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 |
|---|---|---|
| ZFLNCG00762 | 193500 | Waardenburg syndrome, type 1 |
| ZFLNCG04502 | 606768 | Myopathy, distal, with anterior tibial onset |
| ZFLNCG10827 | 207750 | Hyperlipoproteinemia, type Ib |
| ZFLNCG02067 | 184460 | Stapes ankylosis with broad thumb and toes |
| ZFLNCG01974 | 614063 | N-acetylaspartate deficiency |
| ZFLNCG13110 | 613810 | Retinitis pigmentosa 43 |
| ZFLNCG12564 | 612126 | GLUT1 deficiency syndrome 2, childhood onset |
| ZFLNCG06198 | 611638 | Microphthalmia with coloboma 5 |
| ZFLNCG03687 | 300400 | Severe combined immunodeficiency, X-linked |
| ZFLNCG00516 | 234200 | Neurodegeneration with brain iron accumulation 1 |
| ZFLNCG00745 | 122400 | Epithelial recurrent erosion dystrophy |
| ZFLNCG05515 | 269160 | Schizencephaly |
| ZFLNCG12741 | 609622 | Short QT syndrome 3 |
| ZFLNCG09045 | 227810 | Fanconi-Bickel syndrome |
| ZFLNCG01741 | 256030 | Nemaline myopathy 2, autosomal recessive |
| ZFLNCG04372 | 614402 | Microphthalmia, syndromic 11 |
| ZFLNCG01312 | 219200 | Cutis laxa, autosomal recessive, type IIA |
| ZFLNCG01693 | 130000 | Ehlers-Danlos syndrome, classic type |
| ZFLNCG01205 | 600919 | Long QT syndrome 4 |
| ZFLNCG04642 | 600334 | Tibial muscular dystrophy, tardive |
| ZFLNCG00765 | 118210 | Charcot-Marie-Tooth disease, type 2A1 |
| ZFLNCG13205 | 615325 | Muscular dystrophy, limb-girdle, type 2R |
| ZFLNCG08626 | 181400 | Scapuloperoneal syndrome, neurogenic, Kaeser type |
| ZFLNCG12716 | 613810 | Retinitis pigmentosa 43 |
| ZFLNCG06961 | 225400 | Ehlers-Danlos syndrome, type VI |