12 research outputs found

    Image1_Construction of ceRNA network and identification of hub genes in aniridia-associated keratopathy using bioinformatics analysis.JPEG

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    Aniridia-associated keratopathy (AAK) is characteristic at ocular surface of aniridia caused by haploinsufficiency of PAX6. Competing endogenous RNA (ceRNA) has been reported to play an important role in various diseases, whereas its function on AAK is unclear. The microarray data of 20 AAK patients and 20 healthy people were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed lncRNAs, miRNAs, and mRNAs were analyzed using “limma” packages and weighted gene co-expression network analysis (WGCNA). A ceRNA network was constructed by Cytoscape 3.9.1, and miR-224-5p, miR-30a-5p, and miR-204-5p were at the center of the network. CIBERSORTx algorithm and ssGSEA analyses revealed that AAK was associated with immune cell infiltration, showing that activated Mast cells increased while resting Mast cells decreased and NK cells decreased in AAK. Type II INF Response, CCR, parainflammation, T cell co-stimulation, and APC co-stimulation of AAK patients differed from healthy individuals. Additionally, the ROC curve of five genes, MITF(AUC = 0.988), RHOB(AUC = 0.973), JUN(AUC = 0.953), PLAUR (AUC = 0.925), and ARG2 (AUC = 0.915) with high confidence in predicting AAK were identified. Gene set enrichment analysis (GSEA) analysis of hub genes enriched in the IL-17 signaling pathway.</p

    Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails-10

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    <p><b>Copyright information:</b></p><p>Taken from "Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails"</p><p>http://www.biomedcentral.com/1472-6807/7/57</p><p>BMC Structural Biology 2007;7():57-57.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2065866.</p><p></p>5, hsCBP, hsP/CAF, hsBRG1 and the two components from TAF250. The sequences were aligned based on the experimentally determined three-dimensional structures of these bromodomains, highlighted in green. The secondary structure of Brd2 BD2 is indicated above the alignment. Residues identical in all sequences are shown in red and residues conserved are coloured in blue and residues corresponding to Z sheet (hsBRG1) and helix D are represented in yellow. The two amino acids insertion is indicated by triangle symbols (▼)

    Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails-4

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    <p><b>Copyright information:</b></p><p>Taken from "Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails"</p><p>http://www.biomedcentral.com/1472-6807/7/57</p><p>BMC Structural Biology 2007;7():57-57.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2065866.</p><p></p>an value is denoted as a solid line and the mean value plus one standard deviation as a dash line. () A ribbon diagram view mapping the binding interface of H4-AcK12 peptide on Brd2 BD2. The residues, whose combined chemical shift changes were more than the mean value plus one standard deviation and above the mean value, are colored in blue and cyan respectively. The figure B was generated in PyMOL

    Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails-0

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    <p><b>Copyright information:</b></p><p>Taken from "Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails"</p><p>http://www.biomedcentral.com/1472-6807/7/57</p><p>BMC Structural Biology 2007;7():57-57.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2065866.</p><p></p>representation of the average, energy-minimized structure with the secondary structure elements highlighted. The helix nomenclature follows that of hsP/CAF bromodomain [9]. () Contact surface emphasized surface hydrophobic potential (left) and surface electrostatic potential (right) at the acetyl-lysine binding site. Yellow denotes hydrophobic potential; red negative potential; and blue positive potential. () A clear view of showing the conserved or type conserved side chains lined the hydrophobic cavity, and denoting the negative-charged collar formed by residues D330, D338, D341, D385 and D387. A, B, C and D were produced with MOLMOL or PyMOL

    Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails-8

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    <p><b>Copyright information:</b></p><p>Taken from "Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails"</p><p>http://www.biomedcentral.com/1472-6807/7/57</p><p>BMC Structural Biology 2007;7():57-57.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2065866.</p><p></p>as a function of residue number of Brd2 BD2. Only those residues of which H-N cross-peaks are resolved enough to permit accurate measurements of their intensities are included

    Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails-1

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    <p><b>Copyright information:</b></p><p>Taken from "Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails"</p><p>http://www.biomedcentral.com/1472-6807/7/57</p><p>BMC Structural Biology 2007;7():57-57.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2065866.</p><p></p>N5, hsCBP, hsP/CAF, hsBRG1 and the two components from TAF250. The sequences were aligned based on the experimentally determined three-dimensional structures of these bromodomains, highlighted in green. The secondary structure of Brd2 BD2 is indicated above the alignment. Residues identical in all sequences are shown in red and residues conserved are coloured in blue and residues corresponding to Z sheet (hsBRG1) and helix D are represented in yellow. The two amino acids insertion is indicated by triangle symbols (▼)

    Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails-5

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    <p><b>Copyright information:</b></p><p>Taken from "Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails"</p><p>http://www.biomedcentral.com/1472-6807/7/57</p><p>BMC Structural Biology 2007;7():57-57.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2065866.</p><p></p>the unacetylated peptide H4-U. Combined chemical shift perturbation was calculated using the equation, , and R = [peptide]/[bromodomain]

    Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails-2

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    <p><b>Copyright information:</b></p><p>Taken from "Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails"</p><p>http://www.biomedcentral.com/1472-6807/7/57</p><p>BMC Structural Biology 2007;7():57-57.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2065866.</p><p></p>of Brd2 BD1 (pink) [PDB: ]. The figure was generated with MOLMOL

    Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails-7

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    <p><b>Copyright information:</b></p><p>Taken from "Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails"</p><p>http://www.biomedcentral.com/1472-6807/7/57</p><p>BMC Structural Biology 2007;7():57-57.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2065866.</p><p></p> more significant perturbed residue G335 during titrations was followed
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