Dataset Information

Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares.

ABSTRACT:

Background

As presented in the introduction paper, three sets of differentially regulated genes were found after the analysis of the chicken infection data set from EADGENE. Different methods were used to interpret these results.

Results

GOTM, Pathway Studio and Ingenuity softwares were used to investigate the three lists of genes. The three softwares allowed the analysis of the data and highlighted different networks. However, only one set of genes, showing a differential expression between primary and secondary response gave significant biological interpretation.

Conclusion

Combining these databases that were developed independently on different annotation sources supplies a useful tool for a global biological interpretation of microarray data, even if they may contain some imperfections (e.g. gene not or not well annotated).

SUBMITTER: Bonnet A

PROVIDER: S-EPMC2712741 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares.

Bonnet Agnès A Lagarrigue Sandrine S Liaubet Laurence L Robert-Granié Christèle C Sancristobal Magali M Tosser-Klopp Gwenola G

BMC proceedings 20090716

<h4>Background</h4>As presented in the introduction paper, three sets of differentially regulated genes were found after the analysis of the chicken infection data set from EADGENE. Different methods were used to interpret these results.<h4>Results</h4>GOTM, Pathway Studio and Ingenuity softwares were used to investigate the three lists of genes. The three softwares allowed the analysis of the data and highlighted different networks. However, only one set of genes, showing a differential express ...[more]

PMID: 19615111

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Project description:BackgroundThe consolidation of pathway databases, such as KEGG, Reactome and ConsensusPathDB, has generated widespread biological interest, however the issue of pathway redundancy impedes the use of these consolidated datasets. Attempts to reduce this redundancy have focused on visualizing pathway overlap or merging pathways, but the resulting pathways may be of heterogeneous sizes and cover multiple biological functions. Efforts have also been made to deal with redundancy in pathway data by consolidating enriched pathways into a number of clusters or concepts. We present an alternative approach, which generates pathway subsets capable of covering all of genes presented within either pathway databases or enrichment results, generating substantial reductions in redundancy.ResultsWe propose a method that uses set cover to reduce pathway redundancy, without merging pathways. The proposed approach considers three objectives: removal of pathway redundancy, controlling pathway size and coverage of the gene set. By applying set cover to the ConsensusPathDB dataset we were able to produce a reduced set of pathways, representing 100% of the genes in the original data set with 74% less redundancy, or 95% of the genes with 88% less redundancy. We also developed an algorithm to simplify enrichment data and applied it to a set of enriched osteoarthritis pathways, revealing that within the top ten pathways, five were redundant subsets of more enriched pathways. Applying set cover to the enrichment results removed these redundant pathways allowing more informative pathways to take their place.ConclusionOur method provides an alternative approach for handling pathway redundancy, while ensuring that the pathways are of homogeneous size and gene coverage is maximised. Pathways are not altered from their original form, allowing biological knowledge regarding the data set to be directly applicable. We demonstrate the ability of the algorithms to prioritise redundancy reduction, pathway size control or gene set coverage. The application of set cover to pathway enrichment results produces an optimised summary of the pathways that best represent the differentially regulated gene set.

Dataset Information

Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares.

Background

Results

Conclusion

Publications

Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares.

Similar Datasets

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