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 |
|---|---|---|
| ZFLNCG09762 | 612337 | Mental retardation, autosomal dominant 22 |
| ZFLNCG08615 | 131850 | Epidermolysis bullosa, pretibial |
| ZFLNCG13558 | 300243 | Mental retardation, X-linked syndromic, Christianson type |
| ZFLNCG10279 | 215150 | Otospondylomegaepiphyseal dysplasia |
| ZFLNCG09551 | 610093 | Microphthalmia, isolated 2 |
| ZFLNCG07208 | 142680 | Periodic fever, familial |
| ZFLNCG06609 | 245050 | Succinyl CoA:3-oxoacid CoA transferase deficiency |
| ZFLNCG12894 | 609220 | Bruck syndrome 2 |
| ZFLNCG08297 | 614195 | Craniofacial anomalies and anterior segment dysgenesis syndrome |
| ZFLNCG10829 | 600852 | Retinitis pigmentosa 17 |
| ZFLNCG06928 | 108600 | Spastic ataxia 1, autosomal dominant |
| ZFLNCG00623 | 166710 | Osteoporosis, involutional |
| ZFLNCG11072 | 277300 | Spondylocostal dysostosis 1, autosomal recessive |
| ZFLNCG01697 | 277300 | Spondylocostal dysostosis 1, autosomal recessive |
| ZFLNCG08579 | 605115 | Hypertension, early-onset, autosomal dominant, with exacerbation in pregnancy |
| ZFLNCG09861 | 605850 | Dimethylglycine dehydrogenase deficiency |
| ZFLNCG12405 | 612965 | 46XY sex reversal 3 |
| ZFLNCG01593 | 613671 | Mental retardation, anterior maxillary protrusion, and strabismus |
| ZFLNCG11786 | 193400 | von Willebrand disease, type 1 |
| ZFLNCG05097 | 600132 | Retinitis pigmentosa 14 |
| ZFLNCG12302 | 613986 | Pituitary hormone deficiency, combined, 6 |
| ZFLNCG10602 | 262700 | Pituitary hormone deficiency, combined, 4 |
| ZFLNCG11358 | 176807 | Prostate cancer, susceptibility to, somatic |
| ZFLNCG00745 | 226650 | Epidermolysis bullosa, junctional, non-Herlitz type |
| ZFLNCG06107 | 607236 | HARP syndrome |