From each dataset, we filtered splice variants and removed non-coding transcripts, pseudogenes and purely computational gene predictions, and mapped each cDNA on the corresponding genome to extract the Overlapping Gene Clusters (OGCs).
To identify pathogenic variants, a stepwise filtering process was used that firstly removed non-coding, synonymous and common variants (minor allele frequency, MAF >0.005 in the 1000 genome project database or our in-house database of >800 exomes).
We analyzed the microarray generated germline-expressed data with WS160 Wormbase freeze genome annotations and updated gene IDs, removed non-protein coding genes, removed pseudogenes, removed retired genes and removed duplicated data entries.
Read count data were filtered to remove non-protein coding genes and genes with read counts per million <1 in one or more library.
In order to be able to translate the nucleotide sequences to protein sequences, the pipeline first performs a Blast search (blastx) against a RNA database [ 36], to remove non-protein coding unigenes.
Data cleaning removed non-diagnosis and irrelevant ICD-10 codes.
We removed non-significant interactions.
The first was 581 single coding exon genes, retrieved from GeneLoc ([ 97], http://genecards.weizmann.ac.il/geneloc), further curated with the UCSC table tool [ 94] to remove non-protein-coding genes.
The absence of siRNAs cannot account for these differences because experiments with transitive silencing showed that siRNAs are formed from both the central and 3? regions of the transgene., In Arabidopsis, the IBM1 (increase in BONSAI methylation 1) factor was reported to actively remove non-CG methylation from coding regions.
One At U2AF35 homolog (atU2AF35a) is alternatively spliced by removing non-canonical introns with repeated borders in the 3'-end of the coding region.
The actual network reduction algorithm (see pseudo-code below and Fig. 1) starts with a preprocessing step, which checks the feasibility of the protected functions in the original network and removes (non-protected) blocked reactions.
