Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray

Here, we present a protocol for deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray. We describe steps for utilizing NMF-defined group 3/group 4 metagenes to calculate a continuum score between 0 and 1 that can be proje...

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Detalles Bibliográficos
Autores principales: Hacking, James P.R., Thompson, Dean, Schwalbe, Edward C., Clifford, Steven C., Williamson, Daniel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10448413/
https://www.ncbi.nlm.nih.gov/pubmed/37573504
http://dx.doi.org/10.1016/j.xpro.2023.102509
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author Hacking, James P.R.
Thompson, Dean
Schwalbe, Edward C.
Clifford, Steven C.
Williamson, Daniel
author_facet Hacking, James P.R.
Thompson, Dean
Schwalbe, Edward C.
Clifford, Steven C.
Williamson, Daniel
author_sort Hacking, James P.R.
collection PubMed
description Here, we present a protocol for deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray. We describe steps for utilizing NMF-defined group 3/group 4 metagenes to calculate a continuum score between 0 and 1 that can be projected onto new sample data analyzed via RNA-sequencing. We then detail procedures for reverse engineering a continuum score for samples analyzed via DNA methylation microarray using a random forest classifier.
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spelling pubmed-104484132023-08-25 Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray Hacking, James P.R. Thompson, Dean Schwalbe, Edward C. Clifford, Steven C. Williamson, Daniel STAR Protoc Protocol Here, we present a protocol for deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray. We describe steps for utilizing NMF-defined group 3/group 4 metagenes to calculate a continuum score between 0 and 1 that can be projected onto new sample data analyzed via RNA-sequencing. We then detail procedures for reverse engineering a continuum score for samples analyzed via DNA methylation microarray using a random forest classifier. Elsevier 2023-08-11 /pmc/articles/PMC10448413/ /pubmed/37573504 http://dx.doi.org/10.1016/j.xpro.2023.102509 Text en © 2023 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Protocol
Hacking, James P.R.
Thompson, Dean
Schwalbe, Edward C.
Clifford, Steven C.
Williamson, Daniel
Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray
title Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray
title_full Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray
title_fullStr Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray
title_full_unstemmed Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray
title_short Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray
title_sort deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via rna-sequencing or dna methylation microarray
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10448413/
https://www.ncbi.nlm.nih.gov/pubmed/37573504
http://dx.doi.org/10.1016/j.xpro.2023.102509
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