An interactive multi-omics data mining tool for Idiopathic Pulmonary Fibrosis

About IPF

Idiopathic Pulmonary Fibrosis is a progressive pulmonary disease of unknown etiology characterized, among others, by extensive lung scarring and fibrosis. It manifests mainly into older adults, half of which usually decease due to respiratory failure 3-5 years post diagnosis.

Despite many years of relentless attempts, the scientific community has not yet found a cure for IPF. Currently, the discovery and approval of two new anti-fibrotic treatments, nintedanib and pirfenidone, was able to delay disease progression, but not to increase overall survival, while several side effects have also been reported.

Quickly after their first introduction to the everyday laboratory practice, omics technologies have greatly boosted biomedical research leading to several major discoveries and the inevitable accumulation of a great number of datasets. Due to the heterogeneity of the latter, their scattering across the web and the different approaches used for their analysis, a fruitful meta-analysis is a time-consuming and laborious process even for those possessing the required computational skills. Consequently, centralized repositories/web servers dedicated to the carefull collection, selection and communication are urgently needed.

About Fibromine

Fibromine is a Shiny-based web server that aims to accelerate IPF research by providing functionalities for three point-of-view integration and exploration of numerous IPF and IPF-related transcriptomic and proteomic datasets. In addition, Fibromine includes a custom datasets benchmarking strategy in an attempt to reveal otherwise "invisible" datasets characteristics.

All Fibromine functionalities are highly user-tunable and results, as well as Fibromine included data, can be easily downloaded.

  Site map

  • Dataset explorer facilitates transcriptomic and proteomic datasets review and integration. Consensus differentially expressed genes and proteins can be fetched along with exploratory heatmaps and volcano plots for the transcriptomic datasets.
  • Gene explorer enables the interrogation of gene expression patterns for either single or multiple genes at the same time. Apart from basic gene annotation, further data regarding respective gene ontology, RefSeq sequences and miRNA-mRNA interactions are provided.
  • Protein explorer's main functionality is to plot condition-specific protein-protein interaction networks revolving around the protein queried. In addition, protein differential expression pattern is fetched from Fibromine included proteomic datasets.
  • Datasets benchmarking tab displays the results of the deployed custom strategy for Fibromine datasets benchmarking.
  • Download data tab enables on-click download of normalized transcriptomics data and differential expression analysis results for proteomics datasets.

For more in detail information about Fibromine please refer to the application Docs, or search for the green "About" buttons in each of the explorers.

Transcriptomic datasets explorer

Proteomics datasets explorer

Note: batch search for a great number of genes can take some time; please, be patient.

General information

Map to single cell data

miRNA - target DEGs shortlist

Select an miRNA from the drop-down menu and press the 'Search' button to obtain DEA data for that miRNA as well as for the deregulated genes potentially interacting with it.

miRNA expression summary


Potential targets expression summary


Benchmarking backstage