Method of omim prediction
We use the RWRH (random walk with restart on heterogeneous network) algorithm1 to analyze the relationship between lncRNA and OMIM in MATLAB. The upper subnetwork is coding-lncRNA gene co-expression network, and the lower network is OMIM similarity network. OMIM similarity matrix is from Disimweb2 and gene-OMIM relationship is from InterMine3.
1. Li, Y. & Patra, J. C. Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network. Bioinformatics 26, 1219-1224, doi:10.1093/bioinformatics/btq108 (2010).
2. Caniza, H., Romero, A. E. & Paccanaro, A. A network medicine approach to quantify distance between hereditary disease modules on the interactome. Sci Rep 5, 17658, doi:10.1038/srep17658 (2015).
3. Smith, R. N. et al. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics 28, 3163-3165, doi:10.1093/bioinformatics/bts577 (2012).
| ZFLNC lncRNA | OMIM | Phenotype |
|---|---|---|
| ZFLNCG11719 | 601287 | Muscular dystrophy, limb-girdle, type 2F |
| ZFLNCG04372 | 120200 | Coloboma, ocular |
| ZFLNCG05711 | 601003 | Brody myopathy |
| ZFLNCG02067 | 186570 | Tarsal-carpal coalition syndrome |
| ZFLNCG05331 | 610612 | Leber congenital amaurosis 12 |
| ZFLNCG03536 | 615378 | Atrial fibrillation, familial, 14 |
| ZFLNCG09621 | 245570 | Epilepsy, focal, with speech disorder and with or without mental retardation |
| ZFLNCG00470 | 601369 | Deafness, autosomal dominant 9 |
| ZFLNCG06627 | 108600 | Spastic ataxia 1, autosomal dominant |
| ZFLNCG08626 | 608930 | Myasthenic syndrome, congenital, 1B, fast-channel |
| ZFLNCG12405 | 264080 | Progesterone resistance |
| ZFLNCG06494 | 607236 | HARP syndrome |
| ZFLNCG10706 | 612965 | 46XY sex reversal 3 |
| ZFLNCG12294 | 265120 | Surfactant metabolism dysfunction, pulmonary, 1 |
| ZFLNCG05577 | 180000 | Retinal arteries, tortuosity of |
| ZFLNCG00762 | 122880 | Craniofacial-deafness-hand syndrome |
| ZFLNCG12302 | 300088 | Epileptic encephalopathy, early infantile, 9 |
| ZFLNCG00512 | 608747 | Growth retardation with deafness and mental retardation due to IGF1 deficiency |
| ZFLNCG12831 | 615419 | Hypotonia, infantile, with psychomotor retardation and characteristic facies |
| ZFLNCG06945 | 612938 | Growth retardation, developmental delay, facial dysmorphism |
| ZFLNCG02042 | 613980 | Atrial fibrillation, familial, 9 |
| ZFLNCG05559 | 261650 | PEPCK deficiency, mitochondrial |
| ZFLNCG10113 | 233690 | Chronic granulomatous disease, autosomal, due to deficiency of CYBA |
| ZFLNCG03016 | 614402 | Microphthalmia, syndromic 11 |
| ZFLNCG09641 | 610092 | Microphthalmia with coloboma 3 |