hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine
Publication Date
October 04, 2016
Journal
PLOS ONE
Authors
Steffen Falgreen, Anders Ellern Bilgrau, Rasmus Froberg Brøndum, Lasse Hjort Jakobsen, et al
Volume
11
Issue
10
Pages
e0163711
DOI
https://dx.plos.org/10.1371/journal.pone.0163711
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0163711
Web of Science
000385696900017
Scopus
84991216051
Mendeley
http://www.mendeley.com/research/hemaclassorg-online-onebyone-microarray-normalization-classification-hematological-cancers-precision
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Mendeley | Further Information

{"title"=>"HemaClass.org: Online one-by-one microarray normalization and classification of hematological cancers for precision medicine", "type"=>"journal", "authors"=>[{"first_name"=>"Steffen", "last_name"=>"Falgreen", "scopus_author_id"=>"37121752500"}, {"first_name"=>"Anders Ellern", "last_name"=>"Bilgrau", "scopus_author_id"=>"55503521700"}, {"first_name"=>"Rasmus Froberg", "last_name"=>"Br�ndum", "scopus_author_id"=>"57201166077"}, {"first_name"=>"Lasse Hjort", "last_name"=>"Jakobsen", "scopus_author_id"=>"57021325900"}, {"first_name"=>"Jonas", "last_name"=>"Have", "scopus_author_id"=>"57191518626"}, {"first_name"=>"Kasper Lindblad", "last_name"=>"Nielsen", "scopus_author_id"=>"57191480664"}, {"first_name"=>"Tarec Christoffer", "last_name"=>"El-Galaly", "scopus_author_id"=>"22634515900"}, {"first_name"=>"Julie St�ve", "last_name"=>"B�dker", "scopus_author_id"=>"57201046864"}, {"first_name"=>"Alexander", "last_name"=>"Schmitz", "scopus_author_id"=>"36171970600"}, {"first_name"=>"Ken H.", "last_name"=>"Young", "scopus_author_id"=>"36687576100"}, {"first_name"=>"Hans Erik", "last_name"=>"Johnsen", "scopus_author_id"=>"7103033331"}, {"first_name"=>"Karen", "last_name"=>"Dybk�r", "scopus_author_id"=>"57201164528"}, {"first_name"=>"Martin", "last_name"=>"B�gsted", "scopus_author_id"=>"57201047110"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84991216051", "sgr"=>"84991216051", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0163711", "pmid"=>"27701436", "isbn"=>"1932-6203", "pui"=>"612644015"}, "id"=>"da6c614c-2b0a-3a22-920e-4f3f32ebf42b", "abstract"=>"BACKGROUND Dozens of omics based cancer classification systems have been introduced with prognostic, diagnostic, and predictive capabilities. However, they often employ complex algorithms and are only applicable on whole cohorts of patients, making them difficult to apply in a personalized clinical setting. RESULTS This prompted us to create hemaClass.org, an online web application providing an easy interface to one-by-one RMA normalization of microarrays and subsequent risk classifications of diffuse large B-cell lymphoma (DLBCL) into cell-of-origin and chemotherapeutic sensitivity classes. Classification results for one-by-one array pre-processing with and without a laboratory specific RMA reference dataset were compared to cohort based classifiers in 4 publicly available datasets. Classifications showed high agreement between one-by-one and whole cohort pre-processsed data when a laboratory specific reference set was supplied. The website is essentially the R-package hemaClass accompanied by a Shiny web application. The well-documented package can be used to run the website locally or to use the developed methods programmatically. CONCLUSIONS The website and R-package is relevant for biological and clinical lymphoma researchers using affymetrix U-133 Plus 2 arrays, as it provides reliable and swift methods for calculation of disease subclasses. The proposed one-by-one pre-processing method is relevant for all researchers using microarrays.", "link"=>"http://www.mendeley.com/research/hemaclassorg-online-onebyone-microarray-normalization-classification-hematological-cancers-precision", "reader_count"=>26, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>7, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>7, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Nursing and Health Professions"=>1, "Mathematics"=>2, "Agricultural and Biological Sciences"=>4, "Medicine and Dentistry"=>6, "Physics and Astronomy"=>1, "Social Sciences"=>1, "Computer Science"=>5}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Computer Science"=>{"Computer Science"=>5}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"United Kingdom"=>1}, "group_count"=>4}

Scopus | Further Information

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