Posts Tagged ‘encodenets’

uri alon’s coherent/incoherent ffls

March 9, 2017

Function of the FFL network motif
http://www.PNAS.org/content/100/21/11980.abstract Decade-old work defining coherent & incoherent ones based on activation/repression

http://sites.fas.harvard.edu/~mcb195/lectures/Networks-II/Literature/pnas_Mangan03.pdf

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.

The Transcription Factor Titration Effect Dictates Level of Gene Expression

April 6, 2014

Interesting 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

correlated noise in TF co-association / FFLs

March 9, 2013

http://dx.doi.org/10.1016/j.bpj.2013.01.033

Cross Talk and Interference Enhance Information Capacity of a Signaling Pathway Sahand Hormoz
QT:”
A recurring motif in gene regulatory networks is transcription factors (TFs) that regulate each other and then bind to overlapping sites on DNA, where they interact and synergistically control transcription of a target gene. Here, we suggest that this motif maximizes information flow in a noisy network. Gene expression is an inherently noisy process due to thermal fluctuations and the small number of molecules involved. A consequence of multiple TFs interacting at overlapping binding sites is that their binding noise becomes correlated. Using concepts from information theory, we show that in general a signaling pathway transmits more information if 1), noise of one input is correlated with that of the other; and 2), input signals are not chosen independently.

What were the top papers of 2012 on social media? : Nature News Blog

March 8, 2013

http://blogs.nature.com/news/2012/12/what-were-the-top-papers-of-2012-on-social-media.html encodenets within one of the top-10 lists