Telomere Maintenance Pathways in Lower-Grade Gliomas: Insights from Genetic Subtypes and Telomere Length Dynamics

This is the submission accompanying the "Telomere Maintenance Pathways in Lower-Grade Gliomas: Insights from Genetic Subtypes and Telomere Length Dynamics" paper.

The dataset contains the TCGA and CGGA LGG

The dataset is organized as follows:

Folder "CGGA_LGG_IDH_subtype_mean_vis" - The CGGAL GG data IDH subtype pathway visualization and CSV data. Folder "Long_Short_telomeres_path_vis" - The TCGA LGG data ALT and TEL pathway visualization for Long and Short telomeres mean values. Folder ...

Creators: Arsen Arakelyan, Meline Hakobyan, Hans Binder

Submitter: Arsen Arakelyan

External Link
Test model - KEGGParser: parsing and editing KEGG pathway maps in Matlab

KEGG pathway database is a collection of manually drawn pathway maps representing current knowledge on molecular interaction and reaction networks, accompanied with KGML (KEGG pathway xml format) files for automatic computational analyses and modeling of metabolic and signaling networks. In a KGML file the pathway is represented as a graph object with entry elements (gene products, compounds, pathways) as its nodes, and relations between elements as edges. However, in most cases there is a lack ...

Creator: Arsen Arakelyan

Submitter: Arsen Arakelyan

PSF toolkit: an R package for pathway curation and topology-aware analysis.

Abstract (Expand)

Most high throughput genomic data analysis pipelines currently rely on over-representation or gene set enrichment analysis (ORA/GSEA) approaches for functional analysis. In contrast, topology-based … pathway analysis methods, which offer a more biologically informed perspective by incorporating interaction and topology information, have remained underutilized and inaccessible due to various limiting factors. These methods heavily rely on the quality of pathway topologies and often utilize predefined topologies from databases without assessing their correctness. To address these issues and make topology-aware pathway analysis more accessible and flexible, we introduce the PSF (Pathway Signal Flow) toolkit R package. Our toolkit integrates pathway curation and topology-based analysis, providing interactive and command-line tools that facilitate pathway importation, correction, and modification from diverse sources. This enables users to perform topology-based pathway signal flow analysis in both interactive and command-line modes. To showcase the toolkit's usability, we curated 36 KEGG signaling pathways and conducted several use-case studies, comparing our method with ORA and the topology-based signaling pathway impact analysis (SPIA) method. The results demonstrate that the algorithm can effectively identify ORA enriched pathways while providing more detailed branch-level information. Moreover, in contrast to the SPIA method, it offers the advantage of being cut-off free and less susceptible to the variability caused by selection thresholds. By combining pathway curation and topology-based analysis, the PSF toolkit enhances the quality, flexibility, and accessibility of topology-aware pathway analysis. Researchers can now easily import pathways from various sources, correct and modify them as needed, and perform detailed topology-based pathway signal flow analysis. In summary, our PSF toolkit offers an integrated solution that addresses the limitations of current topology-based pathway analysis methods. By providing interactive and command-line tools for pathway curation and topology-based analysis, we empower researchers to conduct comprehensive pathway analyses across a wide range of applications.

Authors: S. Hakobyan, A. Stepanyan, L. Nersisyan, H. Binder, A. Arakelyan

Date Published: 8th Sep 2023

Publication Type: Journal

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