Sentence examples for calculating pathway from inspiring English sources

The main advantage to calculating pathway activities on top of pathway consistencies is that activities can be calculated even when there is not enough data to work with the output, as is the case, for example, when the interaction is based on activating or modifying molecules without the generation of a novel molecule as output.

The pathway activity profiling (PAPi) algorithm (13) was employed for calculating pathway activity based on metabolomic data.

We next assessed the impact of Pten/p53 deletion on PI3K/AKT signaling by calculating pathway activation for AKT, PI3K and p53 (Gatza et al, 2010).

Further, by calculating pathway activation of AKT, PI3K and p53 in the mouse tumors, the AKT pathway was strongly induced in PTEN/p53 deficient tumors.

The probability of the occurrence of x or fewer metabolites within set B in a given pathway is calculated by hypergeometric distribution [ 36] according to the following formula: Ρ = ∑ i − x n m i N − m n − i N n The hypergeometric test is a standard method for calculating pathway enrichment.

Calculating pathway-specific Jaccard distances between interacting proteins (see Methods), we observed that proteins in SI and HC interactions are involved in more similar pathways than proteins in the HTP network (Fig 2B).

More recently, [ 38] described an algorithm, Pathifier, which uses expression data to calculate pathway deregulation scores.

To further measure the quality of structurally inferred interactions, we calculated pathway and functional distances between interacting proteins.

Details of Figure S3: Pathway expression of canonical KEGG signal transduction pathways [ 21] were measured as the normalized mean of the pathway components and subsequently used to calculate pathway perturbation between BC subtypes (see Additional file 4).

Rank normalizations provide robust summary statistics to calculate pathway expression scores [ 6, 13] that can be applied across all technologies, and does not depend on the dynamic range of an array.

In order to evaluate the biological relevance of observed hits, we calculated pathway enrichment scores separately for each pathogen by the Gene Set Enrichment Analysis (GSEA) algorithm [ 42] using as input the results from the three hit ranking algorithms PMM, MTT, and RSA (see Additional file 1).