23 research outputs found
Domain size distribution.
<p>Shown in pink is the density distribution of the lengths of non-capsid proteins, and that of capsid proteins is shown in blue. Viral capsid proteins appear to have overall larger domains compared to their cellular counterparts, with a few exceptionally complex domains having more than 600 residues. 600 was later used as a size cutoff in order to examine the two sets that are of comparable sizes.</p
The 21 folds covered by structural relatives of capsid proteins.
<p>14 out of these 21 folds are either greek-key or jelly-roll (the latter fold being a specific variation of the former). Remarkably, 17 folds are specific to non-capsid proteins, and are only marginally similar to capsid proteins in structure.</p
Capsid shells and the folded topology of a typical capsid protein.
<p>A) Representative icosahedral viral capsid structures with varying sizes. The Satellite Tobacco Mosaic Virus which is a Tā=ā1 virus has a radius of 8.8 nm, and the Paramecium bursaria Chlorella virus 1 (PBCV-1) which is a pTā=ā169 virus has a radius of 92.9 nm. Here pT stands for āpseudo T numberā, which simply means the subunits are not chemically identical (the primary sequences are different). These protein shells are large in that they are assembled from tens of up to hundreds of protein monomers, and they are highly symmetrical. B) The signature jelly-roll of viral capsid proteins, with 8 Ī²-strands forming two antiparallel sheets. The wedge or trapezoidal shape of this particular fold immediately reveals six flat surfaces for monomer-monomer interaction; the sides, the two loop ends and the top and the bottom. The prevalence of the jelly-roll fold among capsid proteins might be related to their relative ease for tiling.</p
Statistical significance of test statistic.
<p>No single case in the 10,000 permutations has resulted in 210 or fewer shared folds between the set of 56 protein domains and their complement set, which makes the p-value of our test statistic less than 0.0001, as an upper bound for the statistical significance.</p
The 56 representative capsid folds.
<p>Domains within one cluster are superimposed on one another to show good structural alignment, with number of members in each cluster indicated. The prevalence of singlet clusters reflects the scarcity of structural data for many viral families.</p
Additional file 1 of A Novel pyroptosis-related signature for predicting prognosis and evaluating tumor immune microenvironment in ovarian cancer
Supplementary Material 1 TableĀ 1 The clinicopathological features of ovarian cancer (OV) patients
Additional file 4 of A Novel pyroptosis-related signature for predicting prognosis and evaluating tumor immune microenvironment in ovarian cancer
Supplementary Material 4 FigureĀ 2 The clinical features of OV patients, stratified by the pyroptosis-associated 6-gene signature
Additional file 2 of A Novel pyroptosis-related signature for predicting prognosis and evaluating tumor immune microenvironment in ovarian cancer
Supplementary Material 2 TableĀ 2 Overview of the six differentially expressed pyroptosis-related
Additional file 3 of A Novel pyroptosis-related signature for predicting prognosis and evaluating tumor immune microenvironment in ovarian cancer
Supplementary Material 3 FigureĀ 1 The Principal Component Analysis (PCA) dimensionality reduction on samples from the TCGA-OV and ovarian normal tissue from GTEx based on their expression of the pyroptosis-related gene signature
Additional file 1: of Amenable epigenetic traits of dental pulp stem cells underlie high capability of xeno-free episomal reprogramming
Table S1. List of commercial and patient-derived dental stem cell samples used. Table S2. DiPS colony counts of dental pulp stem cell samples used for reprogramming under different culture conditions. Figure S1. Transduction efficiencies for reprogramming DPSCs. Figure S2. Generation of iPS cells from DPSCs in the presence of enhancer compounds. Figure S3. Time course during episomal-based reprogramming of DPSCs. Figure S4. Characterisation of DPSCs cultured in xeno-free media. Figure S5. Cytogenetics and in vivo characterisation of DiPS lines generated under xeno-free culture conditions. Table S3. List of differentially methylated regions of selected genes in DPSCs versus ASCs with respect to iPS (DiPS and AiPS) and H1 hES cell lines. Table S4. DNA methylation raw data analysed with multiple probe sets of PAX9 gene that exhibit significant differences between DPSCs and ASCs. Table S5. Top networks by ingenuity pathway analysis (IPA) for differentially methylated genes in ASCs versus AiPS cells that do not exhibit such differences in DPSCs versus DiPS cells. Figure S6. Pluripotent and self-renewal supporting characteristics of DPSCs. (ZIP 8876 kb