Posts Tagged ‘chipseq’

Inferring chromatin-bound protein complexes from genome-wide binding assays – Genome Research

February 26, 2017

Inferring [w. NMF] chromatin-bound protein complexes [of TFs] from [ENCODE ChIP-seq] binding assays, by @ElementoLab
http://genome.cshlp.org/content/23/8/1295.full

Giannopoulou E, Elemento O. 2013. Inferring chromatin-bound
protein complexes from genome-wide binding assays. Genome Research, Published in Advance April 3, 2013, doi: 10.1101/gr.149419.112.

This study uses nonnegative matrix factorization (NMF) of ENCODE CHIP-seq data (transcription
factors and histone modifications) to predict complexes of
transcription factors that bind DNA
together; it then assesses how these predicted complexes regulate gene expression. It goes beyond
previous studies in that it attempts to treat the TFs as complexes rather than individuals. A handful of
the predicted complexes correspond to known regulatory complexes, e.g. PRC2, and overall, the
complexes were enriched for known protein-protein interactions. Linear regression and random forest
models were then used to predict the effects of the complexes on the expression of adjacent genes. In
both models, the complexes performed better than those predicted from a scrambled TF read count
matrix. Overall, this study provides a large set of hypotheses for combinations of TFs that may
function together, as well as potential new components of known complexes.

PLOS Computational Biology: Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

April 3, 2016

Discovering TFBSs in…Repetitive Regions of #Genomes with Multi-Read
Analysis http://journals.PLOS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002111 CSEM uses EM to refine site occupancy

Chung D, Kuan PF, Li B, SanalKumar R, Liang K, Bresnick E, Dewey C, and Keles S (2011), “Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data,” PLoS Computational Biology, 7(7): e1002111

http://www.stat.wisc.edu/~keles/Software/multi-reads/

CSEM

https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=e18c78b20646a2aa&tool_config=database%2Fcommunity_files%2F000%2Frepo_83%2Fcsem.xml&changeset_revision=1438767ad92f

Enhancer Evolution across 20 Mammalian Species: Cell

November 28, 2015

#Enhancer Evolution across 20 Mammal[s is faster than for promoters] by @PaulFlicek lab http://www.cell.com/cell/abstract/S0092-8674(15)00007-0 H3K27ac & H3K4me3 #chipseq

http://www.cell.com/cell/abstract/S0092-8674(15)00007-0

Single-cell ChIP-seq

October 23, 2015

#Singlecell ChIPseq reveals…subpopulations defined by chromatin statehttp://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3383.html Sparse data: on order of 1K uniq. reads/cell

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3383.html

retroelement functional recruitment

May 12, 2014

DUX4 binding to #retroelements creates promoters that are active… Highlights #chipseq binding sites in #repeats
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003947 http://www.ncbi.nlm.nih.gov/pubmed/?term=24278031
PLoS Genet. 2013 Nov;9(11):e1003947. doi:
10.1371/journal.pgen.1003947. Epub 2013 Nov 21.
DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis.
Young JM, Whiddon JL, Yao Z, Kasinathan B, Snider L, Geng LN, Balog J, Tawil R, van der Maarel SM, Tapscott SJ.