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A Survey of Machine Learning Approaches Applied to Gene Expression Analysis for Cancer Prediction

Mahmood Khalsan, Lee R. Machado, Eman Salih Al-Shamery, Suraj Ajit, Karen Anthony, Mu Mu, Michael Opoku Agyeman
2022 IEEE Access  
The survey captures multiple aspects of machine learning associated cancer studies, including cancer classification, cancer prediction, identification of biomarker genes, microarray, and RNA-Seq data.  ...  and gallbladder) for survival prediction, tumor identification and stratification.  ...  Biomarker genes typically represent the identification of a subset of genes that are associated with a specific disease or subset of diseases.  ... 
doi:10.1109/access.2022.3146312 fatcat:m7z6ekvh7re2ncvba6ijki675a

Similar expression profiles in CD34+ cells from chronic phase chronic myeloid leukemia patients with and without deep molecular responses to nilotinib

Ami B. Patel, Thoralf Lange, Anthony D. Pomicter, Christopher J. Conley, Christina A. Harrington, Kimberly R. Reynolds, Todd W. Kelley, Thomas O'Hare, Michael W. Deininger
2018 OncoTarget  
Approximately 60% of patients treated with second generation tyrosine kinase inhibitors achieve a deep molecular response, the prerequisite for a trial of treatmentfree remission.  ...  This result is in contrast to the distinct expression signature of CD34 + chronic phase chronic myeloid leukemia patients failing to achieve a cytogenetic response on imatinib and suggests that deep molecular  ...  ACKNOWLEDGMENTS AND FUNDING Support for this project came from Novartis, the National Institutes of Health Award R01CA178397 (MWD and TO) and P30 CA042014 (MWD and TO).  ... 
doi:10.18632/oncotarget.24954 pmid:29707154 pmcid:PMC5915162 fatcat:g75dnib4xfhdrkcjkdkffwxnju

Identification of two downregulated circRNAs in patients with acute B‑lymphocytic leukemia

Bo Zhou, Liansheng Zhong, Liu Tian, Ye Zhang, Runan Wang, Qun He, Yujie Zhao
2021 Oncology Letters  
The identification of diagnostic and prognostic biomarkers of B-ALL can contribute to the development of novel therapeutic methods and drugs, which can improve the survival outcomes of patients with B-ALL  ...  Thus, these circRNAs may serve as biomarkers for patients with B-ALL.  ...  .), which were subjected to deep sequencing using BioAnalyzer 2100 (Agilent Technologies, Inc.). Identification of circRNAs.  ... 
doi:10.3892/ol.2021.13158 pmid:34966456 pmcid:PMC8669665 fatcat:oaqp2hsmynhkpentgboa5bgemi

High-throughput analysis and functional interpretation of extracellular vesicle content in hematological malignancies

Ilaria Tanasi, Annalisa Adamo, Paul Takam Kamga, Riccardo Bazzoni, Mauro Krampera
2020 Computational and Structural Biotechnology Journal  
Recent advances in high-throughput technologies have allowed the deep characterization and functional interpretation of EV content.  ...  In particular, they are actively involved in the pathogenesis of several hematological malignancies (HM), mainly interacting with a number of target cells and inducing functional and epigenetic changes  ...  Acknowledgments We would like to acknowledge Associazione Italiana contro Leucemie, Linfomi e Mieloma (AIL) -Sezione di Verona for donations and logistic support in managing hematological patients.  ... 
doi:10.1016/j.csbj.2020.09.027 pmid:33101605 pmcid:PMC7554250 fatcat:2ckmijfbr5f53f6v6sw6ikiftm

Genome-wide analysis of microRNA and mRNA expression signatures in cancer

Ming-hui Li, Sheng-bo Fu, Hua-sheng Xiao
2015 Acta Pharmacologica Sinica  
In this review, we summarize the progress in genome-wide analysis of miRNAs and mRNAs as cancer biomarkers, highlighting their diagnostic and prognostic roles.  ...  In the past few decades, DNA microarray and next-generation sequencing techniques have been widely applied to identify miRNA and mRNA signatures for cancers on a genome-wide scale and have provided meaningful  ...  We are entering a new era with enormous amounts of data generated by NGS and microarray analysis.  ... 
doi:10.1038/aps.2015.67 pmid:26299954 pmcid:PMC4648178 fatcat:z5y665ys7ncjton2i2xvg35e4q

Network biomarkers, interaction networks and dynamical network biomarkers in respiratory diseases

Xiaodan Wu, Luonan Chen, Xiangdong Wang
2014 Clinical and Translational Medicine  
Clinical bioinformatics should be a key approach to the identification and validation of disease-specific biomarkers.  ...  Identification and validation of interaction networks and network biomarkers have become more critical and important in the development of disease-specific biomarkers, which are functionally changed during  ...  A transcriptome network analysis method was used to construct gene regulation networks on published microarray data and select candidate genes for squamous lung cancer [39] .  ... 
doi:10.1186/2001-1326-3-16 pmid:24995123 pmcid:PMC4072888 fatcat:qxjchyqltndxhdsyf3rihr5ce4

A Review on Recent Progress in Machine Learning and Deep Learning Methods for Cancer Classification on Gene Expression Data

Aina Umairah Mazlan, Noor Azida Sahabudin, Muhammad Akmal Remli, Nor Syahidatul Nadiah Ismail, Mohd Saberi Mohamad, Hui Wen Nies, Nor Bakiah Abd Warif
2021 Processes  
The development of many machine learning methods for insight analysis in cancer classification has brought a lot of improvement in healthcare.  ...  This paper provides a recent review on recent progress in ML and deep learning (DL) for cancer classification, which has received increasing attention in bioinformatics and computational biology.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/pr9081466 fatcat:mehvzadmn5dafauq4lqifb2vky

How to Translate DNA Methylation Biomarkers Into Clinical Practice

Wolfgang Wagner, Wolfgang Wagner
2022 Frontiers in Cell and Developmental Biology  
Development of an epigenetic biomarker for clinical application is a long and cumbersome process that is only initiated with the identification of an epigenetic signature.  ...  processing, 3) accuracy of DNA methylation measurements, 4) identification of confounding parameters, 5) accreditation as diagnostic procedure, 6) standardized data analysis, 7) turnaround time, and 8  ...  For the deep-sequencing based approaches accuracy depends largely on the sequencing depth.  ... 
doi:10.3389/fcell.2022.854797 pmid:35281115 pmcid:PMC8905294 doaj:34532c2018314d3584e771d153382d0f fatcat:lrkmrlryqjc2rekq3ebmswgdj4

New tools for functional genomic analysis

Xin Chen, Eric Jorgenson, Siu Tim Cheung
2009 Drug Discovery Today  
Functional genomic analyses enable biologists to perform analysis of genetic events on a global scale and they have been widely used in gene discovery, biomarker determination, disease classification,  ...  For the past decade, the development of genomic technology has revolutionized modern biological research and drug discovery.  ...  Bioinformatics Analysis Genomic studies generally generate large amounts of data.  ... 
doi:10.1016/j.drudis.2009.05.005 pmid:19477290 pmcid:PMC2720446 fatcat:xpt6mbny5feqvdpu74si4qkov4

Molecular approaches to the diagnosis and monitoring of production diseases in pigs

Timothy A. Giles, Aouatif Belkhiri, Paul A. Barrow, Neil Foster
2017 Research in Veterinary Science  
Whilst a large number of studies have been carried out in human medicine, further work is needed to identify molecular biomarkers in veterinary medicine and in particular those associated with production  ...  Molecular biomarkers of production disease could be of immense value by improving diagnosis and risk analysis to determine best practice with an impact on increased economic output and animal welfare.  ...  Microarray analysis A DNA microarray is an array of DNA probes arranged in miniature on a solid surface.  ... 
doi:10.1016/j.rvsc.2017.05.016 pmid:28535467 pmcid:PMC7118804 fatcat:ztsbrdb225hhjnydrji652p3pm

Circulating MicroRNA Profiling in Cancer Biomarker Discovery [chapter]

Francesca Scionti, Pierosandro Tagliaferri, Pierfrancesco Tassone, Maria Teresa Di Martino
2018 Biomarker - Indicator of Abnormal Physiological Process  
Circulating miRNAs could be reliable biomarkers for early-stage cancer diagnosis, prognosis and response to therapy.  ...  MicroRNAs (miRNAs) are a class of small non-coding RNA molecules of approximately 22 nucleotides that regulate gene expression at the post-transcriptional level.  ...  Acknowledgements This chapter has been supported by the Italian Association for Cancer Research (AIRC), PI: PT. "Special Program Molecular Clinical Oncology -5 per mille" n. 9980, 2010/15.  ... 
doi:10.5772/intechopen.75981 fatcat:za6tms6thjhl3mqffiwkkar5oe

Comprehensive Analysis of MILE Gene Expression Data Set Advances Discovery of Leukaemia Type and Subtype Biomarkers

Wojciech Labaj, Anna Papiez, Andrzej Polanski, Joanna Polanska
2017 Interdisciplinary Sciences Computational Life Sciences  
Abstract Large collections of data in studies on cancer such as leukaemia provoke the necessity of applying tailored analysis algorithms to ensure supreme information extraction.  ...  In this work, a custom-fit pipeline is demonstrated for thorough investigation of the voluminous MILE gene expression data set.  ...  From this analysis a biomarker identification step is added as it is possible to set an appropriate condition.  ... 
doi:10.1007/s12539-017-0216-9 pmid:28303531 pmcid:PMC5366179 fatcat:zmg753wyn5cn3om5e5e3nrs4jm

Applications of Support Vector Machine (SVM) Learning in Cancer Genomics

2018 Cancer Genomics & Proteomics  
to the discovery of new biomarkers, new drug targets, and a better understanding of cancer driver genes.  ...  There are two main types of ML learning -supervised SVM Model SVM is a powerful method for building a classifier.  ...  Acknowledgements This study has been supported by University of Manitoba Faculty of Science Interdisciplinary/New Directions Research Collaboration Initiation Grant, and partially by the Canadian Breast  ... 
doi:10.21873/cgp.20063 pmid:29275361 pmcid:PMC5822181 fatcat:o6l764hssnh2nbu4fm6b52f3mi

Personalized Medicine: Marking a New Epoch in Cancer Patient Management

M. Diamandis, N. M. A. White, G. M. Yousef
2010 Molecular Cancer Research  
In addition to classic single molecular markers, high-throughput approaches can be used for PM including whole genome sequencing, single-nucleotide polymorphism analysis, microarray analysis, and mass  ...  A common trend among these tools is their ability to analyze many targets simultaneously, thus increasing the sensitivity, specificity, and accuracy of biomarker discovery.  ...  Newer microarray platforms, such as miRNA microarrays, are also showing encouraging preliminary data for their potential use as cancer biomarkers (108) (109) (110) (111) (112) (113) .  ... 
doi:10.1158/1541-7786.mcr-10-0264 pmid:20693306 fatcat:cwrurtnhynbyfduzevnxfgl3eq

Immunocapture strategies in translational proteomics

Claudia Fredolini, Sanna Byström, Elisa Pin, Fredrik Edfors, Davide Tamburro, Maria Jesus Iglesias, Anna Häggmark, Mun-Gwan Hong, Mathias Uhlen, Peter Nilsson, Jochen M Schwenk
2015 Espert Review of Proteomics  
Acknowledgment The authors would like to thank Devin Sullivan (Cellprofiling -Subcellular Human Protein Atlas; SciLifeLab, School of Biotechnology, KTH -Royal Institute of Technology, Sweden) for the great  ...  Financial & competing interests disclosure The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the  ...  [70] Moving to discuss the aspect of study design, the identification of a candidate protein as a biomarker for a disease is often pursued using case-control studies.  ... 
doi:10.1586/14789450.2016.1111141 pmid:26558424 pmcid:PMC4732419 fatcat:fybbxk7bgvdxxa3h33r7by77pi
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