recent publication from the Donnelly group comparing using GENCODE or Refeq annotation when predicting variants effects.
Choice of transcripts and software has a large effect on variant annotation
Genome Medicine 2014, 6:26 doi:10.1186/gm543
Posts Tagged ‘from’
Encode-annotation interesting paper
April 14, 2014Three-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, 2014Citi Bike Rides: September 17th & 18th, 2013 on Vimeo
April 7, 2014Citi #Bike Rides 9/17/2013. Great #visualization of daily #network dynamics. Neat if applicable to cellular networks
http://vimeo.com/89305412
Developmental 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
