June 2017
Volume 58, Issue 8
Open Access
ARVO Annual Meeting Abstract  |   June 2017
A bioinformatics approach to identify molecular pathways that characterize the trabecular meshwork
Author Affiliations & Notes
  • Ilona Liesenborghs
    University Eye Clinic Maastricht, Maastricht University Medical Centre+, Maastricht, Netherlands
    Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
  • Carroll Webers
    University Eye Clinic Maastricht, Maastricht University Medical Centre+, Maastricht, Netherlands
  • Lars Eijssen
    Department of Bioinformatics, BiGCaT, Maastricht University, Maastricht, Netherlands
  • Martina Kutmon
    Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
    Department of Bioinformatics, BiGCaT, Maastricht University, Maastricht, Netherlands
  • Theo G M F Gorgels
    University Eye Clinic Maastricht, Maastricht University Medical Centre+, Maastricht, Netherlands
  • Wouter Hubens
    University Eye Clinic Maastricht, Maastricht University Medical Centre+, Maastricht, Netherlands
  • Chris Evelo
    Department of Bioinformatics, BiGCaT, Maastricht University, Maastricht, Netherlands
    Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
  • Henny J Beckers
    University Eye Clinic Maastricht, Maastricht University Medical Centre+, Maastricht, Netherlands
  • Johannes Schouten
    University Eye Clinic Maastricht, Maastricht University Medical Centre+, Maastricht, Netherlands
  • Footnotes
    Commercial Relationships   Ilona Liesenborghs, None; Carroll Webers, None; Lars Eijssen, None; Martina Kutmon, None; Theo Gorgels, None; Wouter Hubens, None; Chris Evelo, None; Henny Beckers, None; Johannes Schouten, None
  • Footnotes
    Support  None
Investigative Ophthalmology & Visual Science June 2017, Vol.58, 4904. doi:
  • Views
  • Share
  • Tools
    • Alerts
      ×
      This feature is available to Subscribers Only
      Sign In or Create an Account ×
    • Get Citation

      Ilona Liesenborghs, Carroll Webers, Lars Eijssen, Martina Kutmon, Theo G M F Gorgels, Wouter Hubens, Chris Evelo, Henny J Beckers, Johannes Schouten; A bioinformatics approach to identify molecular pathways that characterize the trabecular meshwork. Invest. Ophthalmol. Vis. Sci. 2017;58(8):4904.

      Download citation file:


      © ARVO (1962-2015); The Authors (2016-present)

      ×
  • Supplements
Abstract

Purpose : The pathogenesis of primary open angle glaucoma (POAG) has not been clarified and its treatment is still not based on insights in the underlying molecular mechanisms. We performed in silico pathway analysis based on gene expression datasets of healthy human trabecular meshwork (TM) cells. Identification of the active pathways in this tissue contributes to a better insight in the molecular processes and may provide candidate target genes for new treatment options of POAG.

Methods : A search for datasets was conducted in Gene Expression Omnibus and ArrayExpress. We used five microarray datasets (GSE27276, GSE65240, GSE6298, GSE37474, and GSE16643; n=23 individuals), which contained gene expression profiles of healthy trabecular meshwork cells. All data were subjected to a thorough quality control based on ArrayAnalysis.org and R scripts. Divergent samples were removed from the datasets. Pathway analysis and visualisation was conducted with PathVisio using a curated pathway collection from WikiPathways. Ubiquitous pathways (pathways that are common pathways in almost all body tissues) were excluded based on data from TissueAnalyzer. From each dataset, the top 25% highest expressed genes were identified and used for pathway overrepresentation analysis. The top 20 Z-score ranked pathways from the pathway analysis of each dataset were selected as these are likely the most relevant TM active pathways.

Results : Seven ubiquitous pathways were found in the pathway analysis and excluded. One dataset (GE6298) expressed none of these common pathways and did not show any correlation with the results of the other four datasets. Therefore, this dataset was removed from further analysis. Pathways that were expressed in at least three out of four datasets were considered to be active, non-ubiquitous pathways of the healthy TM. Four pathways were significantly expressed in all the datasets and four pathways in three out of four datasets. Several of these pathways have been associated with processes in TM, for example the pathways TNF alpha signalling (WP231), trans-sulfuration (WP2333), and miRNA targets in extracellular matrix and membrane receptor (WP2911).

Conclusions : We identified eight non-ubiquitous pathways that appear to be active in healthy human trabecular meshwork tissue.

This is an abstract that was submitted for the 2017 ARVO Annual Meeting, held in Baltimore, MD, May 7-11, 2017.

×
×

This PDF is available to Subscribers Only

Sign in or purchase a subscription to access this content. ×

You must be signed into an individual account to use this feature.

×