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Patterns from Gene Expression

eagle-i ID

http://eagle-i.itmat.upenn.edu/i/0000013a-79a9-a8cb-d69a-d90d80000000

Resource Type

  1. Algorithmic software suite

Properties

  1. Resource Description
    "PaGE can be used to produce sets of differentially expressed genes with confidence measures attached. These lists are generated the False Discovery Rate method of controlling the false positives. But PaGE is more than a differential expression analysis tool. PaGE is a tool to attach descriptive , dependable, and easily interpretable expression patterns to genes across multiple conditions, each represented by a set of replicated array experiments. The input consists of (replicated) intensities from a collection of array experiments from two or more conditions (or from a collection of direct comparisons on 2-channel arrays). The output consists of patterns, one for each row identifier in the data file. One condition is used as a reference to which the other types are compared. The length of a pattern equals the number of non-reference sample types. The symbols in the patterns are integers, where positive integers represent up-regulation as compared to the reference sample type and negative integers represent down-regulation. The patterns are based on the false discovery rates for each position in the pattern, so that the number of positive and negative symbols that appear in each position of the pattern is as descriptive as the data variability allows. The patterns generated are easily interpretable in that integers are used to represent different levels of up- or down-regulation as compared to the reference sample type."
  2. Additional Name
    PaGE
  3. Used by
    Penn Center for Bioinformatics
  4. Version
    5.1
  5. Data Input
    Gene expression intensities
  6. Data Output
    Gene expression patterns
  7. Software purpose
    Differential expression analysis objective
  8. Related Publication or Documentation
    A practical false discovery rate approach to identifying patterns of differential expression in microarray data
  9. Website(s)
    http://www.cbil.upenn.edu/PaGE/
  10. Related Technique
    Data analysis
  11. Related Technique
    RNA sequencing
  12. Related Technique
    MeDIP-SEQ assay
  13. Related Technique
    ChIP-seq assay
  14. Developed by
    Grant, Gregory R., Ph.D.
  15. Developed by
    Manduchi, Elisabetta, Ph.D.
  16. Algorithm used
    Multiple testing
  17. Coded in
    Java
  18. Coded in
    Perl
 
RDFRDF
 
Provenance Metadata About This Resource Record
  1. workflow state
    Published
  2. contributor
    fcoldren
  3. created
    2012-10-19T11:47:34.868-04:00
  4. creator
    fcoldren
  5. modified
    2013-04-05T16:54:23.755-04:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016