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obcs / obcs

A biomedical ontology in the domain of biological and clinical statistics.
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new term request from BCBC #6

Closed zhengj2007 closed 9 years ago

zhengj2007 commented 9 years ago

From zhengj2...@gmail.com on February 24, 2015 14:47:42

Three software terms are needed for annotation of data in the Beta Cell Biological Consortium database.

  1. Term: PaGE Definition: PaGE (Patterns from Gene Expression) is a differential expression software that can be used to produce lists of differentially expressed genes with confidence measures attached. These lists are generated via a False Discovery Rate method of controlling the false positives. 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. Details about the PaGE algorithm can be found in Grant G.R., Liu J., Stoeckert C.J.Jr. (2005) A practical false discovery rate approach to identifying patterns of differential expression in microarray data, Bioinformatics, 21(11): 2684-2690.
  2. Term: EDGE Definition: EDGE (Extraction of Differential Gene Expression) is a differential expression software package for the significance analysis of DNA microarray experiments for both standard and time course experiments. The software is based on the following articles:
  3. Storey J.D. (2007) The optimal discovery procedure: A new approach to simultaneous significance testing, Journal of the Royal Statistical Society, Series B, 69: 347-368.
  4. Storey J.D., Dai J.Y., and Leek J.T. (2007) The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments, Biostatistics, 8: 414-432.
  5. Leek J.T,. Monsen E.C., Dabney A.R., and Storey J.D. (2006) EDGE: Extraction and analysis of differential gene expression, Bioinformatics, 22: 507-508.
  6. Storey J.D., Xiao W., Leek J.T., Tompkins R.G., and Davis R.W. (2005) Significance analysis of time course microarray experiments, Proceedings of the National Academy of Sciences, 102: 12837-12842.
  7. Term: GLITR Definition: GLITR (GLobal Identifier of Target Regions) is a peak calling software to identify transcription factor binding sites from ChIP-Seq technology, described in Tuteja G., White P., Schug J., Kaestner K.H. (2009) Extracting transcription factor targets from ChIP-Seq data, Nucleic Acids Res., 37(17): e113. doi: 10.1093/nar/gkp536.

The statistical measures of the software are:

PaGE: confidence values (for both up and down regulation, where confidence is defined as 1-FDR).

EDGE: outputs p-values and q-values.

GLITR: FDR.

Information provided by Dr. Elisabetta Manduchi

Original issue: http://code.google.com/p/obcs/issues/detail?id=6

zhengj2007 commented 9 years ago

The terms were add on Commits on Feb 24, 2015.