A gene recommender algorithm to identify co-expressed genes in C. elegans

Online Supplement

Art B. Owen1,4, Joshua M. Stuart2,3, Kathy E. Mach3, Anne M. Villeneuve3, Stuart K. Kim3,4

1Department of Statistics                                                2Stanford Medical Informatics     

 Sequoia Hall 130                                                          251 Campus Drive, MSOB X-215

 Stanford, CA, 94305                                                     Stanford, California, 94305         

 

3Departments of Developmental Biology and Genetics

 Stanford University School of Medicine

 Stanford, California, 94305

 

4corresponding authors

 A.B.O.                                                                         S.K.K.

 art@stat.stanford.edu.                                             kim@cmgm.stanford.edu

 650.725.2232                                                                650.725.7671

 Fax: 650.725.8977                                                        Fax: 650.725.7739

 http://www.stanford.edu/~owen                               www.cmgm.stanford.edu/~kimlab

 

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Manuscript

Note for Netscape users: To download tables as Excel documents, right click on [EXCEL] links and choose “Save Link As…”.

Supplemental Tables

*  S-Table 1.  The top-scoring 51 genes in the retinoblastoma cassette tested with RNA interference. [EXCEL]

*  S-Table 2.  List of genes found in the search for new major sperm protein candidates. [EXCEL]

*  S-Table 3.  List of genes found in the search for new synaptonemal complex candidates. [EXCEL]

*  S-Table 4.  List of genes found in the search for new repair/recombination candidates. [EXCEL]

 

Supplemental Figures

*  S-Figure 1.  Experiment scores for the non-retinoblastoma queries. [PDF]

 

Program availability and source code

 

*  Web-based search engine.  Search for new candidates related to your own genes of interest.

*  C++ source code [ZIP]  for performing gene recommender analysis (unzipping creates a gene_recommender_src sub-directory; see the README file in that directory for further instructions).  Written by Josh Stuart.

*  Matlab source code  [ZIP] (unzipping creates a gene_recommender_matlab sub-directory; see the README file in that directory for further instructions).  Running requires Matlab version 5 or above.  Written by Art Owen.

 

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Tables from the Paper

*  Table 1. List of genes for each query. [EXCEL]

*  Table 2. Retinoblastoma hits.  See Supplemental Table 1 which contains an expanded version of the list. [EXCEL]

*  Table 3. Size of the retinoblastoma cassette compared to random queries. [EXCEL]

*  Table 4. wrm-1 RNA interference results. [EXCEL]

*  Table 5. Precision of retinoblastoma cassette found by recommender compared to the topomap. [EXCEL]

Figures from the Paper

*  Figure 1.  Experiment scores from retinoblastoma query. [PDF]

*  Figure 2.  Leave-one-out analysis. [PDF]

*  Figure 3.  Expression profiles of the genes in the Rb hit list. [PDF, 884KB]

*  Figure 4.  RNA interference results of JC8.6. [PDF, 2.6MB]