Wednesday 24 April 2013

Using MEMo to Discover Mutual Exclusivity Modules in Cancer

Curr Protoc Bioinformatics. 2013 Mar;Chapter 8:Unit8.17. doi: 10.1002/0471250953.bi0817s41.

Using MEMo to Discover Mutual Exclusivity Modules in Cancer.

Source

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York.

Abstract

Although individual tumors show surprisingly diverse genomic alterations, these events tend to occur in a limited number of pathways, and alterations that affect the same pathway tend to not co-occur in the same patient. While pathway analysis has been a powerful tool in cancer genomics, our knowledge of oncogenic pathway modules is incomplete. To systematically identify such modules, we have developed a novel method, Mutual Exclusivity Modules in Cancer (MEMo). The method searches and identifies modules characterized by three properties: (1) member genes are recurrently altered across a set of tumor samples; (2) member genes are known to or are likely to participate in the same biological process; and (3) alteration events within the modules are mutually exclusive. MEMo integrates multiple data types and maps genomic alterations to biological pathways. MEMo's mutual exclusivity uses a statistical model that preserves the number of alterations per gene and per sample. The MEMo software, source code and sample data sets are available for download at: http://cbio.mskcc.org/memo. Curr. Protoc. Bioinform. 41:8.17.1-8.17.12. © 2013 by John Wiley & Sons, Inc.



http://www.ncbi.nlm.nih.gov/pubmed/23504936

Gene-pair expression signatures reveal lineage control : Nature Methods : Nature Publishing Group

http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.2445.html

Deanna Church on the Reference Genome Past, Present and Future - Bio-IT World

http://www.bio-itworld.com/2013/4/22/church-on-reference-genomes-past-present-future.html

GRC38

( METAGENOMICS) FunFrame: functional gene ecological analysis pipeline

http://bioinformatics.oxfordjournals.org/content/29/9/1212.short?rss=1&utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%253A+bioinformatics_today+%2528Bioinformatics%2529

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

http://bioinformatics.oxfordjournals.org/content/29/9/1210.short?rss=1&utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%253A+bioinformatics_today+%2528Bioinformatics%2529

QIIME Overview Tutorial: de novo OTU picking and diversity analyses

http://qiime.org/tutorials/tutorial.html

Metagenomic analysis.

Saturday 13 April 2013

The FAM ( USP9X) Deubiquitylating Enzyme Localizes to Multiple Points of Protein Trafficking in Epithelia, where It Associates with E-cadherin and -catenin.

http://www.molbiolcell.org/content/15/4/1591.full.pdf


The FAM ( USP9X) Deubiquitylating Enzyme Localizes to Multiple Points of Protein Trafficking in Epithelia,  where It Associates with E-cadherin and -catenin.


USP9X is substrate-specific deubiquitylating enzyme highly expressed in epithelia where it interacts with its
substrate, beta -catenin.


In vivo depletion of USP9X in preimplantation mouse embryos, by addition of siRNA, resulted in a parallel decrease in beta -catenin.

It proves USP9X to be a member of Beta-catenin related pathway.


Cancer Genome Landscapes

http://www.sciencemag.org/content/339/6127/1546

Bert volelstein discusses about the core signalling pathways in human cancers.

Differential principal component analysis of ChIP-seq

http://www.pnas.org/content/early/2013/04/05/1204398110.short

Principal component analysis of chip-seq.

How to identify cancer drivers from tumor somatic mutations?

How to identify cancer drivers from tumor somatic mutations?

http://bg.upf.edu/blog/2012/07/how-to-identify-cancer-drivers-from-tumor-somatic-mutations/

Up, Up, and Array | The Scientist Magazine(R)

http://www.the-scientist.com/?articles.view/articleNo/34779/title/Up--Up--and-Array/

Biography of Todd golub.

Inspiring article.

Form and function : Nature News & Comment

Stories on ENCODE coding and non-coding claims.

USP9x - Smad4 Interaction

http://www.cell.com/retrieve/pii/S0092867408014451



FAM/USP9x, a deubiquitinating enzyme essential for TGFbeta signaling, controls Smad4 monoubiquitination.

Stephen Piccolo' group pointed out that loss of USP9x helps in the promotion of cancer progression through TGF-beta signalling.


http://www.pnas.org/content/109/10/3879.long#ref-23

Read the entire story on

Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing


by Todd Golub team.

Interesting Findings:

Somatic mutations found in  MYD88CARD11EZH2, and CREBBP genes with additional new drivers in MEF2BMLL2,BTG1GNA13ACTBP2RY8PCLO, and TNFRSF14.