Literature DB >> 17906632

A gene expression bar code for microarray data.

Michael J Zilliox1, Rafael A Irizarry.   

Abstract

The ability to measure genome-wide expression holds great promise for characterizing cells and distinguishing diseased from normal tissues. Thus far, microarray technology has been useful only for measuring relative expression between two or more samples, which has handicapped its ability to classify tissue types. Here we present a method that can successfully predict tissue type based on data from a single hybridization. A preliminary web-tool is available online (http://rafalab.jhsph.edu/barcode/).

Mesh:

Year:  2007        PMID: 17906632      PMCID: PMC3154617          DOI: 10.1038/nmeth1102

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  17 in total

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Authors:  Lars Dyrskjøt; Mogens Kruhøffer; Thomas Thykjaer; Niels Marcussen; Jens L Jensen; Klaus Møller; Torben F Ørntoft
Journal:  Cancer Res       Date:  2004-06-01       Impact factor: 12.701

2.  Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS.

Authors:  Ranadip Pal; Aniruddha Datta; Albert J Fornace; Michael L Bittner; Edward R Dougherty
Journal:  Bioinformatics       Date:  2004-12-14       Impact factor: 6.937

3.  Multiple-laboratory comparison of microarray platforms.

Authors:  Rafael A Irizarry; Daniel Warren; Forrest Spencer; Irene F Kim; Shyam Biswal; Bryan C Frank; Edward Gabrielson; Joe G N Garcia; Joel Geoghegan; Gregory Germino; Constance Griffin; Sara C Hilmer; Eric Hoffman; Anne E Jedlicka; Ernest Kawasaki; Francisco Martínez-Murillo; Laura Morsberger; Hannah Lee; David Petersen; John Quackenbush; Alan Scott; Michael Wilson; Yanqin Yang; Shui Qing Ye; Wayne Yu
Journal:  Nat Methods       Date:  2005-04-21       Impact factor: 28.547

4.  An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival.

Authors:  Lance D Miller; Johanna Smeds; Joshy George; Vinsensius B Vega; Liza Vergara; Alexander Ploner; Yudi Pawitan; Per Hall; Sigrid Klaar; Edison T Liu; Jonas Bergh
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-02       Impact factor: 11.205

5.  Progression of Barrett's metaplasia to adenocarcinoma is associated with the suppression of the transcriptional programs of epidermal differentiation.

Authors:  Erik T Kimchi; Mitchell C Posner; James O Park; Thomas E Darga; Masha Kocherginsky; Theodore Karrison; John Hart; Kerrington D Smith; James J Mezhir; Ralph R Weichselbaum; Nikolai N Khodarev
Journal:  Cancer Res       Date:  2005-04-15       Impact factor: 12.701

6.  Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis.

Authors:  Christos Sotiriou; Pratyaksha Wirapati; Sherene Loi; Adrian Harris; Steve Fox; Johanna Smeds; Hans Nordgren; Pierre Farmer; Viviane Praz; Benjamin Haibe-Kains; Christine Desmedt; Denis Larsimont; Fatima Cardoso; Hans Peterse; Dimitry Nuyten; Marc Buyse; Marc J Van de Vijver; Jonas Bergh; Martine Piccart; Mauro Delorenzi
Journal:  J Natl Cancer Inst       Date:  2006-02-15       Impact factor: 13.506

7.  Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements.

Authors:  Scott L Carter; Aron C Eklund; Brigham H Mecham; Isaac S Kohane; Zoltan Szallasi
Journal:  BMC Bioinformatics       Date:  2005-04-25       Impact factor: 3.169

8.  Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts.

Authors:  Yudi Pawitan; Judith Bjöhle; Lukas Amler; Anna-Lena Borg; Suzanne Egyhazi; Per Hall; Xia Han; Lars Holmberg; Fei Huang; Sigrid Klaar; Edison T Liu; Lance Miller; Hans Nordgren; Alexander Ploner; Kerstin Sandelin; Peter M Shaw; Johanna Smeds; Lambert Skoog; Sara Wedrén; Jonas Bergh
Journal:  Breast Cancer Res       Date:  2005-10-03       Impact factor: 6.466

9.  Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential.

Authors:  Leming Shi; Weida Tong; Hong Fang; Uwe Scherf; Jing Han; Raj K Puri; Felix W Frueh; Federico M Goodsaid; Lei Guo; Zhenqiang Su; Tao Han; James C Fuscoe; Z Alex Xu; Tucker A Patterson; Huixiao Hong; Qian Xie; Roger G Perkins; James J Chen; Daniel A Casciano
Journal:  BMC Bioinformatics       Date:  2005-07-15       Impact factor: 3.169

10.  ArrayExpress--a public repository for microarray gene expression data at the EBI.

Authors:  H Parkinson; U Sarkans; M Shojatalab; N Abeygunawardena; S Contrino; R Coulson; A Farne; G Garcia Lara; E Holloway; M Kapushesky; P Lilja; G Mukherjee; A Oezcimen; T Rayner; P Rocca-Serra; A Sharma; S Sansone; A Brazma
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

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  80 in total

1.  Intercohort gene expression co-analysis reveals chemokine receptors as prognostic indicators in Ewing's sarcoma.

Authors:  Idriss M Bennani-Baiti; Aaron Cooper; Elizabeth R Lawlor; Maximilian Kauer; Jozef Ban; Dave N T Aryee; Heinrich Kovar
Journal:  Clin Cancer Res       Date:  2010-06-04       Impact factor: 12.531

Review 2.  Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation.

Authors:  Björn Reinius; Rickard Sandberg
Journal:  Nat Rev Genet       Date:  2015-10-07       Impact factor: 53.242

3.  An empirical Bayesian approach for identifying differential coexpression in high-throughput experiments.

Authors:  John A Dawson; Christina Kendziorski
Journal:  Biometrics       Date:  2011-10-17       Impact factor: 2.571

4.  R/EBcoexpress: an empirical Bayesian framework for discovering differential co-expression.

Authors:  John A Dawson; Shuyun Ye; Christina Kendziorski
Journal:  Bioinformatics       Date:  2012-05-16       Impact factor: 6.937

5.  Multiplatform single-sample estimates of transcriptional activation.

Authors:  Stephen R Piccolo; Michelle R Withers; Owen E Francis; Andrea H Bild; W Evan Johnson
Journal:  Proc Natl Acad Sci U S A       Date:  2013-10-15       Impact factor: 11.205

Review 6.  Genome-scale approaches to the epigenetics of common human disease.

Authors:  Andrew P Feinberg
Journal:  Virchows Arch       Date:  2009-10-21       Impact factor: 4.064

7.  Molecular biomarkers of residual disease after surgical debulking of high-grade serous ovarian cancer.

Authors:  Susan L Tucker; Kshipra Gharpure; Shelley M Herbrich; Anna K Unruh; Alpa M Nick; Erin K Crane; Robert L Coleman; Jamie Guenthoer; Heather J Dalton; Sherry Y Wu; Rajesha Rupaimoole; Gabriel Lopez-Berestein; Bulent Ozpolat; Cristina Ivan; Wei Hu; Keith A Baggerly; Anil K Sood
Journal:  Clin Cancer Res       Date:  2014-04-22       Impact factor: 12.531

8.  Disease signatures are robust across tissues and experiments.

Authors:  Joel T Dudley; Robert Tibshirani; Tarangini Deshpande; Atul J Butte
Journal:  Mol Syst Biol       Date:  2009-09-15       Impact factor: 11.429

9.  TileProbe: modeling tiling array probe effects using publicly available data.

Authors:  Jennifer Toolan Judy; Hongkai Ji
Journal:  Bioinformatics       Date:  2009-07-09       Impact factor: 6.937

10.  A molecular function map of Ewing's sarcoma.

Authors:  Maximilian Kauer; Jozef Ban; Reinhard Kofler; Bob Walker; Sean Davis; Paul Meltzer; Heinrich Kovar
Journal:  PLoS One       Date:  2009-04-30       Impact factor: 3.240

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