A New Ensemble Method for Detecting Anomalies in Gene Expression Matrices

被引：12

作者：

Selicato, Laura ^{[1
,2
]}

Esposito, Flavia ^{[1
,2
]}

Gargano, Grazia ^{[1
]}

Vegliante, Maria Carmela ^{[3
]}

Opinto, Giuseppina ^{[3
]}

Zaccaria, Gian Maria ^{[3
]}

Ciavarella, Sabino ^{[3
]}

Guarini, Attilio ^{[3
]}

Del Buono, Nicoletta ^{[1
,2
]}

机构：

[1] Univ Bari Aldo Moro, Dept Math, I-70125 Bari, Italy

[2] Ist Nazl Alta Matemat, GNCS, Ple Aldo Moro 5, I-00185 Rome, Italy

[3] IRCCS Ist Tumori Giovanni Paolo II, Hematol & Cell Therapy Unit, I-70124 Bari, Italy

来源：

MATHEMATICS | 2021年 / 9卷 / 08期

关键词：

anomaly; low rank decomposition; gene expression; clustering; outliers; FOLLICULAR LYMPHOMA; MICROARRAY; MUTATIONS; NUMBER;

D O I：

10.3390/math9080882

中图分类号：

O1 [数学];

学科分类号：

0701 ; 070101 ;

摘要：

One of the main problems in the analysis of real data is often related to the presence of anomalies. Namely, anomalous cases can both spoil the resulting analysis and contain valuable information at the same time. In both cases, the ability to detect these occurrences is very important. In the biomedical field, a correct identification of outliers could allow the development of new biological hypotheses that are not considered when looking at experimental biological data. In this work, we address the problem of detecting outliers in gene expression data, focusing on microarray analysis. We propose an ensemble approach for detecting anomalies in gene expression matrices based on the use of Hierarchical Clustering and Robust Principal Component Analysis, which allows us to derive a novel pseudo-mathematical classification of anomalies.

引用

页数：26

共 43 条

[11] Biological and Clinical Relevance of Associated Genomic Alterations in MYD88 L265P and non-L265P-Mutated Diffuse Large B-Cell Lymphoma: Analysis of 361 Cases [J].

Dubois, Sydney ;

Viailly, Pierre-Julien ;

Bohers, Elodie ;

Bertrand, Philippe ;

Ruminy, Philippe ;

Marchand, Vinciane ;

Maingonnat, Catherine ;

Mareschal, Sylvain ;

Picquenot, Jean-Michel ;

Penther, Dominique ;

Jais, Jean-Philippe ;

Tesson, Bruno ;

Peyrouze, Pauline ;

Figeac, Martin ;

Desmots, Fabienne ;

Fest, Thierry ;

Haioun, Corinne ;

Lamy, Thierry ;

Copie-Bergman, Christiane ;

Fabiani, Bettina ;

Delarue, Richard ;

Peyrade, Frederic ;

Andre, Marc ;

Ketterer, Nicolas ;

Leroy, Karen ;

Salles, Gilles ;

Molina, Thierry J. ;

Tilly, Herve ;

Jardin, Fabrice .

CLINICAL CANCER RESEARCH, 2017, 23 (09) :2232-2244

[12] An NMF-Based Methodology for Selecting Biomarkers in the Landscape of Genes of Heterogeneous Cancer-Associated Fibroblast Populations [J].

Esposito, Flavia ;

Boccarelli, Angelina ;

Del Buono, Nicoletta .

BIOINFORMATICS AND BIOLOGY INSIGHTS, 2020, 14

[13] EZH2 Mutations in Follicular Lymphoma from Different Ethnic Groups and Associated Gene Expression Alterations [J].

Guo, Shuangping ;

Chan, John K. C. ;

Iqbal, Javeed ;

McKeithan, Timothy ;

Fu, Kai ;

Meng, Bin ;

Pan, Yi ;

Cheuk, Wah ;

Luo, Donglan ;

Wang, Ruian ;

Zhang, Weiwei ;

Greiner, Timothy C. ;

Chan, Wing C. .

CLINICAL CANCER RESEARCH, 2014, 20 (12) :3078-3086

[14] Pathway discovery in mantle cell lymphoma by integrated analysis of high-resolution gene expression and copy number profiling [J].

Hartmann, Elena M. ;

Campo, Elias ;

Wright, George ;

Lenz, Georg ;

Salaverria, Itziar ;

Jares, Pedro ;

Xiao, Wenming ;

Braziel, Rita M. ;

Rimsza, Lisa M. ;

Chan, Wing-Chung ;

Weisenburger, Dennis D. ;

Delabie, Jan ;

Jaffe, Elaine S. ;

Gascoyne, Randy D. ;

Dave, Sandeep S. ;

Mueller-Hermelink, Hans-Konrad ;

Staudt, Louis M. ;

Ott, German ;

Bea, Silvia ;

Rosenwald, Andreas .

BLOOD, 2010, 116 (06) :953-961

[15] ROBPCA: A new approach to robust principal component analysis [J].

Hubert, M ;

Rousseeuw, PJ ;

Vanden Branden, K .

TECHNOMETRICS, 2005, 47 (01) :64-79

[16] A gene-expression profiling score for prediction of outcome in patients with follicular lymphoma: a retrospective training and validation analysis in three international cohorts [J].

Huet, Sarah ;

Tesson, Bruno ;

Jais, Jean-Philippe ;

Feldman, Andrew L. ;

Magnano, Laura ;

Thomas, Emilie ;

Traverse-Glehen, Alexandra ;

Albaud, Benoit ;

Carrere, Marjorie ;

Xerri, Luc ;

Ansell, Stephen M. ;

Baseggio, Lucile ;

Reyes, Cecile ;

Tarte, Karin ;

Boyault, Sandrine ;

Haioun, Corinne ;

Link, Brian K. ;

Feugier, Pierre ;

Lopez-Guillermo, Armando ;

Tilly, Herve ;

Brice, Pauline ;

Hayette, Sandrine ;

Jardin, Fabrice ;

Offner, Fritz ;

Sujobert, Pierre ;

Gentien, David ;

Viari, Alain ;

Campo, Elias ;

Cerhan, James R. ;

Salles, Gilles .

LANCET ONCOLOGY, 2018, 19 (04) :549-561

[17] BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams [J].

Hulsen, Tim ;

de Vlieg, Jacob ;

Alkema, Wynand .

BMC GENOMICS, 2008, 9 (1)

[18]

Hung H., 2020, ARXIV200413914

[19] Adjusting batch effects in microarray expression data using empirical Bayes methods [J].

Johnson, W. Evan ;

Li, Cheng ;

Rabinovic, Ariel .

BIOSTATISTICS, 2007, 8 (01) :118-127

[20] Principal component analysis: a review and recent developments [J].

Jolliffe, Ian T. ;

Cadima, Jorge .

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 2016, 374 (2065)

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