|

楼主 |
发表于 2016-9-6 16:35:26
|
显示全部楼层
GBM is the most common and also the most devastating brain tumor, with a 5-year survival rate below 10%.
article :http://www.sciencedirect.com/sci ... i/S1535610812003649
Cancer Cell
Volume 22, Issue 4, 16 October 2012, Pages 425–437
我也不知道为什么要读它,但是感觉,每篇文献都还有好多不懂的!
里面用到的分类包都已经淘汰了:Package ‘clusterCons’ was removed from the CRAN repository.
We identified six epigenetic GBM subgroups displaying characteristic global DNA methylation patterns, harboring distinct hotspot mutations, DNA copy-number alterations, and transcriptomic patterns.
Based on correlations with mutational status, DNA copy-number aberrations, and gene expression signatures, as outlined below, we have labeled these subgroups “IDH,” “K27,” “G34,” “RTK I (PDGFRA),” “Mesenchymal,” and “RTK II (Classic).”
the TCGA to classify 122 of the above tumors with available transcriptome data into one of four gene expression subtypes: Proneural, Neural, Mesenchymal, and Classical
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34824 paediatric glioblastomas HG-U133_Plus_2
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36245 Glioblastoma HG-U133_Plus_2
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36278 Illumina HumanMethylation450 BeadChip childhood (n=59) and adult GBMs (n=77)
For unsupervised consensus clustering we used the 8,000 most variable methylated probes (by standard deviation) across the data set (R package: clusterCons)
The significance analysis of microarrays (SAM) method was used to identify genes that are differentially methylated or differentially expressed between subgroups.
Kaplan-Meier analysis was performed to estimate the survival time of different GBM subgroups and a log rank test was used to test for differences of more than one survival curve. |
|