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39 results for “protein clustering”
Supplementary Data Files for the paper "Intrinsically disordered compositional bias in proteins: Sequence traits, region clustering, and generation of hypothetical functional associations"
<div> <div> <div> <div> <p><strong>Supplementary data files relating to <a href="https://doi.org/10.1177/11779322241287485">https://doi.org/10.1177/11779322241287485. </a></strong></p> <p><strong><span>Suppl. File 1: Protein Family Clusters.</span></strong></p> <p><strong><span>Suppl. File 2: Cluster GO enrichments/depletions. </span></strong></p> <p><strong><span>Suppl. File 3: The raw ID-CBR data with annotations. </span></strong></p> <p><strong><span>Suppl. File 4: ­ID-CBR Cluster membership.</span></strong></p> <p><strong><span>Each file has an explanatory header. </span></strong></p> <p> </p> </div> </div> </div> </div>
Supplementary Movies and Source Data for: Quantitative real-time in-cell imaging reveals heterogeneous clusters of proteins prior to condensation
<p>Supplementary Movies and raw data for the manuscript: "Quantitative real-time in-cell imaging reveals heterogeneous clusters of proteins prior to condensation":</p> <p>Source_Data.zip: Supplementary Code, Supplementary Data and Weka Analysis</p> <p>Lan_supplementary_movies_AVI.zip: Supplementary movies as AVI</p> <p>Lan_supplementary_movies_MP4.zip: Supplementary movies as MP4</p> <p>Lan_raw_movies.zip: Raw TIFF stacks of the movies.</p> <p>Lan_supplementary_movies.zip: Old version of the movies.</p>
Fig. 3 in Cluster Analysis of Non-conserved Proteins of Trypanosoma cruzi Reference Strains Displays Parity between these Groupings (Peptidemes) and the Consensually Accepted Parasite Lineages
Fig. 3. Phenogram of the peptidemes (P) of eight Trypanosoma cruzi reference strains obtained using the SM coefficient and the UPGMA clustering algorithm, based on data from non-conserved proteins, as seen in SDS-PAGE analysis. The major peptidemes are indicated as mP 1 and mP 2. Their subgroups are identified on the right (P II, P VI, P I), and were numbered following their respective genetic types (TcII, TcVI, TcI), as currently used.
Fig. 1 in Cluster Analysis of Non-conserved Proteins of Trypanosoma cruzi Reference Strains Displays Parity between these Groupings (Peptidemes) and the Consensually Accepted Parasite Lineages
Fig. 1. Total protein profiles of eight Trypanosoma cruzi reference strains separated in 10% SDS-PAGE at 250 V, 25 mA, 90 min, and stained by Coomassie brilliant blue. The position of some conserved proteins is indicated on the right. M: molecular mass markers. (kDa) are indicated on the left.
Fig. 2 in Cluster Analysis of Non-conserved Proteins of Trypanosoma cruzi Reference Strains Displays Parity between these Groupings (Peptidemes) and the Consensually Accepted Parasite Lineages
Fig. 2. Diagrammatic representation of the twenty-two protein bands not shared by all Trypanosoma cruzi reference strains (nonconserved proteins), as visualized in SDS-PAGE. These bands were coded and analyzed by numerical taxonomy procedures. At the top is indicated the number of the major groups they belong, as identified by different approaches. The bands that were exclusive of one or more strains were highlighted with rectangles. M: molecular mass markers. (kDa) are indicated on the left.
Curation of Vibrio biofilm matrix cluster and associated proteins
<p>The supplementary data and other supporting materials for the paper titled "Comprehensive Genomic and Evolutionary Analysis of Biofilm Matrix Clusters and Proteins in the <em>Vibrio </em>Genus".</p>
Mp4-Version of the supplementary Movies for the manuscript: "Quantitative real-time in-cell imaging reveals heterogeneous clusters of proteins prior to condensation"
<p>Videos in 'mp4'-format of the 8 supplementary movies for the manuscript: "Quantitative real-time in-cell imaging reveals heterogeneous clusters of proteins prior to condensation"</p>
Raw Diffraction Images: Formation of a highly dense tetra rhenium cluster in a protein crystal and its implications in medical imaging.
<p>Exploration of a “time on shelf” protein structure containing the radiopharmaceutical synthon <em>fac</em>-[Re(CO)<sub>3</sub>(H<sub>2</sub>O)<sub>3</sub>]<sup>+ </sup>as an <em>in vivo</em> reaction vessel to form tetranuclear rhenium clusters appropriate for theranostic applications.That a protein crystal can serve as a chemical reaction vessel is intrinsically fascinating. That it can produce an electron dense tetranuclear rhenium cluster compound from a rhenium tricarbonyl tribromo starting compound adds to the fascination. The cluster has been synthesised before in vitro when it formed under basic conditions. Therefore its synthesis in a protein crystal grown at pH4.5 is even more unexpected. The X-ray crystal structures presented here are for the protein hen egg white lysozyme incubated with the rhenium tricarbonyl tribromo compound for periods of 1 year and 2 years. These reveal a completed, very well resolved, tetra rhenium cluster after two years and an intermediate state after 1 year where the carbonyl ligands to the rhenium cluster are not yet clearly resolved. A dense tetra-nuclear rhenium cluster, and its technetium form, offers enhanced medical imaging contrast. The raw diffraction images for the one year and two year protein structure, described in the manuscript, is made avaliable on the Zenodo repository.</p>
USE OF NEW CARBON CLUSTER FULLERENES AS ANTIOXIDANTS IN PROTEIN STORAGE COMPOUNDS USED IN STROKE PREVENTION
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MicroRNA Clustering Assists Processing of Suboptimal MicroRNA Hairpins Through the Action of the ERH Protein
GEO Series GSE142818. Homo sapiens. 4 samples. Type: Non-coding RNA profiling by high throughput sequencing.
The major urinary protein gene cluster knockout mouse as a novel model for translational metabolism research
GEO Series GSE188158. Mus musculus. 47 samples. Type: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Yeast zinc cluster proteins paralogs involved in the switch from fermentation to respiration show interdependency for DNA binding revealing a novel type of DNA recognition
GEO Series GSE225348. Saccharomyces cerevisiae. 8 samples. Type: Genome binding/occupancy profiling by array.
Oxygen Toxicity Causes Cyclic Damage by Destabilizing Specific Fe-S Cluster-Containing Protein Complexes
GEO Series GSE224583. Homo sapiens. 10 samples. Type: Other.
Ribosome pausing at the AT-rich codons regulates the protein expression of secondary metabolite gene clusters in the Streptomyces tsukubaensis NRRL 18488
GEO Series GSE97637. Streptomyces tsukubensis. 18 samples. Type: Expression profiling by high throughput sequencing; Other.
Modulation of the microRNA cluster miR-183-96-182 expression by the Epstein-Barr virus latent membrane protein 1
GEO Series GSE65752. Homo sapiens. 9 samples. Type: Non-coding RNA profiling by high throughput sequencing.
The PhtL protein of Pseudomonas syringae pv. phaseolicola NPS3121 affects the expression of both phaseolotoxin cluster (Pht) and Non-Pht encoded genes
GEO Series GSE44554. Pseudomonas savastanoi pv. phaseolicola. 6 samples. Type: Expression profiling by array.
Analysis of a fungus-specific transcription factor family, the Candida albicans zinc cluster proteins, by artificial activation
GEO Series GSE48259. Candida albicans. 15 samples. Type: Expression profiling by array.
Clustered PHD domains in KMT2/MLL proteins are attracted by H3K4me3 and H3 acetylation-rich active promoters and enhancers
GEO Series GSE185921. Homo sapiens. 58 samples. Type: Other.
The cytosolic iron-sulfur cluster assembly protein MMS19 regulates transcriptional gene silencing, DNA repair, and flowering time in Arabidopsis
GEO Series GSE67669. Arabidopsis thaliana. 3 samples. Type: Expression profiling by high throughput sequencing.
Data from: Stoichiometry controls activity of phase-separated clusters of actin signaling proteins
Biomolecular condensates concentrate macromolecules into foci without a surrounding membrane. Many condensates appear to form through multivalent interactions that drive liquid-liquid phase separation (LLPS). LLPS increases the specific activity of actin regulatory proteins toward actin assembly by the Arp2/3 complex. We show that this increase occurs because LLPS of the Nephrin–Nck–N-WASP signaling pathway on lipid bilayers increases membrane dwell time of N-WASP and Arp2/3 complex, consequently increasing actin assembly. Dwell time varies with relative stoichiometry of the signaling proteins in the phase-separated clusters, rendering N-WASP and Arp2/3 activity stoichiometry dependent. This mechanism of controlling protein activity is enabled by the stoichiometrically undefined nature of biomolecular condensates. Such regulation should be a general feature of signaling systems that assemble through multivalent interactions and drive nonequilibrium outputs.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.