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They were in the list of potential non-coding genes because the human genome annotation project is not yet complete and these genes had yet to be annotated with evidence by GENCODE and UniProt.
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Only ∼200 of these are presently supported by experimental evidence, whereas ∼100 are annotated with evidence based on computational prediction, sequence and structure similarity or author statement (GO database release on 16 February 2013).
Moreover we adopt the same way of selecting reliable GO terms as previous study [ 38] and ignore the GO terms that are annotated with evidence code IEA (Inferred from Electronic Annotation), ND (No biological Data available), NAS Statementable Author StatemeNAS Statement
Conversely, more general InterPro family and domain entries may be annotated with a more general GO term, subject to meeting evidence requirements.
Of these 900 proteins, 664 could already be annotated with a GO biological process term using annotation from GOA (Camon et al., 2004) and allowing all evidence types.
Any process action can be annotated with a precondition.
Classes 5, 6 and 7. Genes with weak Protein Evidence (UniProt) Classes 5, 6 and 7. Genes with weak Protein Evidence (UniProt) Genes where all splice isoforms were annotated with Homology evidence or worse had little evidence of protein expression (the best was Homology with a 6.87% peptide detection rate).
Ten thousand, four hundred eighty-seven sequences (17 %) were annotated with high evidence for molecular function, biological process and/or cellular component by 30,843 GO entries.
Our approach is therefore in agreement with "ACMG Recommendations for Reporting of Incidental Findings in Clinical Exome and Genome Sequencing" although until all possible changes in the human genome are annotated with unequivocal evidence to either support or refute the pathogenicity of each variant, there will always be a risk to make a false positive call.
Each GDA is annotated with the supporting evidence (the publications reporting the GDA, a representative sentence describing the association and the original source of provenance) and the PsyGeNET score.
However, if the gene is annotated with more than one evidence code and one evidence code is a superclass of another, the annotation with the more general evidence code does not need to be specified explicitly.
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