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 | 4th out of 898 Unpublished data | Yes, 2.14-fold up- regulation in callipyge individuals across all time points explored.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 |