Bark, Steven J Wegrzyn, Jill Taupenot, Laurent Ziegler, Michael O'Connor, Daniel T Ma, Qi Smoot, Michael Ideker, Trey Hook, Vivian
Published in
PloS one
Secretory vesicles are required for release of chemical messengers to mediate intercellular signaling among human biological systems. It is necessary to define the organization of the protein architecture of the 'human' dense core secretory vesicles (DCSV) to understand mechanisms for secretion of signaling molecules essential for cellular regulato...
Emig-Agius, Dorothea Olivieri, Kevin Pache, Lars Shih, Hsin Ling Pustovalova, Olga Bessarabova, Marina Young, John A T Chanda, Sumit K Ideker, Trey
Published in
PloS one
Recent proteomic and genetic studies have aimed to identify a complete network of interactions between HIV and human proteins and genes. This HIV-human interaction network provides invaluable information as to how HIV exploits the host machinery and can be used as a starting point for further functional analyses. We integrated this network with com...
Bean, Gordon J Jaeger, Philipp A Bahr, Sondra Ideker, Trey
Published in
PloS one
High-throughput genetic screens in model microbial organisms are a primary means of interrogating biological systems. In numerous cases, such screens have identified the genes that underlie a particular phenotype or a set of gene-gene, gene-environment or protein-protein interactions, which are then used to construct highly informative network maps...
Gross, Andrew M Kreisberg, Jason F Ideker, Trey
Published in
PloS one
To identify the transcriptional regulatory changes that are most widespread in solid tumors, we performed a pan-cancer analysis using over 600 pairs of tumors and adjacent normal tissues profiled in The Cancer Genome Atlas (TCGA). Frequency of upregulation was calculated across mRNA expression levels, microRNA expression levels and CpG methylation ...
Joshi, Shweta Singh, Alok R Zulcic, Muamera Bao, Lei Messer, Karen Ideker, Trey Dutkowski, Janusz Durden, Donald L
Published in
PloS one
Although it is well-established that the macrophage M1 to M2 transition plays a role in tumor progression, the molecular basis for this process remains incompletely understood. Herein, we demonstrate that the small GTPase, Rac2 controls macrophage M1 to M2 differentiation and the metastatic phenotype in vivo. Using a genetic approach, combined with...
