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Biological function and network generation was performed using Ingenuity Pathway Analysis (IPA, Ingenuity Systems, Redwood City, CA).
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(iv) The integration of data on transcriptome and interactome in the light of biological functions and network analysis leads us to link cytokinin signaling and immune regulatory hubs in Arabidopsis.
The overlap between putative targets of miRNAs and the expression of mRNAs provides information on the biological functions and networks of genes regulated by specific miRNAs.
IPA was performed to identify the top biological functions and networks enriched in each gene set.
This list of dissimilar genes was further analyzed with IPA to identify altered biological functions and networks.
Feeding the lists of affected genes as input to the IPA library identified associated canonical pathways, biological functions and networks which were used to investigate the biological context.
IPA validation of biological functions and networks that were most significant to the topotecan microarray data set were in agreement with our initial gene expression data.
The corresponding lists were submitted to IPA to get the canonical pathways, biological functions and networks significantly associated with the gene lists.
For the biological functions and networks the significance was linked to the p-value only, calculated by right-tailed Fisher's exact test.
Feeding the aforementioned lists of affected genes as input to the IPA library, significantly associated canonical pathways, biological functions and networks were identified in order to gain biological context and understanding.
We then used the Ingenuity Pathways Analysis (IPA; http://www.ingenuity.com) software to retrieve the canonical pathways, biological functions and networks that were most significantly associated with the lists of affected genes.
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