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To first investigate whether the genes included in the Module are associated with cell wall synthesis or modifications, we analyzed the genes for MapMan ontology term associations [ 77].
However, changes in the H3K4me3 mark (and histone acetylation) due to the loss of REST were significantly correlated with changes in gene expression, while the other histone modifications we analyzed were not.
To evaluate if the molecular changes observed in activated microglia upon exposure to MMF correlates with relevant functional modifications, we analyzed phagocytic function and intracellular Ca2+ concentration ([Ca2+]i), which are linked to executive microglia function such as release of pro- and anti-inflammatory cytokines, nitric oxide or trophic factors [ 7].
To determine where the antibody bound nonspecifically to other histone modifications, we analyzed the ability to detect any signal in H2AV, a mutation that results in a failure to make H2AV (van Daal and Elgin 1992) and compared with to wild-type tissue.
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Finally, in the absence of experimental evidences supporting a selective modification, we analyzed the effect of the double sulfoxidation replacing the sulfur atoms of M206 and M213 side chains by sulfoxide groups.
To determine whether adult lifespan extension in oga-1 mutants arises from excessive O-GlcNAc-modifications, we analyzed the lifespan of the oga-1; ogt-1 double mutant which has a markedly reduced level of O-GlcNAc-modified proteins similar to the ogt-1 mutant (data not shown).
To identify the potential lysine residue (s) for sumo modification, we analyzed Kif18A amino acid sequences for optimal sumoylation using the criteria available at Abgent Inc.
To further explore whether ASHM genes could lead to differences in histone modification, we analyzed the differential modification genes of H3K27me3 or H3K36me3 modifications between the F1 hybrid and the parents.
To further substantiate our hypothesis of the interaction between tyrosine phosphorylation and O-GlcNAc modification, we analyzed the tyrosine phosphorylation status of all O-GlcNAc modified proteins curated at PhosphoSitePlus® http://www.phosphosite.org along with phosphoproteomes [ 12].
Furthermore, we produced new genome-wide maps for seven histone modifications, and we analyzed, for the first time in S. cerevisiae, the genome-wide profile of acetylation of lysine 8 of H4.
To investigate the role of epigenetic modifications in FSHD, we analyzed patterns of DNA methylation at the 4q35 D4Z4 array in family cohorts of myogenic cells from FSHD1-affected subjects, FSHD1-nonmanifesting carriers, and healthy controls.
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