Show/Hide Menu
Hide/Show Apps
anonymousUser
Logout
Türkçe
Türkçe
Search
Search
Login
Login
OpenMETU
OpenMETU
About
About
Open Science Policy
Open Science Policy
Communities & Collections
Communities & Collections
Help
Help
Frequently Asked Questions
Frequently Asked Questions
Videos
Videos
Thesis submission
Thesis submission
Publication submission with DOI
Publication submission with DOI
Publication submission
Publication submission
Contact us
Contact us
Inferring RBP-Mediated Regulation in Lung Squamous Cell Carcinoma
Download
10.1371:journal.pone.0155354.PDF
Date
2016-5-17
Author
Lafzi, Atefeh
Kazan, Hilal
Metadata
Show full item record
This work is licensed under a
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License
.
Item Usage Stats
14
views
9
downloads
Cite This
RNA-binding proteins (RBPs) play key roles in post-transcriptional regulation of mRNAs. Dysregulations in RBP-mediated mechanisms have been found to be associated with many steps of cancer initiation and progression. Despite this, previous studies of gene expression in cancer have ignored the effect of RBPs. To this end, we developed a lasso regression model that predicts gene expression in cancer by incorporating RBP-mediated regulation as well as the effects of other well-studied factors such as copy-number variation, DNA methylation, TFs and miRNAs. As a case study, we applied our model to Lung squamous cell carcinoma (LUSC) data as we found that there are several RBPs differentially expressed in LUSC. Including RBP-mediated regulatory effects in addition to the other features significantly increased the Spearman rank correlation between predicted and measured expression of held-out genes. Using a feature selection procedure that accounts for the adaptive search employed by lasso regularization, we identified the candidate regulators in LUSC. Remarkably, several of these candidate regulators are RBPs. Furthermore, majority of the candidate regulators have been previously found to be associated with lung cancer. To investigate the mechanisms that are controlled by these regulators, we predicted their target gene sets based on our model. We validated the target gene sets by comparing against experimentally verified targets. Our results suggest that the future studies of gene expression in cancer must consider the effect of RBP-mediated regulation.
Subject Keywords
General Biochemistry, Genetics and Molecular Biology
,
General Agricultural and Biological Sciences
,
General Medicine
URI
https://hdl.handle.net/11511/51229
Journal
PLOS ONE
DOI
https://doi.org/10.1371/journal.pone.0155354
Collections
Graduate School of Informatics, Article
Citation Formats
IEEE
ACM
APA
CHICAGO
MLA
BibTeX
A. Lafzi and H. Kazan, “Inferring RBP-Mediated Regulation in Lung Squamous Cell Carcinoma,”
PLOS ONE
, vol. 11, no. 5, 2016, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/51229.