Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis

Abstract Idiopathic pulmonary fibrosis is a lethal lung fibroproliferative disease with limited therapeutic options. Differential expression profiling of affected sites has been instrumental for involved pathogenetic mechanisms dissection and therapeutic targets discovery. However, there have been l...

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Autores principales:	Dionysios Fanidis, Panagiotis Moulos, Vassilis Aidinis
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/46adc8caa74a47a8888ff71b7649eb32
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spelling	oai:doaj.org-article:46adc8caa74a47a8888ff71b7649eb322021-11-08T10:51:06ZFibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis10.1038/s41598-021-01069-w2045-2322https://doaj.org/article/46adc8caa74a47a8888ff71b7649eb322021-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-01069-whttps://doaj.org/toc/2045-2322Abstract Idiopathic pulmonary fibrosis is a lethal lung fibroproliferative disease with limited therapeutic options. Differential expression profiling of affected sites has been instrumental for involved pathogenetic mechanisms dissection and therapeutic targets discovery. However, there have been limited efforts to comparatively analyse/mine the numerous related publicly available datasets, to fully exploit their potential on the validation/creation of novel research hypotheses. In this context and towards that goal, we present Fibromine, an integrated database and exploration environment comprising of consistently re-analysed, manually curated transcriptomic and proteomic pulmonary fibrosis datasets covering a wide range of experimental designs in both patients and animal models. Fibromine can be accessed via an R Shiny application ( http://www.fibromine.com/Fibromine ) which offers dynamic data exploration and real-time integration functionalities. Moreover, we introduce a novel benchmarking system based on transcriptomic datasets underlying characteristics, resulting to dataset accreditation aiming to aid the user on dataset selection. Cell specificity of gene expression can be visualised and/or explored in several scRNA-seq datasets, in an effort to link legacy data with this cutting-edge methodology and paving the way to their integration. Several use case examples are presented, that, importantly, can be reproduced on-the-fly by a non-specialist user, the primary target and potential user of this endeavour.Dionysios FanidisPanagiotis MoulosVassilis AidinisNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Dionysios Fanidis Panagiotis Moulos Vassilis Aidinis Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis
description	Abstract Idiopathic pulmonary fibrosis is a lethal lung fibroproliferative disease with limited therapeutic options. Differential expression profiling of affected sites has been instrumental for involved pathogenetic mechanisms dissection and therapeutic targets discovery. However, there have been limited efforts to comparatively analyse/mine the numerous related publicly available datasets, to fully exploit their potential on the validation/creation of novel research hypotheses. In this context and towards that goal, we present Fibromine, an integrated database and exploration environment comprising of consistently re-analysed, manually curated transcriptomic and proteomic pulmonary fibrosis datasets covering a wide range of experimental designs in both patients and animal models. Fibromine can be accessed via an R Shiny application ( http://www.fibromine.com/Fibromine ) which offers dynamic data exploration and real-time integration functionalities. Moreover, we introduce a novel benchmarking system based on transcriptomic datasets underlying characteristics, resulting to dataset accreditation aiming to aid the user on dataset selection. Cell specificity of gene expression can be visualised and/or explored in several scRNA-seq datasets, in an effort to link legacy data with this cutting-edge methodology and paving the way to their integration. Several use case examples are presented, that, importantly, can be reproduced on-the-fly by a non-specialist user, the primary target and potential user of this endeavour.
format	article
author	Dionysios Fanidis Panagiotis Moulos Vassilis Aidinis
author_facet	Dionysios Fanidis Panagiotis Moulos Vassilis Aidinis
author_sort	Dionysios Fanidis
title	Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis
title_short	Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis
title_full	Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis
title_fullStr	Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis
title_full_unstemmed	Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis
title_sort	fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/46adc8caa74a47a8888ff71b7649eb32
work_keys_str_mv	AT dionysiosfanidis fibromineisamultiomicsdatabaseandminingtoolfortargetdiscoveryinpulmonaryfibrosis AT panagiotismoulos fibromineisamultiomicsdatabaseandminingtoolfortargetdiscoveryinpulmonaryfibrosis AT vassilisaidinis fibromineisamultiomicsdatabaseandminingtoolfortargetdiscoveryinpulmonaryfibrosis
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Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis

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