Seeking gene relationships in gene expression data using support vector machine regression-0

Morley et al. [2]. The Affymetrix probeset IDs are listed in parentheses.<p><b>Copyright information:</b></p><p>Taken from "Seeking gene relationships in gene expression data using support vector machine regression"</p><p>http://www.biomedcentral.com/1753-6561/1/S1/S51</p><p>BMC Proceedings 2007;1(Suppl 1):S51-S51.</p><p>Published online 18 Dec 2007</p><p>PMCID:PMC2367560.</p><p></p

Seeking gene relationships in gene expression data using support vector machine regression-4

The gene pool hit a group of genes that formed set A. The pathway reconstruction was done using 4.0 (Ariadne Genomics, Inc.).<p><b>Copyright information:</b></p><p>Taken from "Seeking gene relationships in gene expression data using support vector machine regression"</p><p>http://www.biomedcentral.com/1753-6561/1/S1/S51</p><p>BMC Proceedings 2007;1(Suppl 1):S51-S51.</p><p>Published online 18 Dec 2007</p><p>PMCID:PMC2367560.</p><p></p

Seeking gene relationships in gene expression data using support vector machine regression-2

Protein genes. Group A is the genes selected for the SVMR training set. Groups B and C are the genes that were targeted and captured in two separate SVMR searches.<p><b>Copyright information:</b></p><p>Taken from "Seeking gene relationships in gene expression data using support vector machine regression"</p><p>http://www.biomedcentral.com/1753-6561/1/S1/S51</p><p>BMC Proceedings 2007;1(Suppl 1):S51-S51.</p><p>Published online 18 Dec 2007</p><p>PMCID:PMC2367560.</p><p></p

Seeking gene relationships in gene expression data using support vector machine regression-1

Iological group, ribosomal proteins. A1 and A2 are from the same gene, . Correlation coefficients for expression of genes and are > 0.987, but they appear to share no direct biological relationship, even though their NPL LOD score distributions show high similarity as well.<p><b>Copyright information:</b></p><p>Taken from "Seeking gene relationships in gene expression data using support vector machine regression"</p><p>http://www.biomedcentral.com/1753-6561/1/S1/S51</p><p>BMC Proceedings 2007;1(Suppl 1):S51-S51.</p><p>Published online 18 Dec 2007</p><p>PMCID:PMC2367560.</p><p></p

Additional file 2: of MAPK1/ERK2 as novel target genes for pain in head and neck cancer patients

Information of the 800 SNPs within the 82 IPA-selected genes from the Illumina HumanOmniExpress-12v1 platform. (DOCX 72 kb

Crystallographic data and refinement information.

a<p>Numbers in parenthesis are for the highest resolution shell (3.06-2.90).</p>b<p>R_sym = Σ|I_h−h>|/ΣI_h over all h, where I_h is the intensity of reflection h.</p>c<p>R_cryst and R_free = Σ∥F_o|−|F_c∥/Σ|F_o|, where F_o and F_c are observed and calculated amplitudes, respectively. Rfree was calculated using 5% of data excluded from the refinement.</p

Co-crystal structure of argyrin B bound to <i>P.aeruginosa</i> EF-G1.

<p>(<b>A</b>) The argyrin B binding pocket localizes to the flexible interface between domains III and V, distinct from the GTP/fusidic acid binding domain (**). (<b>B</b>) Inset view. (<b>C</b>) 2D protein-ligand interaction plot showing the chemical structure of the argyrin B macrocyclic polypeptide and the hydrophobic (cyan) and hydrophilic (yellow) amino-acid residues in EF-G1 which are in binding contact. (<b>D</b>) Interactions between <i>P. aeruginosa</i> EF-G (domain III in yellow and domain V in cyan) and argyrin B (gray). (<b>E</b>) Superposition of Thermus thermophilus EF-G in complex with GTP (magenta), Thermus thermophilus EF-G in complex with the ribosome (ribosome not shown) and fuscidic acid (cyan), and structure of the argyrin B-bound Pseudomonas aeroginosa EF-G (FusA1) (yellow). Superposition was done using domains I and II of each of the protein structures.</p

Key residues involved in resistance to argyrin B are conserved in EF-G homologues.

<p>The amino acid sequence of <i>P. aeruginosa</i> EF-G1 was used to identify EF-G homologues in the indicated organisms by a BLAST search. EF-G sequences were then aligned using ClustalW, and residues conferring resistance to argyrin B are shown in bold.</p

Susceptibility of representative bacteria and resistant mutants to argyrin B.

<p>Susceptibility determinations were conducted using the broth microdilution protocol as described previously <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042657#pone.0042657-Caughlan1" target="_blank">[26]</a>.</p>*<p>Argyrin B was not uniformly soluble and occasionally a small amount of precipitate was visible at concentrations greater than 16–32 µg/ml; therefore values here are reported as susceptibility rather than MIC. Selected on 128^a, 2^b, 4^c, or 16^d µg/ml argyrin B in solid Mueller-Hinton agar.</p

The mode of action of argyrin B is conserved in mammalian cells.

<p>(<b>A</b>) Cytotoxicity profile of argyrin B across 512 mammalian cell lines showing reduced cell viability with an IC₅₀ below 1 µM in 18 cell lines (red). (<b>B</b>) Susceptibility to argyrin B (IC₅₀ and A_max values) was compared to different cytotoxic agents across the cell line panel by calculating Pearson correlation values. (<b>C</b>) RKO and HCT116 cells were treated for 4 days with 1 µM argyrin B, and total proteins were extracted and analyzed by immunoblotting for SDHA and COX2. (<b>D</b>) Cells were transfected with non-targeting (NT) or GFM1 (encoding mEF-G1) siRNA for 7 days, and total proteins were extracted and analyzed by immunoblotting for mEF-G1 and GAPDH. (<b>E</b>) siRNA-transfected cells were treated for 7 days with increasing doses of Argyrin B or MG132, and cell viability was assessed using CellTiter Glo. A representative example of three independent experiments is shown.</p