linkstream2 microblog

RUNX1 is most connected in TLX1 & 3 expr. net. It’s a tumor suppressor disabled by LOF mutations.

Rev. engineering…identifies RUNX1 as tumor suppressor in T-ALL http://www.nature.com/nm/journal/v18/n3/full/nm.2610.html It’s the most connected TF in the expression network

Nat Med. Author manuscript; available in PMC 2012 Sep 1.
Nat Med. 2012 Feb 26; 18(3): 436–440.
Published online 2012 Feb 26. doi: 10.1038/nm.2610

Giusy Della Gatta,1 Teresa Palomero,1,2 Arianne Perez-Garcia,1 Alberto Ambesi-Impiombato,1 Mukesh Bansal,3Zachary W. Carpenter,1 Kim De Keersmaecker,4,5 Xavier Sole,6,7 Luyao Xu,1 Elisabeth Paietta,8,9 Janis Racevskis,8,9Peter H Wiernik,8,9 Jacob M Rowe,10 Jules P Meijerink,11 Andrea Califano,1,3 and Adolfo A. Ferrando1,2,12

Is Biomedical Innovation Happening Outside the Peer-Reviewed Literature? http://jama.jamanetwork.com/article.aspx?articleid=2110977 Focuses on diagnostics company, #Theranos

QT:{{”
This Viewpoint discusses the need for scientific transparency when biomedical innovation takes place outside of the peer-reviewed literature.
“}}

by J Ioannidis

From noncoding variant to phenotype…at…#cholesterol locus http://www.nature.com/nature/journal/v466/n7307/full/nature09266.html
Gold standard ex of #SNP functional effect: LDL changes

Kiran Musunuru,
Alanna Strong,
Maria Frank-Kamenetsky,
et al.

Nature 466, 714–719 (05 August 2010) doi:10.1038/nature09266

Changes LDL level

Disease-disease relationships through the incomplete interactome, by @barabasi http://www.sciencemag.org/content/347/6224/1257601.abstract #Network modules for 226 diseases

QT:{{”
Altogether, disease genes associated with 226 of the 299 diseases show a statistically significant tendency to form disease modules based on both Si andP(ds) (fig. S4).
“}}

Genome sequence-independent identification of #RNA editing
siteshttp://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3314.html GIREMI uses LD to separate edit sites from #SNPs

Qing Zhang
& Xinshu Xiao

Nature Methods (2015) doi:10.1038/nmeth.3314Received

Linking #signaling pathways [phospho-proteins in samples] to transcriptional programs [TFs & targets], via matrices
http://genome.cshlp.org/content/24/11/1869.long

More verbosely:
using matrices to linking TF & targets and phosphorsylated proteins in particular samples to gene expression in specific samples

Linking signaling pathways to transcriptional programs in breast cancer

Hatice U. Osmanbeyoglu1,
Raphael Pelossof1,
Jacqueline F. Bromberg2 and
Christina S. Leslie1

Genome Research

Convergent…specializations in brains of humans & songbirds http://www.sciencemag.org/content/346/6215/1256846.long Both have matching expression patterns across regions

Statistical Basis for Predicting Technological Progress

http://trancik.scripts.mit.edu/home/data/
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052669

Béla Nagy,
J. Doyne Farmer,
Quan M. Bui,
Jessika E. Trancik

Published: February 28, 2013
DOI: 10.1371/journal.pone.0052669

http://www.sciencemag.org/content/early/2009/12/10/science.1181421

Published Online December 10 2009

Science DOI: 10.1126/science.1181421

REPORT

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

Sergei Nechaev1,
David C. Fargo2,
Gilberto dos Santos1,
Liwen Liu3,
Yuan Gao4 and
Karen Adelman1,*

http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html