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 |
|---|---|---|
| ZFLNCG05449 | 607323 | Duane-radial ray syndrome |
| ZFLNCG01372 | 219200 | Cutis laxa, autosomal recessive, type IIA |
| ZFLNCG09861 | 612718 | Cerebral creatine deficiency syndrome 3 |
| ZFLNCG12858 | 121050 | Contractural arachnodactyly, congenital |
| ZFLNCG12907 | 178300 | Ptosis, congenital |
| ZFLNCG01621 | 229100 | Glutamate formiminotransferase deficiency |
| ZFLNCG12557 | 610093 | Microphthalmia, isolated 2 |
| ZFLNCG01080 | 615418 | Mitochondrial DNA depletion syndrome 12 (cardiomyopathic type) |
| ZFLNCG08627 | 610828 | Holoprosencephaly-7 |
| ZFLNCG00547 | 219730 | Ventriculomegaly with cystic kidney disease |
| ZFLNCG04674 | 159950 | Spinal muscular atrophy with progressive myoclonic epilepsy |
| ZFLNCG05559 | 232220 | Glycogen storage disease Ib |
| ZFLNCG01532 | 173200 | Pityriasis rubra pilaris |
| ZFLNCG07461 | 609622 | Short QT syndrome 3 |
| ZFLNCG05735 | 261740 | Glycogen storage disease of heart, lethal congenital |
| ZFLNCG08395 | 610227 | Seborrhea-like dermatitis with psoriasiform elements |
| ZFLNCG11358 | 300633 | Hypospadias 1, X-linked |
| ZFLNCG03410 | 162300 | Multiple endocrine neoplasia IIB |
| ZFLNCG10755 | 602481 | Migraine, familial hemiplegic, 2 |
| ZFLNCG08477 | 227810 | Fanconi-Bickel syndrome |
| ZFLNCG01693 | 114000 | Caffey disease |
| ZFLNCG13058 | 264600 | Pseudovaginal perineoscrotal hypospadias |
| ZFLNCG07651 | 128230 | Dystonia, DOPA-responsive, with or without hyperphenylalaninemia |
| ZFLNCG07651 | 233910 | Hyperphenylalaninemia, BH4-deficient, B |
| ZFLNCG09948 | 610743 | Spinocerebellar ataxia, autosomal recessive 8 |