QT:{{"
“The NCI will continue to supply the NCI-60 cell lines to researchers, but will eventually refocus its drug screening on newer models. It is developing hundreds of ‘patient-derived xenografts’ (PDXs), which are created by implanting small chunks of human tumours into mice. There, the tumours grow in an environment that, although not human, better mimics their native environment”
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Genes, environment & bad luck
http://science.ScienceMag.org/content/355/6331/1266 To what degree are #cancer mutations due to replication error (3rd factor), not 1st 2?
discusses R v D correlation
Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention Cristian Tomasetti1,2,*, Lu Li2, Bert Vogelstein3,*
Science 24 Mar 2017:
Vol. 355, Issue 6331, pp. 1330-1334
DOI: 10.1126/science.aaf9011
http://science.sciencemag.org/content/355/6331/1330
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 [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.
#IHECpapers rollout http://www.Cell.com/consortium/ihec Gr8 work! incl. #privacy, normal breast epigenetics, ETG links, deconvolution, #allelic activity
De novo prediction of cis-regulatory…modules through integrative analysis of a large number of ChIP datasets
http://BMCGenomics.BiomedCentral.com/articles/10.1186/1471-2164-15-1047 [1/2]
Only calls modules w/ overrepresented pairs of TFBSes – based on observation that well-known promotors have extensive co-regulation [2/2]
De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets
Meng Niu,
Ehsan S Tabari and
Zhengchang Su
lncRNA-mediated sponge regulatory network in prostate cancer http://www.nature.com/ncomms/2016/160315/ncomms10982/full/ncomms10982.html Few explicitly noted #pseudogenes besides PTENP1
Kinome-wide Decoding of #Network-Attacking Mutations Rewiring Cancer http://www.cell.com/cell/abstract/S0092-8674(15)01108-3 Mapping NAMs onto well-known signaling pathways
