(placeholder)

This page contains supplemental information and code for the following papers:

Implications of Functional Similarity for Gene Regulatory Interactions, K. Glass, E. Ott, W. Losert and M. Girvan, J. Royal Society Interface, 2012.

Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets, K. Glass and M. Girvan, Scientific Reports, 2013.




(placeholder)

Implications of Functional Similarity for Gene Regulatory Interactions

This section is the online supplement to “Implications of Functional Similarity for Gene Regulatory Interactions.” Here we provide C++ code as well as several example files which can be used to calculate the scaled similarity between pairs of genes. It is academic code and provided without warranty. However, if issues are brought to my attention I will make every effort to address them in a timely manner.

The code only requires two inputs, ontology and annotation files, which are available from the Gene Ontology website for many different species. Do note that the paper focused on two smaller organisms, E.coli and yeast, and has not been tested or optimized for larger genomes. The output is a list of all gene-gene pairs and their corresponding scaled similarity values. We provide the results for E.coli and yeast from the paper, cacuclated using all ontologies in the case of large α.

Finally, we also supply code to calculate the informational importance of edges in a given network. The input is a text file containing pairs of edges and the output is a text file containing those edges and their corresponding informational importance values.

Further information for running the programs is contained in README files provided with the code. If you have any comments or questions do not hesitate to contact Kimberly Glass at kglass at jimmy dot harvard dot edu.

Useful links/downloads:

     PDF of Paper

     Supplemental Material

     Gene Ontology Main Page

(placeholder)

Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets

This section is the online supplement to “Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets.” Here we provide C++ code as well as several example files which can be used to run Annotation Enrichment Anlysis (AEA) to evaluate the enrichment of a given set (or sets) of genes in branches (or sets of terms) from the Gene Ontology.

A detailed explanation of how to run the code is contained in the README file provided with the code. Note that this is academic code and provided without warranty. However, if issues are brought to the author's attention she will make every effort to address them in a timely manner. If you have any comments or questions do not hesitate to contact the author at kglass at jimmy dot harvard dot edu.

Useful links/downloads:

     PDF of Paper

     Supplemental Material

     Gene Ontology Main Page