We propose that these may serve as potential breast cancer prediction genes, and should be prioritized for further clinical studies on breast cancer. This new model allows for the assignment of values to the αi ∗ parameters associated with gene expression. It was noted that some αi ∗ parameters are associated with genes previously described as breast cancer biomarkers, as well as other genes not yet studied in relation to this disease.
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Affiliation(s)
- Francielly Morais-Rodrigues
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil.
| | - Rita Silv Erio-Machado
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Rodrigo Bentes Kato
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Diego Lucas Neres Rodrigues
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Juan Valdez-Baez
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Vagner Fonseca
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Emmanuel James San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Lucas Gabriel Rodrigues Gomes
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Roselane Gonçalves Dos Santos
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Marcus Vinicius Canário Viana
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil; Federal University of Pará, UFPA, Brazil
| | - Joyce da Cruz Ferraz Dutra
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Mariana Teixeira Dornelles Parise
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Doglas Parise
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Frederico F Campos
- Department of Computer Science, Federal University of Minas Gerais, Brazil Av Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | | | - José Miguel Ortega
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal 721172, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Vasco A C Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Marcos A Dos Santos
- Department of Computer Science, Federal University of Minas Gerais, Brazil Av Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
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