User:Robert M. MacCallum/WTFGSB Reportback: Difference between revisions
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A review of several years' network work. Including some Venter ocean sample sequence analysis (map to pathways, correlate with environmental factors with some canonical ..... method (is this like bi-clustering?)) | A review of several years' network work. Including some Venter ocean sample sequence analysis (map to pathways, correlate with environmental factors with some canonical ..... method (is this like bi-clustering?)) | ||
==Day two== | ==Day two, am== | ||
===Seth Grant=== | ===Seth Grant=== | ||
Revision as of 04:35, 1 December 2009
Welcome Trust Functional Genomics and Systems Biology Workshop
30 November to 1 December 2009
Day one
Edison Liu
Estrogen (or is it EGF) receptor (ER) binding site analysis (ChIP and bioinf) - "Cosmic" score, correlation with RNA PolII binding and H3K4meX marks.
Some functional binding is 1Mb away from gene!! Only 9% in 5k "promoter".
Cool ChIA-PET (ChiA-seq) method to determine chromosomal loops.
Looping for efficient transcription, grouping of coregulated genes ("looped out" genes don't respond to ER)
Johan Rung
GWAS for type 2 diabetes
F Pradezynski
Y2H between various virus proteomes and human proteins.
Many human pathways interfered with, in particular the ones you'd expect (interferon reponse)
Seems to be a remarkable number of targets (100s) from such a few viral proteins.
Chris Bakal
Wounding, cell morphology, image analysis -> 100+ feature profile of cell's, morphology.
"canalised" morphology space (jumps between states)
Keith Baggerly
Reproducibility in hi-thru biology
More to come on this
Nick Luscombe
Nuclear lamins known to tether transcriptionally inactive DNA
Nucleoporins now shown to be assoc with active gene expression.
Also through ChIP some proteins bind to enable X chromosome dosage compensation.
Mark Gerstein
A review of several years' network work. Including some Venter ocean sample sequence analysis (map to pathways, correlate with environmental factors with some canonical ..... method (is this like bi-clustering?))
Day two, am
Seth Grant
Complexity of post-synaptic molecular machinery (several thousand proteins). Conserved in invertebrates (50% of prots) and single celled (25%). Evolution of the machinery (including plasticity) preceded evolution of synapses.
Very slow evolution.
Many diseases.
Caleb Webber
CNV in mouse
What's special about pathological CNVs? (vs. benign)
Human CNVs look up mouse phenotypes (somehow!)
Enrichment!
Florian Markowetz
ES cell histone modifications
days 1 3 5 of ES development - 4 analyses
Protein MS ChIP-chip histone Rna pol II Microarrays
day 0 nanog TF downreg -> network of TFs
clustering of smoothed histone profiles (around TSS)
when mRNA upreg, small local acetylation around TSS when mRNA down, wider deacetylation around TSS.
increased correlation between H acet and gene expression through time (more at day 5 than day 1) genome-wide
predict gene expr from histone acetylation using LOTS of ML methods (in R)
Grant Belgard
brain transcriptomics
by sequencing
6 layers of neocortex
many cell types spanning several layers
paired end 50bp reads
(you get some intronic reads)
some intergenic regions detected (a few percent of reads)
layer specific genes, various layers show various GO enrichments.
John Hogenesch
Circadian clock genes through hi-thru func genomics. nice robot video.
siRNA screen (seems to be tunable to desired knockdown level)
clock pathway is robust - surprising lack of lethal knock outs
