|Causal genes correctly highlighted by RIF across a range of species and biological circumstances|
|Gene||Species, Phenotype||Independent evidence for gene function||RIF ranking||Differentially expressed|
|MSTN||Cattle muscle, Piedmontese hyper-muscularity versus normal||Mapping, deep sequencing ||1st out of 920 ||No|
|Alpha-Synuclein||Human brain, Parkinson’s disease versus healthy||Range of evidence including GWAS reviewed in ||Not formally stated in patent , presumably 1st||Unknown. Patent was established to identify causal variants by transcriptome wiring, even when not DE|
|CDK8||Human colon, colorectal cancer versus healthy||Colorectal cancer oncogene regulates B-catenin ||4th out of 1,292 ||No|
|P107||Human, brown fat tissue versus white fat tissue||P107 knockout mouse exhibits a uniform white to brown fat transition ||5th out of 552 ||No|
|DLK1||Sheep muscle, Callipyge hyper- muscularity versus normal||Not proven, but DLK1 is the most DE highly abundant gene, and its expression is maintained post-natally in effected muscles only.||4th out of 898 Unpublished data||Yes, 2.14-fold up- regulation in callipyge individuals across all time points explored.|
|INSM1||Pig, 6 CNS tissues versus 21 other tissues||Neuroendocrine differentiation ||1st out of 1,072 (submitted)||Yes, 3.8-Fold up- regulation in CNS|
|OXTR||Cattle muscle, steroid hormone induced muscling||No direct evidence, but OXT precursor is the most DE gene in this experiment, and is known to drive cardiac development.||2nd out of 2,944 ||No|
|CARM1||Human breast, breast cancer high survival versus low survival||Regulates estrogen stimulated breast cancer via E2F1 ||2nd out of 892 ||No|
RIF highlights the correct molecules irrespective of whether they are DE.
Hudson et al.
Hudson et al. BMC Genomics 2012 13:356 doi:10.1186/1471-2164-13-356