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 |
|---|---|---|
| ZFLNCG10725 | 615034 | Dystonia 24 |
| ZFLNCG05213 | 615771 | Cortical dysplasia, complex, with other brain malformations 6 |
| ZFLNCG12733 | 192950 | Vertical talus, congenital |
| ZFLNCG05238 | 269840 | Selective T-cell defect |
| ZFLNCG07651 | 601800 | Skin/hair/eye pigmentation 3, light/dark/freckling skin |
| ZFLNCG01064 | 125852 | Diabetes mellitus, insulin-dependent, 2 |
| ZFLNCG03375 | 276880 | Urocanase deficiency |
| ZFLNCG05735 | 600858 | Cardiomyopathy, hypertrophic 6 |
| ZFLNCG06931 | 147250 | Single median maxillary central incisor |
| ZFLNCG12274 | 609622 | Short QT syndrome 3 |
| ZFLNCG12387 | 600132 | Retinitis pigmentosa 14 |
| ZFLNCG11719 | 300066 | Deafness, X-linked 4 |
| ZFLNCG04982 | 604219 | Cataract 9, multiple types |
| ZFLNCG03308 | 613443 | Mental retardation, stereotypic movements, epilepsy, and/or cerebral malformations |
| ZFLNCG07039 | 253250 | Mulibrey nanism |
| ZFLNCG06555 | 613003 | Attention deficit-hyperactivity disorder, susceptibility to, 7 |
| ZFLNCG00567 | 264600 | Pseudovaginal perineoscrotal hypospadias |
| ZFLNCG13482 | 612838 | Cardiac conduction defect, nonspecific |
| ZFLNCG10413 | 108600 | Spastic ataxia 1, autosomal dominant |
| ZFLNCG07109 | 127750 | Dementia, Lewy body |
| ZFLNCG02018 | 610227 | Seborrhea-like dermatitis with psoriasiform elements |
| ZFLNCG04391 | 611875 | Brugada syndrome 3 |
| ZFLNCG03410 | 607476 | Newfoundland rod-cone dystrophy |
| ZFLNCG04642 | 611705 | Myopathy, early-onset, with fatal cardiomyopathy |
| ZFLNCG03922 | 613443 | Mental retardation, stereotypic movements, epilepsy, and/or cerebral malformations |