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641
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Dataset results
641 results for “Protein interaction”
Next-generation interaction screening to discover Mla6aa1-161 related protein-protein interactions regulating barley powdery mildew disease immunity and susceptibility.
GEO Series GSE164814. Hordeum vulgare; Blumeria hordei. 6 samples. Type: Other.
Identification of differential expression gene of LncRNA interacting with NLRP3 protein in RAW264.7 cells infected with Salmonella typhimurium and uninfected cells
GEO Series GSE250407. Mus musculus. 6 samples. Type: Other.
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP II]
GEO Series GSE248461. Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing.
Heat shock protein gp96 induces Foxp3 expression in Regulatory T Cells via interaction with TLRs for treatment of Auto-immune Diseases [Foxp3Cre Myd88fl/fl]
GEO Series GSE154172. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide analysis of HDAC9 and BRG1 protein-RNA interactions in TAA by CLIP-seq
GEO Series GSE93744. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
easyCLIP Quantifies RNA-Protein Interactions and Characterizes Recurrent PCBP1 Mutations in Cancer
GEO Series GSE131210. Homo sapiens. 50 samples. Type: Other.
The B-cell CLL/lymphoma 7 (BCL7) protein family members drive gene expression changes via interactions with the Brahma Related Gene 1 (BRG1) Helicase-Sant Associated domain (HSA) domain [24 hours]
GEO Series GSE188726. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing.
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription
GEO Series GSE120110. Homo sapiens. 152 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Using fish models to understand the role of aryl hydrocarbon receptor (AHR)-interacting protein (AIP) in controlling sensitivity and resistance to dioxin-like compounds in vivo 5dpf
GEO Series GSE295203. Danio rerio. 24 samples. Type: Expression profiling by high throughput sequencing.
Genomic and Proteomic Analyses of Prdm5 Reveal Interactions with Insulator Binding Proteins in Embryonic Stem Cells (ChIP-seq)
GEO Series GSE51816. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
SARS-CoV-2 Nucleocapsid protein attenuates stress granule formation and interacts directly with mRNAs to impair host stress response (iCLIP-Seq)
GEO Series GSE171008. Homo sapiens. 18 samples. Type: Other.
Next-generation interaction screening to discover Mla6aa1-225 related protein-protein interactions regulating barley powdery mildew disease immunity and susceptibility.
GEO Series GSE164815. Hordeum vulgare; Blumeria hordei. 6 samples. Type: Other.
MP3-seq: Massively parallel measurement of protein-protein interactions by sequencing
GEO Series GSE271790. Saccharomyces cerevisiae. 36 samples. Type: Other.
Data from "Reversible Control of Protein Corona Formation on Gold Nanoparticles Using Host–Guest Interactions"
<p>This file contains raw data for the manuscript:<br> "Reversible Control of Protein Corona Formation on Gold Nanoparticles Using Host–Guest Interactions"<br> <em>ACS Nano</em> 2020, 14, 5, 5382–5391, DOI: <a href="https://doi.org/10.1021/acsnano.9b08752">10.1021/acsnano.9b08752</a></p> <p>The data is transmission electron microscopy (TEM) images of of gold nanoparticles.</p> <p> </p> <p> </p> <p> </p>
Data from: Coevolution-based inference of amino acid interactions underlying protein function
Protein function arises from a poorly understood pattern of energetic interactions between amino acid residues. Sequence-based strategies for deducing this pattern have been proposed, but lack of benchmark data has limited experimental verification. Here, we extend deep-mutation technologies to enable measurement of many thousands of pairwise amino acid couplings in several homologs of a protein family – a deep coupling scan (DCS). The data show that cooperative interactions between residues are loaded in a sparse, evolutionarily conserved, spatially contiguous network of amino acids. The pattern of amino acid coupling is quantitatively captured in the coevolution of amino acid positions, especially as indicated by the statistical coupling analysis (SCA), providing experimental confirmation of the key tenets of this method. This work exposes the collective nature of physical constraints on protein function and clarifies its link with sequence analysis, enabling a general practical approach for understanding the structural basis for protein function.
Supplements for "The Proteomic Code: Novel Amino Acid Residue Pairing Models "Encode" Protein Folding and Protein-Protein Interactions"
<p><strong>Supplements for "The Proteomic Code: Novel Amino Acid Residue Pairing Models “Encode” Protein Folding and Protein-Protein Interactions"</strong></p> <p>This supplement includes the following files:</p> <ul> <li>Main_v02.R --- Script in R language to process protein structures and produce the datasets.</li> <li>datasets_v02.zip --- final filtered version of datasets produced in R language (by "Main_v02.R"). </li> <li>Dataset key v02.txt --- key and descriptions to column names in ("datasets.zip"). </li> </ul> <p>The article featuring these datasets is submitted to:</p> <p>Journal: Computers in Biology and Medicine (Reference: CBM_110033)<br>Title: "The Proteomic Code: Novel Amino Acid Residue Pairing Models "Encode" Protein Folding and Protein-Protein Interactions"<br>Authors: Hameduh, Tareq; Miller, Andrew D. ; Heger, Zbynek; Haddad, Yazan</p> <p> </p> <p> </p>
Structural basis of Omicron immune evasion: A comparative computational study of Spike protein-Antibody interaction
<p>The COVID-19 pandemic has caused more than 424 million infections and 5.9 million deaths so far. The vaccines used against SARS-COV-2 by now have been able to develop some neutralising antibodies in the vaccinated human population and slow down the infection rate. The effectiveness of the vaccines has been challenged by the emergence of the new strains with numerous mutations in the spike (S) protein of SARS-CoV-2. Since S protein is the major immunogenic protein of the virus and also contains Receptor Binding Domain (RBD) that interacts with the human Angiotensin-Converting Enzyme 2 (ACE2) receptors, any mutations in this region should affect the neutralisation potential of the antibodies leading to the immune evasion. Several variants of concern (VOC) of the virus have emerged so far. Among them, the most critical are Delta (B.1.617.2), and recently reported Omicron (B. 1.1.529) which have acquired a lot of mutations in the spike protein. We have mapped those mutations on the modelled RBD and evaluated the binding affinities of various human antibodies with it. Docking and molecular dynamics simulation studies have been used to explore the effect of the mutations on the structure of the RBD and the RBD-antibody interaction. The analysis shows that the mutations mostly at the interface of a nearby region lower the binding affinity of the antibody by ten to forty per cent, with a downfall in the number of interactions formed as a whole and therefore, it implies the generation of immune escape variants. Notable mutations and their effect was characterised by performing various analyses that explain the structural basis of antibody efficacy in Delta and a compromised neutralisation effect for the Omicron variant. Our results pave the way for robust vaccine design that can be effective for many variants.</p>
Kinases in motion: impact of protein and small molecule interactions on kinase conformations
<p><span>Protein kinases act as central molecular switches in the control of cellular functions. Alterations in the regulation and function of protein kinases may provoke diseases including cancer. In this study we investigate the conformational states of such disease associated kinases using the high sensitivity of the Kinase Conformation (KinCon)reporter system. We first tracked BRAF kinase activity conformation changes upon melanoma drug binding. Second, we also use the KinCon reporter technology to examine the impact of regulatory protein interactions on LKB1kinase tumor suppressor functions. Third, we explore the conformational dynamics of RIP kinases in response to TNF pathway activation and small molecule interactions. Finally, we show that CDK4/6 interactions with regulatory proteins alter conformations which remain unaffected in the presence of clinically applied inhibitors. Apart from its predictive value, the KinCon technology helps identify cellular factors that impact drug efficacies. The understanding of the dynamics of full-length protein kinases when interacting with small molecule inhibitors or regulatory proteins is crucial for designing more effective therapeutic strategies.</span></p>
Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions
<p>for manuscript "Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions"</p>
ROS-Specific Huntingtin Interactions: Huntingtin pulldown of PARylated proteins
<p>Huntingtin co-immunoprecipitation of proteins modified by poly ADP ribose.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.