FunRich: An open access standalone functional enrichment and interaction network analysis tool

@article{Pathan2015FunRichAO,
  title={FunRich: An open access standalone functional enrichment and interaction network analysis tool},
  author={Mohashin Pathan and Shivakumar Keerthikumar and Ching-Seng Ang and Lahiru Gangoda and Camelia Y.J. Quek and Nicholas A. Williamson and Dmitri Mouradov and Oliver M. Sieber and Richard J. Simpson and Agus Salim and Antony Bacic and Andrew F. Hill and David A. Stroud and Michael T. Ryan and Johnson I. Agbinya and John M. Mariadason and Antony Wilks Burgess and Suresh Mathivanan},
  journal={PROTEOMICS},
  year={2015},
  volume={15}
}
As high‐throughput techniques including proteomics become more accessible to individual laboratories, there is an urgent need for a user‐friendly bioinformatics analysis system. Here, we describe FunRich, an open access, standalone functional enrichment and network analysis tool. FunRich is designed to be used by biologists with minimal or no support from computational and database experts. Using FunRich, users can perform functional enrichment analysis on background databases that are… 

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References

SHOWING 1-8 OF 8 REFERENCES

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

TLDR
The survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

TLDR
By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.

Onto-Tools: new additions and improvements in 2006

TLDR
A new tool, Onto-Express-to-go (OE2GO), is a tool for functional profiling using custom annotations that removes the necessity to use any specific database, and makes the functional profiling available for all organisms, with annotations using any ontology.

Visualization of omics data for systems biology

TLDR
How visualization tools are being used to help interpret protein interaction, gene expression and metabolic profile data is discussed, and emerging new directions are highlighted.

A travel guide to Cytoscape plugins

TLDR
A travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5–2.8 and ongoing efforts to distribute, organize and maintain the quality of the collection.

The model organism as a system: integrating 'omics' data sets

TLDR
Researchers are rising to the challenge by using omics data integration to address fundamental biological questions that would increase the understanding of systems as a whole.

Real-time single-molecule observation of rolling-circle DNA replication

TLDR
By attaching a rolling-circle substrate to a TIRF microscope-mounted flow chamber, this method allows for rapid and precise characterization of the kinetics of DNA synthesis and the effects of replication inhibitors.

Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data

TLDR
Different tools for functionally annotating gene sets and identifying significantly enriched GO categories differ widely in their results when applied to a test annotation gene set and an experimental dataset from chicken, emphasizing the need for care when interpreting the results of such analysis and the lack of standardization of approaches.