Posts Tagged ‘biokdd’

Laboratory of Computational Proteomics – Tools – Quilts

August 31, 2014

http://www.fenyolab.org/tools/tools.html

QT:{{”
QUILTS is a tools for creating sample specific protein sequence databased. It uses genomic and transcriptomic information to create comprehensive sample specific protein database that supports the identification of novel proteins, resulting from single nucleotide variants, splice variants and fusion genes.
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Similar to the alleleseq personal genome for proteomics

Fenyo: Nice discussion of Quilts Tools for making up sample specific protein databases to identify novel proteins in cancer. Similar to personal genome construction #kdd2014 #biokdd

Fenyo: Quilts Tools for sample-specific DBs to identify novel proteins in cancer. Similar to personal genome construction #kdd2014 #biokdd

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups : Nature : Nature Publishing Group

August 31, 2014

metabric 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

BMC Bioinformatics | Full text | BicSPAM: flexible biclustering using sequential patterns

August 31, 2014

Related to BIP KDD talk, dealing with overlapping biclusters http://www.biomedcentral.com/1471-2105/15/130