PhenPath: A tool for characterizing biological functions underlying different phenotypes
| العنوان: | PhenPath: A tool for characterizing biological functions underlying different phenotypes |
|---|---|
| المؤلفون: | Pier Luigi Martelli, Giulia Babbi, Rita Casadio |
| المساهمون: | Babbi G, Martelli P, Casadio R |
| المصدر: | BMC Genomics, Vol 20, Iss S8, Pp 1-11 (2019) BMC Genomics |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | 0106 biological sciences, lcsh:QH426-470, Molecular pathway, lcsh:Biotechnology, Diseases, Computational biology, Biology, Proteomics, 01 natural sciences, Biological process, 03 medical and health sciences, lcsh:TP248.13-248.65, Databases, Genetic, Human Phenotype Ontology, Genetics, Humans, Disease, KEGG, Gene, 030304 developmental biology, 0303 health sciences, Research, Computational Biology, Phenotype Diseases Molecular pathway Biological process Enrichment, Gene Annotation, Phenotype, lcsh:Genetics, Biological Ontologies, Enrichment, Human genome, DNA microarray, 010606 plant biology & botany, Biotechnology |
| الوصف: | Background Many diseases are associated with complex patterns of symptoms and phenotypic manifestations. Parsimonious explanations aim at reconciling the multiplicity of phenotypic traits with the perturbation of one or few biological functions. For this, it is necessary to characterize human phenotypes at the molecular and functional levels, by exploiting gene annotations and known relations among genes, diseases and phenotypes. This characterization makes it possible to implement tools for retrieving functions shared among phenotypes, co-occurring in the same patient and facilitating the formulation of hypotheses about the molecular causes of the disease. Results We introduce PhenPath, a new resource consisting of two parts: PhenPathDB and PhenPathTOOL. The former is a database collecting the human genes associated with the phenotypes described in Human Phenotype Ontology (HPO) and OMIM Clinical Synopses. Phenotypes are then associated with biological functions and pathways by means of NET-GE, a network-based method for functional enrichment of sets of genes. The present version considers only phenotypes related to diseases. PhenPathDB collects information for 18 OMIM Clinical synopses and 7137 HPO phenotypes, related to 4292 diseases and 3446 genes. Enrichment of Gene Ontology annotations endows some 87.7, 86.9 and 73.6% of HPO phenotypes with Biological Process, Molecular Function and Cellular Component terms, respectively. Furthermore, 58.8 and 77.8% of HPO phenotypes are also enriched for KEGG and Reactome pathways, respectively. Based on PhenPathDB, PhenPathTOOL analyzes user-defined sets of phenotypes retrieving diseases, genes and functional terms which they share. This information can provide clues for interpreting the co-occurrence of phenotypes in a patient. Conclusions The resource allows finding molecular features useful to investigate diseases characterized by multiple phenotypes, and by this, it can help researchers and physicians in identifying molecular mechanisms and biological functions underlying the concomitant manifestation of phenotypes. The resource is freely available at http://phenpath.biocomp.unibo.itTest. Electronic supplementary material The online version of this article (10.1186/s12864-019-5868-x) contains supplementary material, which is available to authorized users. |
| وصف الملف: | ELETTRONICO |
| اللغة: | English |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::088a421baa4b38b146e441ac49baf3a0Test http://hdl.handle.net/11585/712232Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....088a421baa4b38b146e441ac49baf3a0 |
| قاعدة البيانات: | OpenAIRE |
| الوصف غير متاح. |