NSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics

NSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics

Bibliographic Details
Main Author: Zhang, Zhihan
Language:English
Published: Case Western Reserve University School of Graduate Studies / OhioLINK 2017
Subjects:
Bioinformatics
Oncology
Cancer
Brain
Tumor
Glioma
LGG
Subtype
Network
Subnetwork
Enumeration
Algorithm
Clustering
Prognostics
MAPK
NOTCH
Methylation
Online Access:http://rave.ohiolink.edu/etdc/view?acc_num=case148595901371196
id ndltd-OhioLink-oai-etd.ohiolink.edu-case148595901371196
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spelling ndltd-OhioLink-oai-etd.ohiolink.edu-case1485959013711962021-08-03T06:39:57Z NSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics Zhang, Zhihan Bioinformatics Oncology Cancer Brain Tumor Glioma LGG Subtype Network Subnetwork Enumeration Algorithm Clustering Prognostics MAPK NOTCH Methylation Motivation: The prognosis of low-grade-glioma (LGG) patients is very poor. Identifying subnetworks related to LGG can better describe the genetic make-up of the tumor. Methods: n-Node Subnetwork Enumeration Algorithm (nSEA) was developed to identify significantly dysregulated subnetworks. We utilized a filtered protein network to enumerate n-node subnetworks exhaustively and score each subnetwork to carry out feature selection. These subnetwork seeds were expanded to identify tumor-specific subnetworks. Clustering these subnetworks provided patient groups with different subnetwork states.Results: We identified 92 subnetwork features, 8 subnetwork groups and 5 patient groups. A new patient group was identified with favorable outcomes. By decision tree modeling, the new group were characterized as down-regulated MAPK/B-Raf pathway and up-regulated Notch pathway. It had fewer mutations of candidate genes, hypomethylation of NIPBL and hypermethylation of KALRN.Conclusions: These results could provide opportunities for improved treatment options and personalized interventions of LGG. 2017-06-06 English text Case Western Reserve University School of Graduate Studies / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=case148595901371196 http://rave.ohiolink.edu/etdc/view?acc_num=case148595901371196 unrestricted This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws.
collection NDLTD
language English
sources NDLTD
topic Bioinformatics
Oncology
Cancer
Brain
Tumor
Glioma
LGG
Subtype
Network
Subnetwork
Enumeration
Algorithm
Clustering
Prognostics
MAPK
NOTCH
Methylation
spellingShingle Bioinformatics
Oncology
Cancer
Brain
Tumor
Glioma
LGG
Subtype
Network
Subnetwork
Enumeration
Algorithm
Clustering
Prognostics
MAPK
NOTCH
Methylation
Zhang, Zhihan
NSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics
author Zhang, Zhihan
author_facet Zhang, Zhihan
author_sort Zhang, Zhihan
title NSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics
title_short NSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics
title_full NSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics
title_fullStr NSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics
title_full_unstemmed NSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics
title_sort nsea: n-node subnetwork enumeration algorithm identifies lower grade glioma subtypes with altered subnetworks and distinct prognostics
publisher Case Western Reserve University School of Graduate Studies / OhioLINK
publishDate 2017
url http://rave.ohiolink.edu/etdc/view?acc_num=case148595901371196
work_keys_str_mv AT zhangzhihan nseannodesubnetworkenumerationalgorithmidentifieslowergradegliomasubtypeswithalteredsubnetworksanddistinctprognostics
_version_ 1719440901019795456

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