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Biological pathway analysis by ArrayUnlock and Ingenuity Pathway Analysis.

Jiménez-Marín A, Collado-Romero M, Ramirez-Boo M, Arce C, Garrido JJ - BMC Proc (2009)

Bottom Line: Once a list of differentially expressed genes has been identified from a microarray experiment, a subsequent post-analysis task is required in order to find the main biological processes associated to the experimental system.ArrayUnlock let an improvement of the annotations of the chicken genome adding InterPro annotations to the data set file.IPA provides two powerful tools to understand the pathway analysis results: the networks and canonical pathways that showed several pathways related to an adaptative immune response.

View Article: PubMed Central - HTML - PubMed

Affiliation: Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Campus de Rabanales, Edificio C-5, 14071 Córdoba, Spain. gm2jimaa@uco.es

ABSTRACT

Background: Once a list of differentially expressed genes has been identified from a microarray experiment, a subsequent post-analysis task is required in order to find the main biological processes associated to the experimental system. This paper describes two pathways analysis tools, ArrayUnlock and Ingenuity Pathways Analysis (IPA) to deal with the post-analyses of microarray data, in the context of the EADGENE and SABRE post-analysis workshop. Dataset employed in this study proceeded from an experimental chicken infection performed to study the host reactions after a homologous or heterologous secondary challenge with two species of Eimeria.

Results: Analysis of the same microarray data source employing both commercial pathway analysis tools in parallel let to identify several biological and/or molecular functions altered in the chicken Eimeria maxima infection model, including several immune system related pathways. Biological functions differentially altered in the homologous and heterologous second infection were identified. Similarly, the effect of the timing in a homologous second infection was characterized by several biological functions.

Conclusion: Functional analysis with ArrayUnlock and IPA provided information related to functional differences with the three comparisons of the chicken infection leading to similar conclusions. ArrayUnlock let an improvement of the annotations of the chicken genome adding InterPro annotations to the data set file. IPA provides two powerful tools to understand the pathway analysis results: the networks and canonical pathways that showed several pathways related to an adaptative immune response.

No MeSH data available.


Related in: MedlinePlus

T cell receptor signalling canonical pathway obtained by IPA obtained in comparison MM8_PM8. Up- and down-regulated genes in red and green, respectively.
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Figure 1: T cell receptor signalling canonical pathway obtained by IPA obtained in comparison MM8_PM8. Up- and down-regulated genes in red and green, respectively.

Mentions: IPA identified significant networks, top functions and canonical pathways associated with the differentially expressed genes for each comparison analyzed (see Additional file 8). The first networks scored for the MM8_MM24 and MM8_PM8 comparisons are presented in Additional file 9. A similar result to that obtained with ArrayUnlock was obtained for the comparison MM8_MA8, a lower number of genes significantly associated to biological functions (a maximum of five genes per function) compared with the other two comparisons. Similarly, in this comparison, only five canonical pathways were significant. In the comparison MM8_MM24 seven out of the ten most significant canonical pathways were related to cellular signalling, e.g.: cAMP signalling; integrin signalling; actin cytoskeleton mediated signalling; and G-coupled receptor signaling. Interestingly, in this comparison the functions more significant and with higher number of genes implicated correspond to 'cell morphology', 'cellular assembly and organization', and 'cellular development' being most genes down-regulated. In the comparison MM8_PM8 the 'immune response' and 'immune and lymphatic system development and function' are among the most significant functions altered. Then, most genes related to proliferation and maturation of B lymphocytes, recruitment of macrophages and antigen presenting cells, increasing of NK cells and T-cells were up-regulated. As an example, the T cell receptor signalling canonical pathway obtained by IPA and associated with the differentially expressed genes for the comparison MM8_PM8 is shown Figure 1.


Biological pathway analysis by ArrayUnlock and Ingenuity Pathway Analysis.

Jiménez-Marín A, Collado-Romero M, Ramirez-Boo M, Arce C, Garrido JJ - BMC Proc (2009)

T cell receptor signalling canonical pathway obtained by IPA obtained in comparison MM8_PM8. Up- and down-regulated genes in red and green, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2712749&req=5

Figure 1: T cell receptor signalling canonical pathway obtained by IPA obtained in comparison MM8_PM8. Up- and down-regulated genes in red and green, respectively.
Mentions: IPA identified significant networks, top functions and canonical pathways associated with the differentially expressed genes for each comparison analyzed (see Additional file 8). The first networks scored for the MM8_MM24 and MM8_PM8 comparisons are presented in Additional file 9. A similar result to that obtained with ArrayUnlock was obtained for the comparison MM8_MA8, a lower number of genes significantly associated to biological functions (a maximum of five genes per function) compared with the other two comparisons. Similarly, in this comparison, only five canonical pathways were significant. In the comparison MM8_MM24 seven out of the ten most significant canonical pathways were related to cellular signalling, e.g.: cAMP signalling; integrin signalling; actin cytoskeleton mediated signalling; and G-coupled receptor signaling. Interestingly, in this comparison the functions more significant and with higher number of genes implicated correspond to 'cell morphology', 'cellular assembly and organization', and 'cellular development' being most genes down-regulated. In the comparison MM8_PM8 the 'immune response' and 'immune and lymphatic system development and function' are among the most significant functions altered. Then, most genes related to proliferation and maturation of B lymphocytes, recruitment of macrophages and antigen presenting cells, increasing of NK cells and T-cells were up-regulated. As an example, the T cell receptor signalling canonical pathway obtained by IPA and associated with the differentially expressed genes for the comparison MM8_PM8 is shown Figure 1.

Bottom Line: Once a list of differentially expressed genes has been identified from a microarray experiment, a subsequent post-analysis task is required in order to find the main biological processes associated to the experimental system.ArrayUnlock let an improvement of the annotations of the chicken genome adding InterPro annotations to the data set file.IPA provides two powerful tools to understand the pathway analysis results: the networks and canonical pathways that showed several pathways related to an adaptative immune response.

View Article: PubMed Central - HTML - PubMed

Affiliation: Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Campus de Rabanales, Edificio C-5, 14071 Córdoba, Spain. gm2jimaa@uco.es

ABSTRACT

Background: Once a list of differentially expressed genes has been identified from a microarray experiment, a subsequent post-analysis task is required in order to find the main biological processes associated to the experimental system. This paper describes two pathways analysis tools, ArrayUnlock and Ingenuity Pathways Analysis (IPA) to deal with the post-analyses of microarray data, in the context of the EADGENE and SABRE post-analysis workshop. Dataset employed in this study proceeded from an experimental chicken infection performed to study the host reactions after a homologous or heterologous secondary challenge with two species of Eimeria.

Results: Analysis of the same microarray data source employing both commercial pathway analysis tools in parallel let to identify several biological and/or molecular functions altered in the chicken Eimeria maxima infection model, including several immune system related pathways. Biological functions differentially altered in the homologous and heterologous second infection were identified. Similarly, the effect of the timing in a homologous second infection was characterized by several biological functions.

Conclusion: Functional analysis with ArrayUnlock and IPA provided information related to functional differences with the three comparisons of the chicken infection leading to similar conclusions. ArrayUnlock let an improvement of the annotations of the chicken genome adding InterPro annotations to the data set file. IPA provides two powerful tools to understand the pathway analysis results: the networks and canonical pathways that showed several pathways related to an adaptative immune response.

No MeSH data available.


Related in: MedlinePlus