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Axonal guidance signaling 1A, 1U 0.0089125094 1A Family 1 affected twin, 1U Family 1 unaffected twin, 2A Family 2 affected twin, 2U Family 2 unaffected twin Fig. 6 Analysis of ingenuity pathway results Fig. 7 a Dopamine feedback in cAMP signaling pathway identified using ingenuity pathway analysis (IPA).
The core analysis of Ingenuity delivers significantly enriched themes for the input dataset; in terms of biological functions, canonical pathways and molecular networks.
These analyses were performed with core analysis of Ingenuity Pathway Analysis (IPA) with Benjamini-Hochberg multiple testing correction method and with the Database for Annotation, Visualization and Integrated Discovery system (DAVID) [ 47, 48].
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We used the core analysis component of Ingenuity Pathway Analysis (IPA) to categorize these genes according to biological functions.
The upstream pathway analysis module of Ingenuity Pathway Analysis (IPA) (Build 320386 M, Version 21249400) was used to calculate upstream regulator enrichments and to determine whether the regulators identified are either in an activated or an inhibited state [ 35].
Molecular networks are presented which were generated by the core analysis of the Ingenuity knowledge database (see also Methods section and www.ingenuity.com for explanation and details).
The ROH from CFA 26 mapped to two adjacent syntenic regions on Homo sapiens chromosome (Hs) 12. Advantage was taken of the fact that the region in the human genome syntenic to the region of interest on CFA 26 was better annotated and could be used to perform functional annotation analysis through the use of Ingenuity Pathways Analysis software [ 12].
To show the robustness of the MADAD transcriptome versus a single study, we conducted an over-representation analysis (see Methods) of ingenuity canonical pathways (IPA) and of previously published immune and barrier gene-sets [ 12, 48].
In fact, analysis of PC1 by Ingenuity, Kegg, and GeneGo approaches identified multiple potential pathways that might be responsible for the observed molecular subclassification (Additional File 1).
Bio-informatics-based analysis using the demonstration version 7.1 of Ingenuity Pathway Analysis software (IPA; Ingenuity® Systems, www.ingenuity.com) associated with manual and litterature-based analysis was carried out to identify the most relevant functional processes associated with the identified DSS gene signature.
This goes alongside originality of analysis, ingenuity, persuasiveness and power of arguments.
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CEO of Professional Science Editing for Scientists @ prosciediting.com