http://www.nature.com/ncomms/2014/140409/ncomms4644/full/ncomms4644.html
Archive for the 'SciLit' Category
Access : Surfing the p53 network : Nature
April 12, 2014Original article emphasizing the importance of networks to cancer
http://www.nature.com/nature/journal/v408/n6810/full/408307a0.html
A paper that was done by Vogelstein, Lane and Levine in Nature (2000, November 16) that talks about how cancer is associated with a network and these network of genes associated with p53. This is in response to the idea that p53 is such a crucial molecule in cancer as a tumor suppressor and it marks well known cancer biologists discussing this from a network perspective.
Three-Dimensional Genome Architecture Influences Partner Selection for Chromosomal Translocations in Human Disease
April 10, 2014QT:"We show that many translocation-prone pairs of regions genome-wide, including the cancer translocation partners BCR-ABL and MYC-IGH, display elevated Hi-C contact frequencies in normal human cells."
Overlap of Hi-C & gene fusions
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0044196
Synonymous mutations as driver mutations for cancer
April 10, 2014Developmental dynamics and disease potential of random monoallelic gene expression.
April 6, 2014Developmental dynamics… of random monoallelic gene expression. #RNAseq on 100s of instances without causative SNPs
An analysis of differentiated cell lines.
http://www.cell.com/developmental-cell/abstract/S1534-5807(14)00057-4
The Transcription Factor Titration Effect Dictates Level of Gene Expression
April 6, 2014Interesting study looking at the effect of gene duplication on TF binding
"…when a TF is shared among many binding sites, either due to multiple identical copies of a gene regulated by that TF or due to unrelated genes that also independently bind the TF, the correlation in occupancy between the binding sites will lead to a complex dosage response to that TF." http://www.cell.com/abstract/S0092-8674(14)00221-9
Genome-wide signals of positive selection in human evolution
April 6, 2014http://genome.cshlp.org/content/early/2014/03/11/gr.164822.113.abstract
“We further demonstrate that the observed signatures of positive selection correlate better with the presence of regulatory sequences, as predicted by the ENCODE Project Consortium, than with the positions of amino acid substitutions. Our results suggest that adaptation was frequent in human evolution and provide support for the hypothesis of King and Wilson that adaptive divergence is primarily driven by regulatory changes.”
Similar to conclusion positive-section section in FunSeq paper
Finding the lost treasures in exome sequencing data
April 6, 2014Finding lost treasures in #exome sequencing data. Mining off-target, often noncoding, reads from 1000G, TCGA, ESP, &c
http://www.ncbi.nlm.nih.gov/pubmed/23972387
paper on cancer driver genes in RECOMB 2014
April 6, 2014paper from RECOMB 2014 might be interesting to you, which uses
hitting time in random walk to identify cancer drivers.
http://link.springer.com/chapter/10.1007%2F978-3-319-05269-4_23
HIT.nDRIVE: Multi-Driver Gene Prioritization based on Hitting Time
Raunak Shrestha, Ermin Hodzic, Jake Yeung, Kendric Wang, Thomas
Sauerwald, Phuong Dao, Shawn Anderson, Himisha Beltran, Mark A. Rubin,
Colin Collins, Gholamreza Haffari and S. Cenk Sahinalp.
After TopHat, Bowtie and Cufflinks — here’s Ballgown !
April 6, 2014“Flexible isoform-level differential expression analysis with Ballgown” http://biorxiv.org/content/early/2014/03/30/003665
linkstream2 microblog 