Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia

Oncology Letters
Shuxiang SuiDong-Mei Ji

Abstract

Pediatric acute lymphoblastic leukemia (ALL) accounts for over one-quarter of all pediatric cancers. Interacting genes and proteins within the larger human gene interaction network of the human genome are rarely investigated by studies investigating pediatric ALL. In the present study, interaction networks were constructed using the empirical Bayesian approach and the Search Tool for the Retrieval of Interacting Genes/proteins database, based on the differentially-expressed (DE) genes in pediatric ALL, which were identified using the RankProd package. Enrichment analysis of the interaction network was performed using the network-based methods EnrichNet and PathExpand, which were compared with the traditional expression analysis systematic explored (EASE) method. In total, 398 DE genes were identified in pediatric ALL, and LIF was the most significantly DE gene. The co-expression network consisted of 272 nodes, which indicated genes and proteins, and 602 edges, which indicated the number of interactions adjacent to the node. Comparison between EASE and PathExpand revealed that PathExpand detected more pathways or processes that were closely associated with pediatric ALL compared with the EASE method. There were 294 nodes and 1,5...Continue Reading

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Citations

Feb 10, 2018·Oncotarget·Haixiu YangDesi Shang

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Datasets Mentioned

BETA
E-GEOD-34670
E-GEOD-42221

Methods Mentioned

BETA
chip

Software Mentioned

makeMyD
Bioconductor RankProd
AffyBatch
Cytoscape
PathExpand
DAVID
EASE
JEPETTO
RankProd
TopoGSA

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