Celltype & region–resolved mouse brain proteome
http://www.nature.com/neuro/journal/v18/n12/full/nn.4160.html proteins enriched there v liver & in specific regions (eg NCX v STR)
http://www.nature.com/neuro/journal/v18/n12/full/nn.4160.html
Posts Tagged ‘brainspan’
Cell type- and brain region-resolved mouse brain proteome : Nature Neuroscience : Nature Publishing Group
December 13, 2015Understanding multicellular function and disease with human tissue-specific networks : Nature Genetics : Nature Publishing Group
November 28, 2015Human tissue-specific #networks by @TroyanskayaLab
http://www.nature.com/ng/journal/v47/n6/full/ng.3259.html
Brain-specific ones & NetWAS approach for combining #GWAS genes
access all tissue networks including the brain-specific
networks at giant.princeton.edu
expression patterns in brain
November 18, 2015Canonical genetic signatures [across 132 structures] of the adult human #brain [in 6 individuals]
http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4171.html HT @ozgunharmanci
QT:{{”
We applied a correlation-based metric called differential stability to assess reproducibility of gene expression patterning across 132 structures in six individual brains, revealing mesoscale genetic organization. The genes with the highest differential stability are highly biologically relevant, with enrichment for brain-related annotations, disease associations, drug targets and literature citations.
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Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events : Nature Biotechnology : Nature Publishing Group
June 25, 2015#Transcriptome analysis [focusing on brain tissue]
using…long-read[s]…reveals…co-association of
distant…exonshttp://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.3242.html
Mostly protein coding genes
His brain, her brain?
May 13, 2015His brain, her brain? http://www.sciencemag.org/content/346/6212/915.summary Neurosexism potentially results from multiple testing & only publishing positives
Convergent transcriptional specializations in the brains of humans and song-learning birds
March 15, 2015Convergent…specializations in brains of humans & songbirds http://www.sciencemag.org/content/346/6215/1256846.long Both have matching expression patterns across regions
Sign in to read: Brain boosting: It’s not just grey matter that matters – life – 18 February 2015 – Control – New Scientist
March 8, 2015Brain boosting: It’s not just grey matter that matters http://www.newscientist.com/article/mg22530090.600-brain-boosting-its-not-just-grey-matter-that-matters.html Learning involves changes to myelin sheaths, not just synapses
Genotype to phenotype relationships in autism spectrum disorders : Nature Neuroscience : Nature Publishing Group
February 26, 2015Genotype to phenotype relationships in ASD http://www.nature.com/neuro/journal/v18/n2/abs/nn.3907.html Expression differences in #brain development for LOF-containing, M v F, &c
Also, netbag finds subnets assoc w autism
NEw paper using BrainSpan data
January 12, 2015The discovery of integrated gene networks for autism and related disorders
Fereydoun Hormozdiari
Osnat Penn
Elhanan Borenstein
Evan E. Eichler
Published in Advance November 5, 2014, doi:10.1101/gr.178855.114 Genome Res. 2015. 25: 142-154
QT:{{”
Motivated by this observation, we have developed a novel method that simultaneously integrates information from both PPI and coexpression networks to identify highly connected modules in both types of networks that are also enriched in mutations in cases and not in controls. We call this method MAGI, short for merging affected genes into integrated networks. MAGI is based on a combinatorial
optimization algorithm that aims to maximize the number of mutations in the modules while accounting for gene length and distribution of putative LoF and missense mutations in cases and controls. MAGI is generic and can be applied to any disease, given a list of de novo mutations in cases and relevant coexpression information. Using neurodevelopmental RNA-seq data from the BrainSpan Atlas
(http://www.brainspan.org/), we have applied it to exome sequence data generated from ASD, ID, epilepsy, and schizophrenia, providing a comprehensive comparison of common and specific gene modules for these diseases.
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Blood transciptome paper
September 28, 2014Splicing changes along the blood lineage, good ex. of the
state-of-the-art in human transcriptomics
http://www.sciencemag.org/content/345/6204/1251033.abstract
Science 26 September 2014:
Vol. 345 no. 6204
DOI: 10.1126/science.1251033
Transcriptional diversity during lineage commitment of human blood progenitors
Chen et al.
linkstream2 microblog 