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

Bonnet A, Lagarrigue S, Liaubet L, Robert-Granié C, Sancristobal M, Tosser-Klopp G - BMC Proc (2009)

Bottom Line: Different methods were used to interpret these results.However, only one set of genes, showing a differential expression between primary and secondary response gave significant biological interpretation.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).

View Article: PubMed Central - HTML - PubMed

Affiliation: INRA, UMR444, Laboratoire de Génétique Cellulaire, F-31326 Castanet-Tolosan, France. agnes.bonnet@toulouse.inra.fr

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).

No MeSH data available.


Related in: MedlinePlus

Combined pathway from the Sub Network Enrichment Analysis of Pathway Studio (primary or secondary response effect). Molecules are identified with their HUGO symbol. Red colour shows up regulated genes in the PM8 (primary response) condition versus MM8 (secondary response). Blue colour shows down regulated genes in the PM8 (primary response) condition versus MM8 (secondary response).
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Figure 1: Combined pathway from the Sub Network Enrichment Analysis of Pathway Studio (primary or secondary response effect). Molecules are identified with their HUGO symbol. Red colour shows up regulated genes in the PM8 (primary response) condition versus MM8 (secondary response). Blue colour shows down regulated genes in the PM8 (primary response) condition versus MM8 (secondary response).

Mentions: The SNEA analysis gave significant results only for the MM8-PM8 gene list. Expression targets of JUN, CD8A, IL13 and SP1 were found as significantly over-represented (p-value <0.05). The combined pathway is represented in Figure 1. The software allowed to visualise the regulation of the target genes in this combined pathway, using the two other lists of genes (MM8-MA8) and (MM8-MM24) and showed 1 to 4 regulated targets (data not shown).


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

Bonnet A, Lagarrigue S, Liaubet L, Robert-Granié C, Sancristobal M, Tosser-Klopp G - BMC Proc (2009)

Combined pathway from the Sub Network Enrichment Analysis of Pathway Studio (primary or secondary response effect). Molecules are identified with their HUGO symbol. Red colour shows up regulated genes in the PM8 (primary response) condition versus MM8 (secondary response). Blue colour shows down regulated genes in the PM8 (primary response) condition versus MM8 (secondary response).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2712741&req=5

Figure 1: Combined pathway from the Sub Network Enrichment Analysis of Pathway Studio (primary or secondary response effect). Molecules are identified with their HUGO symbol. Red colour shows up regulated genes in the PM8 (primary response) condition versus MM8 (secondary response). Blue colour shows down regulated genes in the PM8 (primary response) condition versus MM8 (secondary response).
Mentions: The SNEA analysis gave significant results only for the MM8-PM8 gene list. Expression targets of JUN, CD8A, IL13 and SP1 were found as significantly over-represented (p-value <0.05). The combined pathway is represented in Figure 1. The software allowed to visualise the regulation of the target genes in this combined pathway, using the two other lists of genes (MM8-MA8) and (MM8-MM24) and showed 1 to 4 regulated targets (data not shown).

Bottom Line: Different methods were used to interpret these results.However, only one set of genes, showing a differential expression between primary and secondary response gave significant biological interpretation.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).

View Article: PubMed Central - HTML - PubMed

Affiliation: INRA, UMR444, Laboratoire de Génétique Cellulaire, F-31326 Castanet-Tolosan, France. agnes.bonnet@toulouse.inra.fr

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).

No MeSH data available.


Related in: MedlinePlus