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

Zhang, Zhihan
http://orcid.org/0000-0001-7824-9437
http://rave.ohiolink.edu/etdc/view?acc_num=case148595901371196

Abstract Details

2017, Master of Sciences, Case Western Reserve University, Systems Biology and Bioinformatics.
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.
Gurkan Bebek (Committee Chair)
Mark Cameron (Committee Member)
Jean-Eudes Dazard (Committee Member)
75 p.
Bioinformatics; Oncology
Cancer; Brain; Tumor; Glioma; LGG; Subtype; Network; Subnetwork; Enumeration; Algorithm; Clustering; Prognostics; MAPK; NOTCH; Methylation

Recommended Citations

Citations

  • Zhang, Z. (2017). NSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics [Master's thesis, Case Western Reserve University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=case148595901371196

    APA Style (7th edition)

  • Zhang, Zhihan. NSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics. 2017. Case Western Reserve University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=case148595901371196.

    MLA Style (8th edition)

  • Zhang, Zhihan. "NSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics." Master's thesis, Case Western Reserve University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=case148595901371196

    Chicago Manual of Style (17th edition)

case148595901371196
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© 2017, all rights reserved.
This open access ETD is published by Case Western Reserve University School of Graduate Studies and OhioLINK.