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 |
|---|---|---|
| ZFLNCG05355 | 612551 | Glomerulosclerosis, focal segmental, 4, susceptibility to |
| ZFLNCG12408 | 608898 | Hemophagocytic lymphohistiocytosis, familial, 3 |
| ZFLNCG05355 | 194200 | Wolff-Parkinson-White syndrome |
| ZFLNCG01693 | 259420 | Osteogenesis imperfecta, type III |
| ZFLNCG09421 | 112600 | Brachydactyly, type A2 |
| ZFLNCG06562 | 228520 | Fibrochondrogenesis 1 |
| ZFLNCG10738 | 312700 | Retinoschisis |
| ZFLNCG09301 | 613013 | Neuroblastoma with Hirschsprung disease |
| ZFLNCG10301 | 231095 | Ghosal hematodiaphyseal syndrome |
| ZFLNCG02428 | 614335 | Arthrogryposis, distal, type 1B |
| ZFLNCG04642 | 608807 | Muscular dystrophy, limb-girdle, type 2J |
| ZFLNCG07522 | 612337 | Mental retardation, autosomal dominant 22 |
| ZFLNCG12741 | 613980 | Atrial fibrillation, familial, 9 |
| ZFLNCG05132 | 300752 | Protoporphyria, erythropoietic, X-linked |
| ZFLNCG03410 | 171400 | Multiple endocrine neoplasia IIA |
| ZFLNCG10716 | 127300 | Leri-Weill dyschondrosteosis |
| ZFLNCG04391 | 611876 | Brugada syndrome 4 |
| ZFLNCG04893 | 615530 | Parkinson disease 20, early-onset |
| ZFLNCG08626 | 615325 | Muscular dystrophy, limb-girdle, type 2R |
| ZFLNCG07054 | 614495 | Pseudohypoaldosteronism, type IID |
| ZFLNCG05957 | 608807 | Muscular dystrophy, limb-girdle, type 2J |
| ZFLNCG01104 | 607236 | HARP syndrome |
| ZFLNCG10318 | 608232 | Leukemia, chronic myeloid, somatic |
| ZFLNCG10602 | 611804 | Elliptocytosis-1 |
| ZFLNCG07994 | 609069 | Pancreatic and cerebellar agenesis |