To elude false positive results of experimental detection for physical interactions and to create a high confident set of physical interactions, the pairs of interactions that are supported by at least three publications and that have an MI-score of at least 0.431 remain (http://wodaklab.org/iRefWeb/).
We merged the high confident results of the individual tools to obtain the high confident annotation of structured RNAs (see Table 1 for the applied cutoffs).
To generate a high confident set of evolutionary conserved novel transcripts with annotated information, we filtered the PNTs with phastCons score > 0.8 and obtained a set of 3982 genes satisfying these criteria.
In particular, a high confident network of mouse NSCs (NSC-GN2) was predicted.
Based on this measure, we proposed a method to select high confident neighbors of a phenotype and detect gene modules that are highly connected to these high confident neighbors.
We obtained high confident annotation of 3,556 structured RNAs distributed over 3,348 (full length) ncRNA genes, 11 conflict loci, 139 cis-regulatory elements, as well as 58 lncRNA loci.
We required a block of at least 10 reads overlapping with at least 20 nucleotides of the annotation and found overlap with 780 of the high confident annotations and 819 of the low confident annotations (308 and 329 of those were miRNAs at the respective annotation levels).
Overall we annotated 3,556 high confident structured RNAs of which a subset was inspected leading to 571 curated annotations.
(b) Experimental validation by RT-PCR analysis of a selected set of high confident skipped exonic events reveals that selected mRNA isoforms with skipped events are more abundant during embryonic and perinatal stages.
We proceed with a summary of the complete curated annotation The high confident annotation is a combination of the results of the high confident homology pipeline and the miRDeep detected miRNA candidates.
