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The most informative terms for each cluster and their IC values are listed in Table 3.
We used the information contained in the resulting directed acyclic graph (DAG) [ 50] to systematize the selection of the most informative terms that are significantly enriched among interactors (Additional file 2: Figure S1).
Structured annotations provide further useful information: relationships between the biological terms in a hierarchical structure codify for the specificity of some terms with respect to others and can help to associate genes to the most informative terms avoiding redundant annotations.
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To obtain the p-value for a cluster with the size k, we generated 10000 random clusters with size k and computed IC of the most informative term in each cluster.
IC scores are used to calculate the semantic distance of a category-assigned parent GO term from the root node, the semantic distance of the GO term to be categorized and its category-assigned parent term from their most informative child terms and the semantic distance between the category-assigned parent term and the GO term to be categorized.
Next, the average distance of the GO term to be categorized (G32) and its category-assigned parent term (G22) from their most informative child terms is calculated.
Significant genes are associated to both the most informative functional terms, avoiding redundancy of information, and the most representative temporal patterns, thus improving the readability of the results.
The most informative in terms of phenotypic identification of CSCs is CD44 molecule expression, which either itself or in combination with other surface markers are used to isolate this cell population from various tumors, including EC.
In these instances the most informative GO terms within the top 10 identified are presented.
To gain further insight into the clusters, we extracted the most informative GO terms for each cluster.
The goal for clinical care is to select the battery of molecular markers that are most informative in terms of unmasking the individual biological profile of each tumour, thereby laying out the molecular targets for the most effective therapeutic intervention.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com