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Gene network reconstruction from microarray data.

Jaffrezic F, Tosser-Klopp G - BMC Proc (2009)

Bottom Line: No significant edges were found for the list of differentially expressed genes between conditions MM8 and MA8.On the other hand, a large number of significant edges were found among 85 differentially expressed genes between conditions MM8 and MM24.Further biological validation is therefore needed for these networks, using for example in vitro invalidation of genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: INRA AgroParisTech, Animal Genetics and Integrative Biology, Populations Statistics Genomes, 78350 Jouy-en-Josas, France. florence.jaffrezic@jouy.inra.fr

ABSTRACT

Background: Often, software available for biological pathways reconstruction rely on literature search to find links between genes. The aim of this study is to reconstruct gene networks from microarray data, using Graphical Gaussian models.

Results: The GeneNet R package was applied to the Eadgene chicken infection data set. No significant edges were found for the list of differentially expressed genes between conditions MM8 and MA8. On the other hand, a large number of significant edges were found among 85 differentially expressed genes between conditions MM8 and MM24.

Conclusion: Many edges were inferred from the microarray data. Most of them could, however, not be validated using other pathway reconstruction software. This was partly due to the fact that a quite large proportion of the differentially expressed genes were not annotated. Further biological validation is therefore needed for these networks, using for example in vitro invalidation of genes.

No MeSH data available.


Related in: MedlinePlus

Gene network for condition MM24. Gene network for condition MM24 obtained with the GeneNet R package, for the 20 most significant edges. Legend for this graph is the same as for Figure 1.
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Figure 2: Gene network for condition MM24. Gene network for condition MM24 obtained with the GeneNet R package, for the 20 most significant edges. Legend for this graph is the same as for Figure 1.

Mentions: Figures 1 and 2 show the graphs of the 20 most significant edges for both conditions, and Tables 1 and 2 provide the correspondence between the gene numbers given in the figures and their RIGG names and Human orthologs. It can be seen that there is very little overlapping between the two networks. In fact, only three genes were found in common in both graphs, and no link was conserved between both graphs. Furthermore, for condition MM8, among the 18 genes present in the graph, only 8 were annotated and for condition MM24, only 7 genes were annotated, which made it very difficult to validate the links found here using literature based pathway reconstruction software. Among the annotated genes present in these graphs, no links were found between them using either Ingenuity or Pathway Studio. Further biological validation is therefore required for this experiment using, for example, in vitro invalidation of genes, in order to confirm the links inferred here based on the gene expression measurements.


Gene network reconstruction from microarray data.

Jaffrezic F, Tosser-Klopp G - BMC Proc (2009)

Gene network for condition MM24. Gene network for condition MM24 obtained with the GeneNet R package, for the 20 most significant edges. Legend for this graph is the same as for Figure 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2712742&req=5

Figure 2: Gene network for condition MM24. Gene network for condition MM24 obtained with the GeneNet R package, for the 20 most significant edges. Legend for this graph is the same as for Figure 1.
Mentions: Figures 1 and 2 show the graphs of the 20 most significant edges for both conditions, and Tables 1 and 2 provide the correspondence between the gene numbers given in the figures and their RIGG names and Human orthologs. It can be seen that there is very little overlapping between the two networks. In fact, only three genes were found in common in both graphs, and no link was conserved between both graphs. Furthermore, for condition MM8, among the 18 genes present in the graph, only 8 were annotated and for condition MM24, only 7 genes were annotated, which made it very difficult to validate the links found here using literature based pathway reconstruction software. Among the annotated genes present in these graphs, no links were found between them using either Ingenuity or Pathway Studio. Further biological validation is therefore required for this experiment using, for example, in vitro invalidation of genes, in order to confirm the links inferred here based on the gene expression measurements.

Bottom Line: No significant edges were found for the list of differentially expressed genes between conditions MM8 and MA8.On the other hand, a large number of significant edges were found among 85 differentially expressed genes between conditions MM8 and MM24.Further biological validation is therefore needed for these networks, using for example in vitro invalidation of genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: INRA AgroParisTech, Animal Genetics and Integrative Biology, Populations Statistics Genomes, 78350 Jouy-en-Josas, France. florence.jaffrezic@jouy.inra.fr

ABSTRACT

Background: Often, software available for biological pathways reconstruction rely on literature search to find links between genes. The aim of this study is to reconstruct gene networks from microarray data, using Graphical Gaussian models.

Results: The GeneNet R package was applied to the Eadgene chicken infection data set. No significant edges were found for the list of differentially expressed genes between conditions MM8 and MA8. On the other hand, a large number of significant edges were found among 85 differentially expressed genes between conditions MM8 and MM24.

Conclusion: Many edges were inferred from the microarray data. Most of them could, however, not be validated using other pathway reconstruction software. This was partly due to the fact that a quite large proportion of the differentially expressed genes were not annotated. Further biological validation is therefore needed for these networks, using for example in vitro invalidation of genes.

No MeSH data available.


Related in: MedlinePlus