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Table 3 Causal genes correctly highlighted by RIF across a range of species and biological circumstances

From: Beyond differential expression: the quest for causal mutations and effector molecules

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most DE highly abundant gene, and its expression is maintained post-natally in effected muscles only. 4th out of 898 Unpublished data Yes, 2.14-fold up- regulation in callipyge individuals across all time points explored.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
  1. RIF highlights the correct molecules irrespective of whether they are DE.