Literature DB >> 19381961

Developing classifiers for the detection of cancer using multi-analytes.

Adi Laurentiu Tarca1, Sorin Draghici, Roberto Romero.   

Abstract

The development of a successful classifier from multiple predictors (analytes) is a multistage process complicated typically by the paucity of the data samples when compared to the number of available predictors. Choosing an adequate validation strategy is key for drawing sound conclusions about the usefulness of the classifier. Other important decisions have to be made regarding the type of prediction model to be used and training algorithm, as well as the way in which the markers are selected. This chapter describes the principles of the classifier development and underlines the most common pitfalls. A simulated dataset is used to illustrate the main concepts involved in supervised classification.

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Year:  2009        PMID: 19381961      PMCID: PMC3748835          DOI: 10.1007/978-1-60327-811-9_19

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  12 in total

1.  Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions.

Authors:  R L Somorjai; B Dolenko; R Baumgartner
Journal:  Bioinformatics       Date:  2003-08-12       Impact factor: 6.937

2.  Systematic variation in gene expression patterns in human cancer cell lines.

Authors:  D T Ross; U Scherf; M B Eisen; C M Perou; C Rees; P Spellman; V Iyer; S S Jeffrey; M Van de Rijn; M Waltham; A Pergamenschikov; J C Lee; D Lashkari; D Shalon; T G Myers; J N Weinstein; D Botstein; P O Brown
Journal:  Nat Genet       Date:  2000-03       Impact factor: 38.330

3.  HykGene: a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data.

Authors:  Yuhang Wang; Fillia S Makedon; James C Ford; Justin Pearlman
Journal:  Bioinformatics       Date:  2004-12-07       Impact factor: 6.937

4.  Analysis of microarray experiments of gene expression profiling.

Authors:  Adi L Tarca; Roberto Romero; Sorin Draghici
Journal:  Am J Obstet Gynecol       Date:  2006-08       Impact factor: 8.661

5.  Multiclass cancer diagnosis using tumor gene expression signatures.

Authors:  S Ramaswamy; P Tamayo; R Rifkin; S Mukherjee; C H Yeang; M Angelo; C Ladd; M Reich; E Latulippe; J P Mesirov; T Poggio; W Gerald; M Loda; E S Lander; T R Golub
Journal:  Proc Natl Acad Sci U S A       Date:  2001-12-11       Impact factor: 11.205

6.  Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays.

Authors:  U Alon; N Barkai; D A Notterman; K Gish; S Ybarra; D Mack; A J Levine
Journal:  Proc Natl Acad Sci U S A       Date:  1999-06-08       Impact factor: 11.205

7.  Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.

Authors:  A A Alizadeh; M B Eisen; R E Davis; C Ma; I S Lossos; A Rosenwald; J C Boldrick; H Sabet; T Tran; X Yu; J I Powell; L Yang; G E Marti; T Moore; J Hudson; L Lu; D B Lewis; R Tibshirani; G Sherlock; W C Chan; T C Greiner; D D Weisenburger; J O Armitage; R Warnke; R Levy; W Wilson; M R Grever; J C Byrd; D Botstein; P O Brown; L M Staudt
Journal:  Nature       Date:  2000-02-03       Impact factor: 49.962

8.  Diagnostic markers of ovarian cancer by high-throughput antigen cloning and detection on arrays.

Authors:  Madhumita Chatterjee; Saroj Mohapatra; Alexei Ionan; Gagandeep Bawa; Rouba Ali-Fehmi; Xiaoju Wang; James Nowak; Bin Ye; Fatimah A Nahhas; Karen Lu; Steven S Witkin; David Fishman; Adnan Munkarah; Robert Morris; Nancy K Levin; Natalie N Shirley; Gerard Tromp; Judith Abrams; Sorin Draghici; Michael A Tainsky
Journal:  Cancer Res       Date:  2006-01-15       Impact factor: 12.701

9.  Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.

Authors:  T R Golub; D K Slonim; P Tamayo; C Huard; M Gaasenbeek; J P Mesirov; H Coller; M L Loh; J R Downing; M A Caligiuri; C D Bloomfield; E S Lander
Journal:  Science       Date:  1999-10-15       Impact factor: 47.728

10.  Autoantibody approach for serum-based detection of head and neck cancer.

Authors:  Ho-Sheng Lin; Harvinder S Talwar; Adi L Tarca; Alexei Ionan; Madhumita Chatterjee; Bin Ye; Jerzy Wojciechowski; Saroj Mohapatra; Marc D Basson; George H Yoo; Brian Peshek; Fulvio Lonardo; Chuan-Ju G Pan; Adam J Folbe; Sorin Draghici; Judith Abrams; Michael A Tainsky
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2007-11       Impact factor: 4.254

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  4 in total

1.  De novo dominant ASXL3 mutations alter H2A deubiquitination and transcription in Bainbridge-Ropers syndrome.

Authors:  Anshika Srivastava; K C Ritesh; Yao-Chang Tsan; Rosy Liao; Fengyun Su; Xuhong Cao; Mark C Hannibal; Catherine E Keegan; Arul M Chinnaiyan; Donna M Martin; Stephanie L Bielas
Journal:  Hum Mol Genet       Date:  2015-12-08       Impact factor: 6.150

2.  RNA-sequencing Identifies Novel Pathways in Sarcoidosis Monocytes.

Authors:  Jaya Talreja; Pershang Farshi; Adnan Alazizi; Francesca Luca; Roger Pique-Regi; Lobelia Samavati
Journal:  Sci Rep       Date:  2017-06-02       Impact factor: 4.379

3.  A Novel S100A8/A9 Induced Fingerprint of Mesenchymal Stem Cells associated with Enhanced Wound Healing.

Authors:  Abhijit Basu; Saira Munir; Medanie A Mulaw; Karmveer Singh; Diana Crisan; Anca Sindrilaru; Nicolai Treiber; Meinhard Wlaschek; Markus Huber-Lang; Florian Gebhard; Karin Scharffetter-Kochanek
Journal:  Sci Rep       Date:  2018-04-18       Impact factor: 4.379

4.  A comparison of prediction approaches for identifying prodromal Parkinson disease.

Authors:  Mark N Warden; Susan Searles Nielsen; Alejandra Camacho-Soto; Roman Garnett; Brad A Racette
Journal:  PLoS One       Date:  2021-08-26       Impact factor: 3.240

  4 in total

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