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Journal of Translational Medicine
Published in: Journal of Translational Medicine 1/2018

Open Access 01-12-2018 | Research

Improving knowledge on the activation of bone marrow fibroblasts in MGUS and MM disease through the automatic extraction of genes via a nonnegative matrix factorization approach on gene expression profiles

Authors: Angelina Boccarelli, Flavia Esposito, Mauro Coluccia, Maria Antonia Frassanito, Angelo Vacca, Nicoletta Del Buono

Published in: Journal of Translational Medicine | Issue 1/2018

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Abstract

Background

Multiple myeloma (MM) is a cancer of terminally differentiated plasma that is part of a spectrum of blood diseases. The role of the micro-environment is crucial for MM clonal evolution.

Methods

This paper describes the analysis carried out on a limited number of genes automatically extracted by a nonnegative matrix factorization (NMF) based approach from gene expression profiles of bone marrow fibroblasts of patients with monoclonal gammopathy of undetermined significance (MGUS) and MM.

Results

Automatic exploration through NMF, combined with a motivated post-processing procedure and a pathways analysis of extracted genes, allowed to infer that a functional switch is required to lead fibroblasts to acquire pro-tumorigenic activity in the progression of the disease from MGUS to MM.

Conclusion

The extracted biologically relevant genes may be representative of the considered clinical conditions and may contribute to a deeper understanding of tumor behavior.
Appendix
Available only for authorised users
Footnotes
3
Heatmap tool is frequently adopted to illustrate trends in genetic data which are not clearly visible using other visualization techniques. This plot associates a color to each numerical values in a matrix so that the relevance of a row element in a column can be easily highlighted.
 
4
This divergence is frequently adopted in microarray data analysis since it corresponds to the maximum likelihood estimation under independent Poisson assumption. [39]
 
5
WebGestalt is a functional enrichment analysis web tool that using statistics is able to translate gene lists into biological insights [44].
 
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Metadata
Title
Improving knowledge on the activation of bone marrow fibroblasts in MGUS and MM disease through the automatic extraction of genes via a nonnegative matrix factorization approach on gene expression profiles
Authors
Angelina Boccarelli
Flavia Esposito
Mauro Coluccia
Maria Antonia Frassanito
Angelo Vacca
Nicoletta Del Buono
Publication date
01-12-2018
Publisher
BioMed Central
Published in
Journal of Translational Medicine / Issue 1/2018
Electronic ISSN: 1479-5876
DOI
https://doi.org/10.1186/s12967-018-1589-1

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