Statistical evaluation of SAGE libraries: consequences for experimental design.

No abstract is available for this paper.

• Publication year

  2002

• Venue

  Physiological Genomics

• Publication date

  2002-10-29

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1152/PHYSIOLGENOMICS.00042.2002PMID 12407185
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• [Serial analysis of gene expression].

  2002cited by this paper
• eSAGE: managing and analysing data generated with Serial Analysis of Gene Expression (SAGE)

  2000cited by this paper
• USAGE: a web-based approach towards the analysis of SAGE data

  2000cited by this paper
• POWER_SAGE: comparing statistical tests for SAGE experiments

  2000influential reference
• Transcriptome analysis of fibroblast cells immediate-early after human cytomegalovirus infection.

  2000cited by this paper
• A quantitative evaluation of SAGE.

  2000cited by this paper
• SAGEmap: a public gene expression resource.

  2000cited by this paper
• Genes differentially expressed in medulloblastoma and fetal brain.

  1999cited by this paper
• A public database for gene expression in human cancers.

  1999cited by this paper
• Computational methods for the identification of differential and coordinated gene expression.

  1999cited by this paper
• Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources.

  1999cited by this paper
• Computational aspects of expression data

  1999cited by this paper
• Characterization of Gene Expression in Resting and Activated Mast Cells

  1998cited by this paper
• The significance of digital gene expression profiles.

  1997influential reference
• Gene expression profiles in normal and cancer cells.

  1997influential reference
• SAGE transcript profiles for p53-dependent growth regulation

  1997influential reference
• Serial Analysis of Gene Expression

  1995cited by this paper
• [A Survey of Exact Inference for Contingency Tables]: Comment

  1992cited by this paper
• Practical statistics for medical research

  1990influential reference
• Practical Nonparametric Statistics

  1972cited by this paper

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  2017cites this paper
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  2016cites this paper
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  2015cites this paper
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  2015cites this paper
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• [Serological diagnosis of tumors: methods of marker's search].

  2013cites this paper
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  2011cites this paper
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  2011cites this paper
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  2011cites this paper
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  2010cites this paper
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  2010cites this paper
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  2010influential citation
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  2010cites this paper
• Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

  2009cites this paper
• A review of gene expression profiling of human embryonic stem cell lines and their differentiated progeny.

  2009cites this paper
• Methods for quantitation of gene expression.

  2009cites this paper
• Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays

  2009cites this paper
• Functional genomic analyses of the impact of global hypomethylation and of tumor microenvironment in a rat model of human chondrosarcoma

  2009cites this paper
• Clustering-based approaches to SAGE data mining

  2008cites this paper
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  2008cites this paper
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  2008cites this paper
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  2008cites this paper
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  2008cites this paper
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  2008cites this paper
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  2008cites this paper
• A comparative Analysis by SAGE of Gene Expression Profiles of Esophageal Adenocarcinoma and Esophageal Squamous Cell Carcinoma

  2008cites this paper
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  2008cites this paper
• Evaluation of Combining Several Statistical Methods with a Flexible Cutoff for Identifying Differentially Expressed Genes in Pairwise Comparison of EST Sets

  2008cites this paper
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  2008cites this paper
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  2008cites this paper
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  2008cites this paper
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  2008cites this paper
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  2008cites this paper
• Regulation of a virus-induced lethal disease in tomato revealed by LongSAGE analysis.

  2007influential citation
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  2007cites this paper
• Reaping the Benefits of SAGE.

  2007cites this paper
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  2007cites this paper
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  2007cites this paper
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  2007cites this paper
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  2007cites this paper
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  2007cites this paper
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  2007cites this paper
• New technologies used in the study of human melanoma.

  2007cites this paper
• Transcriptional Profiling Reveals Novel Markers of Liver Fibrogenesis

  2006influential citation
• Bayesian Hierarchical Models for Serial Analysis of Gene Expression

  2006cites this paper
• Expression profiling of the mouse early embryo: Reflections and perspectives

  2006cites this paper
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  2006cites this paper
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  2006cites this paper
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  2006cites this paper
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  2006influential citation
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  2006cites this paper
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  2006cites this paper
• An Introduction to High-Throughput Bioinformatics Data

  2006cites this paper
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  2005cites this paper
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  2005cites this paper
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  2005cites this paper
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  2005cites this paper
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  2005cites this paper
• Efficiency and limits of the Serial Analysis of Gene Expression (SAGE) method: discussions based on first results in bovine trypanotolerance.

  2005cites this paper
• Gene expression analysis of Tek/Tie2 signaling.

  2005cites this paper
• A comparative analysis by SAGE of gene expression profiles of Barrett's esophagus, normal squamous esophagus, and gastric cardia.

  2005cites this paper
• WEBSAGE: a web tool for visual analysis of differentially expressed human SAGE tags

  2005cites this paper
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  2005cites this paper
• Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line

  2004cites this paper
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  2004cites this paper
• Functional genomics of lung disease. Second annual Pittsburgh International Lung Conference, October 2003.

  2004cites this paper
• Computational approaches for in-depth analysis of cDNA sequence tags

  2004cites this paper
• Serial analysis of gene expression (SAGE): unraveling the bioinformatics tools.

  2004cites this paper
• Overdispersed logistic regression for SAGE: Modelling multiple groups and covariates

  2004cites this paper
• Hematopoietic Stem Cells Identify Known and Novel Transcripts Overexpressed in Microarray and Serial Analysis of Gene Expression Analyses

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