E-PROT-140
Ontology highlight
ABSTRACT:
PROVIDER: E-PROT-140 | ExpressionAtlas | 2024-06-05
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-PROT-140-MappedToGeneID.txt | Txt | |||
| E-PROT-140-analysis-methods.tsv | Tabular | |||
| E-PROT-140-configuration.xml | Xml | |||
| E-PROT-140-factors.xml | Xml | |||
| E-PROT-140-pipeline.pdf |
Items per page: 5 1 - 5 of 11 |
Similar Datasets
Project description:Animal toxins are of interest to a wide range of scientists, due to their numerous applications in pharmacology, neurology, hematology, medicine, and drug research. This, and to a lesser extent the development of new performing tools in transcriptomics and proteomics, has led to an increase in toxin discovery. In this context, providing publicly available data on animal toxins has become essential. The UniProtKB/Swiss-Prot Tox-Prot program (http://www.uniprot.org/program/Toxins) plays a crucial role by providing such an access to venom protein sequences and functions from all venomous species. This program has up to now curated more than 5000 venom proteins to the high-quality standards of UniProtKB/Swiss-Prot (release 2012_02). Proteins targeted by these toxins are also available in the knowledgebase. This paper describes in details the type of information provided by UniProtKB/Swiss-Prot for toxins, as well as the structured format of the knowledgebase.
| S-EPMC3393831 | biostudies-literature
Project description:Expression Profiling of Early Myogenesis - Affymetrix Dataset
2015-09-07 | E-GEOD-16992 | ExpressionAtlas
Project description:During development of heart failure, capacity for cardiomyocyte fatty acid oxidation (FAO) and ATP production is progressively diminished contributing to pathologic cardiac hypertrophy and contractile dysfunction. Receptor interacting protein 140 (RIP140; Nrip1) has been shown to function as a transcriptional co-repressor of oxidative metabolism. Here we show that mice lacking RIP140 in striated muscle (strRIP140-/-) have increased expression of a broad array of involved in a broad array of mitochondrial energy metabolism and contractile function in heart and skeletal muscle. strRIP140-/- mice were resistant to the development of pressure overload-induced cardiac hypertrophy, and cardiomyocyte-specific RIP140 deficient (csRIP140-/-) mice were defended against development of heart failure caused by pressure overload combined with myocardial infarction. Genomic enhancers activated by RIP140 deficiency in cardiomyocytes were enriched in binding motifs for transcriptional regulators of mitochondrial function (estrogen-related receptor) and cardiac contractile proteins (myocyte enhancer factor 2). Consistent with a role in the control of cardiac fuel metabolism, loss of RIP140 in heart resulted in augmented triacylglyceride turnover and FA utilization. We conclude that RIP140 functions as a suppressor of a transcriptional regulatory network that controls cardiac fuel metabolism and contractile function, representing a potential therapeutic target for heart failure.
2023-03-30 | GSE205315 | GEO
Project description:BackgroundThe accuracy of protein 3D structure prediction has been dramatically improved with the help of advances in deep learning. In the recent CASP14, Deepmind demonstrated that their new version of AlphaFold (AF) produces highly accurate 3D models almost close to experimental structures. The success of AF shows that the multiple sequence alignment of a sequence contains rich evolutionary information, leading to accurate 3D models. Despite the success of AF, only the prediction code is open, and training a similar model requires a vast amount of computational resources. Thus, developing a lighter prediction model is still necessary.ResultsIn this study, we propose a new protein 3D structure modeling method, A-Prot, using MSA Transformer, one of the state-of-the-art protein language models. An MSA feature tensor and row attention maps are extracted and converted into 2D residue-residue distance and dihedral angle predictions for a given MSA. We demonstrated that A-Prot predicts long-range contacts better than the existing methods. Additionally, we modeled the 3D structures of the free modeling and hard template-based modeling targets of CASP14. The assessment shows that the A-Prot models are more accurate than most top server groups of CASP14.ConclusionThese results imply that A-Prot accurately captures the evolutionary and structural information of proteins with relatively low computational cost. Thus, A-Prot can provide a clue for the development of other protein property prediction methods.
| S-EPMC8925138 | biostudies-literature
Project description:The ever-growing global health threat of antibiotic resistance is compelling researchers to explore alternatives to conventional antibiotics. Antimicrobial peptides (AMPs) are emerging as a promising solution to fill this need. Naturally occurring AMPs are produced by all forms of life as part of the innate immune system. High-throughput bioinformatics tools have enabled fast and large-scale discovery of AMPs from genomic, transcriptomic, and proteomic resources of selected organisms. Public protein sequence databases, comprising over 200 million records and growing, serve as comprehensive compendia of sequences from a broad range of source organisms. Yet, large-scale in silico probing of those databases for novel AMP discovery using modern deep learning techniques has rarely been reported. In the present study, we propose an AMP mining workflow to predict novel AMPs from the UniProtKB/Swiss-Prot database using the AMP prediction tool, AMPlify, as its discovery engine. Using this workflow, we identified 8008 novel putative AMPs from all eukaryotic sequences in the database. Focusing on the practical use of AMPs as suitable antimicrobial agents with applications in the poultry industry, we prioritized 40 of those AMPs based on their similarities to known chicken AMPs in predicted structures. In our tests, 13 out of the 38 successfully synthesized peptides showed antimicrobial activity against Escherichia coli and/or Staphylococcus aureus. AMPlify and the companion scripts supporting the AMP mining workflow presented herein are publicly available at https://github.com/bcgsc/AMPlify.
| S-EPMC11917140 | biostudies-literature
Project description:Diversification of Root Hair Development Genes in Vascular Plants - rice dataset
2020-04-03 | E-CURD-28 | ExpressionAtlas
Project description:Diversification of Root Hair Development Genes in Vascular Plants - arabidopsis thaliana dataset
2020-04-03 | E-CURD-29 | ExpressionAtlas
Project description:We present RVDB-prot, a database corresponding to the protein equivalent of the nucleic acid reference virus database RVDB. Protein databases can be helpful to perform more sensitive protein sequence comparisons. Similarly to its homologous public repository, RVDB-prot aims to provide reliable and accurately annotated unique entries, while including also an Hidden Markov Model (HMM) protein profiles database for distant protein searching.
| S-EPMC7492780 | biostudies-literature
Project description:Proline acquired via specific transporters can serve as a proteinogenic substrate, carbon and nitrogen source, or osmolyte. Previous reports have documented that Staphylococcus aureus, a major community and nosocomial pathogen, encodes at least four proline transporters, PutP, OpuC, OpuD, and ProP. A combination of genetic approaches and 3H-proline transport assays reveal that a previously unrecognized transporter, ProT, in addition to PutP, are the major proline transporters in S. aureus. Complementation experiments using constitutively expressed non-cognate promoters found that proline transport via OpuD, OpuC, and ProP is minimal. Both proline biosynthesis from arginine and proline transport via ProT are critical for growth when S. aureus is grown under conditions of high salinity. Further, proline transport mediated by ProT or PutP are required for growth in media with and without glucose, indicating both transporters function to acquire proline for proteinogenic purposes in addition to acquisition of proline as a carbon/nitrogen source. Lastly, inactivation of proT and putP resulted in a significant reduction (5 log10) of bacterial burden in murine skin-and-soft tissue infection and bacteremia models, suggesting that proline transport is required to establish a S. aureus infection.
| S-EPMC9886301 | biostudies-literature
Project description:The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at swiss-prot@expasy.org.
| S-EPMC165542 | biostudies-literature