Research article
Identifying disease-specific genes based on their topological significance in protein networks
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* Corresponding author: Andrej Bugrim andrej@genego.com
1 GeneGo Inc, Renaissance Drive, Saint Joseph, Michigan 49085, USA
2 Program of Translational Medicine, Van Andel Research Institute, Bostwick Avenue NE, Grand Rapids, MI 49503, USA
3 Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Str, Moscow, Russia
BMC Systems Biology 2009, 3:36 doi:10.1186/1752-0509-3-36
Published: 23 March 2009Additional files
Additional file 1:
List of differentially expressed genes in psoriasis. Two hundred sixty-six genes were identified as being differentially expressed in psoriasis by comparing gene expression of psoriatic and healthy skin (p < 0.05, t-test).
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Additional file 2:
Topological scoring of genes. The set of differentially expressed genes in psoriasis was used as an input for the topological scoring algorithm. All nodes (3,652) from the shortest path network connecting the differentially expressed genes were assigned p-values.
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Additional file 3:
Topological scoring of differentially expressed genes. One hundred forty-five differentially expressed genes were part of the shortest path network and were assigned p values.
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Additional file 4:
Top scoring maps and analysis of pub-med hits with other diseases. Images and detailed description of top scoring maps from the enrichment analysis of the combined set of differentially expressed and topologically significant genes. The file also includes the functional analysis of down-regulated genes in psoriasis and pub-med hit statistics for glaucoma and multiple sclerosis.
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Additional file 5:
Topologically significant genes. Topologically significant genes were selected from the shortest path nodes by applying false discovery rate. A total of 202 genes passed FDR filtering using the experiment significance level of 0.001.
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Additional file 6:
Drug targets and functional hubs. From the set of 202 topologically significant genes, we identified 97 drug targets and 20 functional hubs.
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Additional file 7:
Enrichment analysis of functional hubs. We built network modules consisting of sets of genes linked to functional hubs by upstream or downstream functional connections. Functional enrichment analysis was performed to prioritize hubs based on their relevance to psoriasis-related processes or psoriasis-related genes.
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