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SpeCond: a method to detect condition-specific gene expression

Florence MG Cavalli1*, Richard Bourgon12, Wolfgang Huber2, Juan M Vaquerizas1 and Nicholas M Luscombe13

Author Affiliations

1 EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK

2 Department of Bioinformatics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA

3 EMBL-Heidelberg Genome Biology Unit, Meyerhofstra├če 1, 69117 Heidelberg, Germany

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Genome Biology 2011, 12:R101  doi:10.1186/gb-2011-12-10-r101

Published: 18 October 2011

Additional files

Additional file 1:

Supplementary material. The document file contains further information about data processing (ROC curve, GO analysis). Additionally, we provide a more detailed description of the SpeCond parameters.

Format: PDF Size: 125KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Table of human tissue-specific genes. The table lists the 2,673 human genes detected as specific. For each of the 32 tissues (column) the gene has a value of 1 if detected as specifically expressed, -1 if detected as specifically repressed or 0 if it does not present specific expression in the tissue.

Format: XLS Size: 698KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Individual SpeCond specific HTML page; output for a specific probe set. Example of the 121_at probe set detected as specific in two tissues. The HTML page displays the probe set (or gene) name and a set of tables and figures: the parameters used in the analysis (top table), the expression profile (first figure), and the density curves of the mixture model fitting the expression values (normals 1, 2 and 3, in blue, green and yellow, respectively), as well as the null distribution (red) (second figure). The parameters of each normal distribution as well as the SpeCond parameter values are presented in the table below the second figure. Finally, the tissues in which the gene is detected as specific with their corresponding adjusted P-value are presented in the bottom table.

Format: PDF Size: 304KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data