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Proteome-wide discovery of mislocated proteins in cancer.

Lee, KiYoung Byun, Kyunghee Hong, Wonpyo Chuang, Han-Yu Pack, Chan-Gi Bayarsaikhan, Enkhjargal Paek, Sun Ha Kim, Hyosil Shin, Hye Young Ideker, Trey ...

Published in Genome research

Several studies have sought systematically to identify protein subcellular locations, but an even larger task is to map which of these proteins conditionally relocates in disease (the mislocalizome). Here, we report an integrative computational framework for mapping conditional location and mislocation of proteins on a proteome-wide scale, called a...

Genome-wide profiling of salt fractions maps physical properties of chromatin.

Henikoff, Steven Henikoff, Jorja G Sakai, Akiko Loeb, Gabriel B Ahmad, Kami

Published in Genome research

We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosome...

Systematic identification of functional orthologs based on protein network comparison.

Bandyopadhyay, S Sharan, R Trey Ideker

Published in Genome Research

Annotating protein function across species is an important task that is often complicated by the presence of large paralogous gene families. Here, we report a novel strategy for identifying functionally related proteins that supplements sequence-based comparisons with information on conserved protein-protein interactions. First, the protein interac...

Coevolution within a transcriptional network by compensatory trans and cis mutations.

Kuo, D Kate Licon Bandyopadhyay, S Chuang, R Luo, C Catalana, J Ravasi, T Tan, K Trey Ideker

Published in Genome Research

Transcriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis-acting DNA sequences near genes as the main cause of divergence. What is less clear is how these changes interact wit...

Mining SNPs from EST databases.

Picoult-Newberg, L Trey Ideker Pohl, Mg Taylor, Sl Donaldson, Ma Nickerson, Da Boyce-Jacino, M

Published in Genome Research

There is considerable interest in the discovery and characterization of single nucleotide polymorphisms (SNPs) to enable the analysis of the potential relationships between human genotype and phenotype. Here we present a strategy that permits the rapid discovery of SNPs from publicly available expressed sequence tag (EST) databases. From a set of E...

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Shannon, P Markiel, A Ozier, O Baliga, Ns Wang, Jt Ramage, D Amin, N Schwikowski, B Trey Ideker

Published in Genome Research

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of pr...

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