@markgerstein: Navin mentions: Tracing the tumor lineage
http://t.co/pDTQBxmd54 Has nice schematic showing different tumor progression models #BTGCG14
http://www.sciencedirect.com/science/article/pii/S1574789110000323?via=ihub
Posts Tagged ‘cancer’
Tracing the tumor lineage — ScienceDirect
October 13, 2014OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes
October 13, 2014@markgerstein: .nlbigas mentions: OncodriveCLUST: exploiting the [local] positional clustering of somatic mutations…
http://t.co/JbMYp6C7bF #BTGCG14
http://bioinformatics.oxfordjournals.org/content/29/18/2238.long
Access : Evolution of the cancer genome : Nature Reviews Genetics
October 13, 2014@markgerstein: .@nlbigas mentions: Evolution of the cancer genome http://t.co/DLwrOlzqch Drivers provide selective advantage #BTGCG14
Criteria for Inference of Chromothripsis in Cancer Genomes — ScienceDirect
October 13, 2014@markgerstein: Korbel mentions: Criteria for Inference of
Chromothripsis in Cancer Genome
http://t.co/TslcrZsmNv #BTGCG14
http://www.sciencedirect.com/science/article/pii/S0092867413002122
Analysis of noncoding regulatory mutations in cancer
September 29, 2014http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3101.html
An interesting report of potential non-coding drivers without actually doing any wet lab work.
“These methods identify recurrent mutations in regulatory elements upstream of PLEKHS1, WDR74 and SDHD, as well as previously identified mutations in the TERT promoter”. In the text they mention “Khurana et al. also reported WDR74 promoter mutations in 2 of the 20 prostate cancer genomes analyzed”.
Constructing structural networks of signaling pathways on the proteome scale
September 6, 2014Structural networks of signaling pathways
http://www.sciencedirect.com/science/article/pii/S0959440X1200070X Prism on IL10 #networks, mapping on Cosmic, disrupting mutations as drivers
WIRED August 2014: The Price of Life
September 1, 2014The Price of Life http://contentviewer.adobe.com/s/Wired/5857345fd35d4d1f9a1f00273013f68a/WI0814_10_Folio/2000_2208IN_deathvmoney.html Nice #visualization of NIH #funding, showing emphasis on #cancer & diabetes v heart disease
CPTAC – Office of Cancer Clinical Proteomics Research – National Cancer Institute
August 31, 2014contains proteomics on some of the TCGA samples
http://proteomics.cancer.gov/programs/cptacnetwork
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups : Nature : Nature Publishing Group
August 31, 2014metabric consortium
gene expression & copy number data available and survival data (on request) for the 4 main breast cancer types (basal, her2 , luma, lumb)
similar to TCGA but from the UK
Allows construction of discovery & validation sets to compare segregation of survival with mRNA level
compare segreg. of survival with inferred protein activity v mRNA level
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
August 30, 2014#Singlecell #RNAseq highlights intratumoral heterogeneity http://www.sciencemag.org/content/344/6190/1396.abs Subtype classifiers variably expressed across indiv. cells
Patel AP(1), Tirosh I(2), Trombetta JJ(2), Shalek AK(2), Gillespie SM(3),
Wakimoto H(4), Cahill DP(4), Nahed BV(4), Curry WT(4), Martuza RL(4), Louis
DN(5), Rozenblatt-Rosen O(2), Suvà ML(6), Regev A(7), Bernstein BE(8).
Published Online June 12 2014
Science 20 June 2014:
Vol. 344 no. 6190 pp. 1396-1401
DOI: 10.1126/science.1254257
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