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Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD)
Complex human traits such as chronic kidney disease (CKD) are a major health and financial burden in modern societies. Currently, the description of the CKD onset and progression at the molecular level is still not fully understood. Meanwhile, the prolific use of high-throughput omic technologies in...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5227717/ https://www.ncbi.nlm.nih.gov/pubmed/28079125 http://dx.doi.org/10.1038/srep40367 |
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author | Fernandes, Marco Husi, Holger |
author_facet | Fernandes, Marco Husi, Holger |
author_sort | Fernandes, Marco |
collection | PubMed |
description | Complex human traits such as chronic kidney disease (CKD) are a major health and financial burden in modern societies. Currently, the description of the CKD onset and progression at the molecular level is still not fully understood. Meanwhile, the prolific use of high-throughput omic technologies in disease biomarker discovery studies yielded a vast amount of disjointed data that cannot be easily collated. Therefore, we aimed to develop a molecule-centric database featuring CKD-related experiments from available literature publications. We established the Chronic Kidney Disease database CKDdb, an integrated and clustered information resource that covers multi-omic studies (microRNAs, genomics, peptidomics, proteomics and metabolomics) of CKD and related disorders by performing literature data mining and manual curation. The CKDdb database contains differential expression data from 49395 molecule entries (redundant), of which 16885 are unique molecules (non-redundant) from 377 manually curated studies of 230 publications. This database was intentionally built to allow disease pathway analysis through a systems approach in order to yield biological meaning by integrating all existing information and therefore has the potential to unravel and gain an in-depth understanding of the key molecular events that modulate CKD pathogenesis. |
format | Online Article Text |
id | pubmed-5227717 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-52277172017-01-17 Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD) Fernandes, Marco Husi, Holger Sci Rep Article Complex human traits such as chronic kidney disease (CKD) are a major health and financial burden in modern societies. Currently, the description of the CKD onset and progression at the molecular level is still not fully understood. Meanwhile, the prolific use of high-throughput omic technologies in disease biomarker discovery studies yielded a vast amount of disjointed data that cannot be easily collated. Therefore, we aimed to develop a molecule-centric database featuring CKD-related experiments from available literature publications. We established the Chronic Kidney Disease database CKDdb, an integrated and clustered information resource that covers multi-omic studies (microRNAs, genomics, peptidomics, proteomics and metabolomics) of CKD and related disorders by performing literature data mining and manual curation. The CKDdb database contains differential expression data from 49395 molecule entries (redundant), of which 16885 are unique molecules (non-redundant) from 377 manually curated studies of 230 publications. This database was intentionally built to allow disease pathway analysis through a systems approach in order to yield biological meaning by integrating all existing information and therefore has the potential to unravel and gain an in-depth understanding of the key molecular events that modulate CKD pathogenesis. Nature Publishing Group 2017-01-12 /pmc/articles/PMC5227717/ /pubmed/28079125 http://dx.doi.org/10.1038/srep40367 Text en Copyright © 2017, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Fernandes, Marco Husi, Holger Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD) |
title | Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD) |
title_full | Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD) |
title_fullStr | Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD) |
title_full_unstemmed | Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD) |
title_short | Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD) |
title_sort | establishment of a integrative multi-omics expression database ckddb in the context of chronic kidney disease (ckd) |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5227717/ https://www.ncbi.nlm.nih.gov/pubmed/28079125 http://dx.doi.org/10.1038/srep40367 |
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