Glossaries

Meta-stable structure

Meta-stable structure refers to the most prevalent secondary structures of a given RNA sequence in the cellular contents. In SSRTool, the meta-stable structure is obtained by weighted aggregation of functionally interpretable predictions from the collection of predictions calculated by other tools. Moreover, this is also the suggested most native-like structure for the given RNA sequence.

Best Functional Significance

The lowest interpretability q-value among the four functional aspects for each predicted structure. The results are in the form of q-values.

Cellular Fitness Interpretability

This functional test evaluates the significance that the secondary structure performs vital cellular fitness determining functions. The results are in the form of q-values. In SSRTool, the cellular fitness interpretability significance is calculated using the fitness profiling coherence test.

RNA-Protein Interaction (RPI) Interpretability

This functional test evaluates the significance for the structure to carry out its functions cooperatively with proteins that contain corresponding RNA sequence/structure binding domains. The results are in the form of q-values. In SSRTool, the RPI interpretability significance is estimated using the interaction complex prevalence test and the gene ontology enrichment test on the proteins interacting with the RPI ncRNA similar set of the structure prediction.

Translational Regulation Interpretability

This functional test evaluates the significance of the structure in affecting start codon accessibility that results in translation initiation regulation. The results are in the form of q-values. In SSRTool, the cellular fitness interpretability significance is computed using the ribosome profiling coherence test on the 5’UTR structural similar set of the structure prediction.

Post-transcriptional Regulation Interpretability

This functional test evaluates the significance of the structure in participating in post-transcriptional regulation. The results are in the form of q-values. In SSRTool, the cellular fitness interpretability significance is evaluated using the interaction complex prevalence test and the gene ontology enrichment test on the genes transcribed to contain the 3’UTR structural similar set of the structure prediction.