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

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 n...

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Autores principales: SUI, SHUXIANG, WANG, XIN, ZHENG, HUA, GUO, HUA, CHEN, TONG, JI, DONG-MEI
Formato: Online Artículo Texto
Lenguaje:English
Publicado: D.A. Spandidos 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4665311/
https://www.ncbi.nlm.nih.gov/pubmed/26788135
http://dx.doi.org/10.3892/ol.2015.3761
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author SUI, SHUXIANG
WANG, XIN
ZHENG, HUA
GUO, HUA
CHEN, TONG
JI, DONG-MEI
author_facet SUI, SHUXIANG
WANG, XIN
ZHENG, HUA
GUO, HUA
CHEN, TONG
JI, DONG-MEI
author_sort SUI, SHUXIANG
collection PubMed
description 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 1,588 edges in the protein-protein interaction network, with the processes of hematopoietic cell lineage and porphyrin metabolism demonstrating a close association with pediatric ALL. Network enrichment analysis based on the PathExpand algorithm was revealed to be more powerful for the analysis of interaction networks in pediatric ALL compared with the EASE method. LIF and MLLT11 were identified as the most significantly DE genes in pediatric ALL. The process of hematopoietic cell lineage was the pathway most significantly associated with pediatric ALL.
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spelling pubmed-46653112016-01-19 Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia SUI, SHUXIANG WANG, XIN ZHENG, HUA GUO, HUA CHEN, TONG JI, DONG-MEI Oncol Lett Articles 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 1,588 edges in the protein-protein interaction network, with the processes of hematopoietic cell lineage and porphyrin metabolism demonstrating a close association with pediatric ALL. Network enrichment analysis based on the PathExpand algorithm was revealed to be more powerful for the analysis of interaction networks in pediatric ALL compared with the EASE method. LIF and MLLT11 were identified as the most significantly DE genes in pediatric ALL. The process of hematopoietic cell lineage was the pathway most significantly associated with pediatric ALL. D.A. Spandidos 2015-12 2015-09-29 /pmc/articles/PMC4665311/ /pubmed/26788135 http://dx.doi.org/10.3892/ol.2015.3761 Text en Copyright: © Sui et al. This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
spellingShingle Articles
SUI, SHUXIANG
WANG, XIN
ZHENG, HUA
GUO, HUA
CHEN, TONG
JI, DONG-MEI
Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia
title Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia
title_full Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia
title_fullStr Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia
title_full_unstemmed Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia
title_short Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia
title_sort gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4665311/
https://www.ncbi.nlm.nih.gov/pubmed/26788135
http://dx.doi.org/10.3892/ol.2015.3761
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