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microRNAs (miRNA) play important roles in regulating immunity. Here we utilize the systems biology approach to predict the regulatory network of miRNAs among the most down-regulated genes by the lipopolysaccharides (LPS) treatment in the macrophage RAW267.4 cell line. We combine the proteome and transcriptome data sets to define 200 target genes that are(More)
In mass spectrometry-based protein quantification, peptides that are shared across different protein sequences are often discarded as being uninformative with respect to each of the parent proteins. We investigate the use of shared peptides which are ubiquitous (~50% of peptides) in mass spectrometric data-sets for accurate protein identification and(More)
Ischemia-reperfusion (I/R) has critical consequences in the heart. Recent studies on the functions of I/R-activated kinases, such as p38 mitogen-activated protein kinase (MAPK), showed that I/R injury is reduced in the hearts of transgenic mice that overexpress the p38 MAPK activator MAPK kinase 6 (MKK6). This protection may be fostered by changes in the(More)
In analyzing the proteome using mass spectrometry, the mass values help identify the molecules, and the intensities help quantify them, relative to their abundance in other samples. Peptides that are shared across different protein sequences are typically discarded as being uninformative w.r.t each of the parent proteins. In this paper, we investigate the(More)
Fibrosis is a pervasive disease in which the excessive deposition of extracellular matrix (ECM) compromises tissue function. Although the underlying mechanisms are mostly unknown, matrix stiffness is increasingly appreciated as a contributor to fibrosis rather than merely a manifestation of the disease. Here we show that the loss of Fibulin-5, an elastic(More)
The community working on model organisms is growing steadily and the number of model organisms for which proteome data are being generated is continuously increasing. To standardize efforts and to make optimal use of proteomics data acquired from model organisms, a new Human Proteome Organisation (HUPO) initiative on model organism proteomes (iMOP) was(More)
kinase kinase 6 overexpress the p38 MAP kinase activator, MAP proteins in the hearts of transgenic mice that Alterations in oxidative phosphorylation complex You might find this additional info useful... α Transcriptional control of mitochondrial biogenesis: the central role of PGC-1 α Transcriptional control of mitochondrial biogenesis: the central role of(More)
Eukaryotic RNA polymerase II contains a C-terminal repeated domain (CTD) consisting of 52 consensus heptad repeats of Y1S2P3T4S5P6S7 that mediate interactions with many cellular proteins to regulate transcription elongation, RNA processing and chromatin structure. A number of CTD-binding proteins have been identified and the crystal structures of several(More)
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