Table 3.

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 [60]	1st out of 920 [1]	No
Alpha-Synuclein	Human brain, Parkinson’s disease versus healthy	Range of evidence including GWAS reviewed in [61]	Not formally stated in patent [55], 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 [54]	4th out of 1,292 [53]	No
P107	Human, brown fat tissue versus white fat tissue	P107 knockout mouse exhibits a uniform white to brown fat transition [62]	5th out of 552 [4]	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most DE highly abundant gene, and its expression is maintained post-natally in effected muscles only.	4th out of 898 Unpublished data	Yes, 2.14-fold up- regulation in callipyge individuals across all time points explored.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 [63]	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 [52]	No
CARM1	Human breast, breast cancer high survival versus low survival	Regulates estrogen stimulated breast cancer via E2F1 [64]	2nd out of 892 [4]	No

RIF highlights the correct molecules irrespective of whether they are DE.