| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T926 |
0-37 |
Sentence |
denotes |
Clustering of phosphorylation changes |
| T927 |
38-369 |
Sentence |
denotes |
Phosphorylation sites with one-to-one mapping to human S, T or Y amino acids and showing significant change in phosphorylation (abs(log2FC) > 1 and adjusted p value < 0.05) in one or more conditions were selected and clustered using hierarchical clustering (complete-linkage) with pearson correlation (1-r) as the distance measure. |
| T928 |
370-569 |
Sentence |
denotes |
The cluster tree was cut into 5 clusters using a dynamic tree cutting method, cutreeHybrid function in dynamicTreeCut (Langfelder et al., 2008) package in R, with a minimum cluster size of 130 sites. |
| T929 |
570-680 |
Sentence |
denotes |
Phosphorylated proteins in each cluster were tested for enrichment of Reactome pathways (Jassal et al., 2020). |
| T930 |
681-857 |
Sentence |
denotes |
The over-representation analysis (ORA) was based on the hypergeometric distribution and performed using the enricher function of clusterProfiler package in R (Yu et al., 2012). |
| T931 |
858-967 |
Sentence |
denotes |
The pathway terms were obtained from the c2 category (Reactome) of Molecular Signature Database (MSigDBv6.1). |
