ExpressHeart: Web Portal to Visualize Transcriptome Profiles of Non-Cardiomyocyte Cells.
Ontology highlight
ABSTRACT:
SUBMITTER: Li G
PROVIDER: S-EPMC8396223 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundWeb-based portals can enhance communication between patients and providers to support IBD self-management and improve care. We aimed to identify portal use patterns of patients with inflammatory bowel disease (IBD) to inform future web portal-based interventions and portal design.MethodsPatients with IBD receiving care at the University of Michigan between 2012 and 2021 were identified. Meta-data from electronic logs of each patient's most recent year of portal use were abstracted. Portal engagement was characterized in terms of intensity (ie, frequency of use); comprehensiveness (ie, number of portal functions used); and duration (ie, quarters per year of portal use). We used k-means clustering, a machine-learning technique, to identify groupings of portal users defined in terms of engagement features.ResultsWe found 5605 patients with IBD who had accessed their portal account at least once. The average age was 41.2 years (SD 16.7), 3035 (54.2%) were female, and 2214 (39.5%) received immune-targeted therapies. We identified 3 patterns of portal engagement: (1) low intensity users (29.5%); (2) moderate intensity, comprehensive, and sustained users (63.3%); and (3) high intensity, comprehensive, sustained users (7.2%). Patients with more intense, comprehensive, and sustained use of the portal were older, female, with more comorbidities, and were more likely to receive immune-targeted therapies.ConclusionUnderstanding distinct patterns of portal use can inform portal-based interventions and portal design. Patient portals may be particularly helpful in delivering assistance to those with comorbidities and those receiving immune-targeted therapies-many of whom demonstrate more intense, comprehensive, and sustained portal use.
| S-EPMC10769793 | biostudies-literature
Project description:BACKGROUND:With the advancement of next generation sequencing technology, researchers are now able to identify important variants and structural changes in DNA and RNA in cancer patient samples. With this information, we can now correlate specific variants and/or structural changes with actionable therapeutics known to inhibit these variants. We introduce the creation of the IMPACT Web Portal, a new online resource that connects molecular profiles of tumors to approved drugs, investigational therapeutics and pharmacogenetics associated drugs. RESULTS:IMPACT Web Portal contains a total of 776 drugs connected to 1326 target genes and 435 target variants, fusion, and copy number alterations. The online IMPACT Web Portal allows users to search for various genetic alterations and connects them to three levels of actionable therapeutics. The results are categorized into 3 levels: Level 1 contains approved drugs separated into two groups; Level 1A contains approved drugs with variant specific information while Level 1B contains approved drugs with gene level information. Level 2 contains drugs currently in oncology clinical trials. Level 3 provides pharmacogenetic associations between approved drugs and genes. CONCLUSION:IMPACT Web Portal allows for sequencing data to be linked to actionable therapeutics for translational and drug repurposing research. The IMPACT Web Portal online resource allows users to query genes and variants to approved and investigational drugs. We envision that this resource will be a valuable database for personalized medicine and drug repurposing. IMPACT Web Portal is freely available for non-commercial use at http://tanlab.ucdenver.edu/IMPACT .
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Project description:UnlabelledMonkeySNP is a web-based resource created by the Genetic Resource and Informatics Program at the Oregon National Primate Research Center to facilitate access to non-human primate (NHP) single nucleotide polymorphisms (SNP) data. MonkeySNP is a mirror of the NCBI dbSNP database and contains additional NHP subpopulation genotype data and visual genotype displays to support SNP review and selection.Availabilityhttp://monkeysnp.ohsu.edu/snp/Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC2579713 | biostudies-literature
Project description:CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to address the needs of the cyanobacterial research and biotechnology communities. The 277 annotated cyanobacterial genomes currently in CyanoCyc are supplemented with computational inferences including predicted metabolic pathways, operons, protein complexes, and orthologs; and with data imported from external databases, such as protein features and Gene Ontology (GO) terms imported from UniProt. Five of the genome databases have undergone manual curation with input from more than a dozen cyanobacteria experts to correct errors and integrate information from more than 1,765 published articles. CyanoCyc has bioinformatics tools that encompass genome, metabolic pathway and regulatory informatics; omics data analysis; and comparative analyses, including visualizations of multiple genomes aligned at orthologous genes, and comparisons of metabolic networks for multiple organisms. CyanoCyc is a high-quality, reliable knowledgebase that accelerates scientists' work by enabling users to quickly find accurate information using its powerful set of search tools, to understand gene function through expert mini-reviews with citations, to acquire information quickly using its interactive visualization tools, and to inform better decision-making for fundamental and applied research.
| S-EPMC10864581 | biostudies-literature
Project description:Circadian rhythms play a fundamental role at all levels of biological organization. Understanding the mechanisms and implications of circadian oscillations continues to be the focus of intense research. However, there has been no comprehensive and integrated way for accessing and mining all circadian omic datasets. The latest release of CircadiOmics (http://circadiomics.ics.uci.edu) fills this gap for providing the most comprehensive web server for studying circadian data. The newly updated version contains high-throughput 227 omic datasets corresponding to over 74 million measurements sampled over 24 h cycles. Users can visualize and compare oscillatory trajectories across species, tissues and conditions. Periodicity statistics (e.g. period, amplitude, phase, P-value, q-value etc.) obtained from BIO_CYCLE and other methods are provided for all samples in the repository and can easily be downloaded in the form of publication-ready figures and tables. New features and substantial improvements in performance and data volume make CircadiOmics a powerful web portal for integrated analysis of circadian omic data.
| S-EPMC6030824 | biostudies-literature
Project description:Circadian rhythms are a foundational aspect of biology. These rhythms are found at the molecular level in every cell of every living organism and they play a fundamental role in homeostasis and a variety of physiological processes. As a result, biomedical research of circadian rhythms continues to expand at a rapid pace. To support this research, CircadiOmics (http://circadiomics.igb.uci.edu/) is the largest annotated repository and analytic web server for high-throughput omic (e.g. transcriptomic, metabolomic, proteomic) circadian time series experimental data. CircadiOmics contains over 290 experiments and over 100 million individual measurements, across >20 unique tissues/organs, and 11 different species. Users are able to visualize and mine these datasets by deriving and comparing periodicity statistics for oscillating molecular species including: period, amplitude, phase, P-value and q-value. These statistics are obtained from BIO_CYCLE and JTK_CYCLE and are intuitively aggregated and displayed for comparison. CircadiOmics is the most up-to-date and cutting-edge web portal for searching and analyzing circadian omic data and is used by researchers around the world.
| S-EPMC9252794 | biostudies-literature
Project description:Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are genomic regions conserved among multiple species, is key to understanding genomic architecture and the evolutionary history of genomes. However, the construction and visualization of such synteny blocks from multiple species are very challenging, especially for biologists with a lack of computational skills. Here, we present Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at http://bioinfo.konkuk.ac.kr/synteny_portal.
| S-EPMC4987893 | biostudies-other
Project description:ABC portal (http://abc.sklehabc.com) is a database and web portal containing 198 single-cell transcriptomic datasets of development, differentiation and disorder of blood/immune cells. All the datasets were re-annotated with a manually curated and unified single-cell reference, especially for the haematopoietic stem and progenitor cells. ABC portal provides web-based interactive analysis modules, especially a comprehensive cell-cell communication analysis and disease-related gene signature analysis. Importantly, ABC portal allows customized sample selection based on a combination of several metadata for downstream analysis and comparison analysis across datasets. ABC portal also allows users to select multiple cell types for analysis in the modules. Together, ABC portal provides an interactive interface of single-cell data exploration and re-analysis with customized analysis modules for the researchers and clinicians, and will facilitate understanding of haematopoiesis and blood/immune disorders.
| S-EPMC9825444 | biostudies-literature
Project description:PurposeTo evaluate participant opinions on the appropriateness of different viewing angles by asking 8 questions, using visual content techniques.MethodsSurvey information from participants was used in this study. We used images of a patient who was operated on for symptomatic knee instability. Participants were asked whether the visual angle could determine the femoral tunnel entry point or evaluate anterior cruciate ligament (ACL) integrity.ResultsQuestionnaires were completed by 40 participants. When all responses were evaluated, participant opinions on the accessory medial portal (AMP) were more positive than opinions on images taken from the anterolateral portal (ALP). These observations were statistically significant (P < .005). Both ACL integrity assessments and femoral tunnel entry site questions were evaluated, we observed that participant opinions on the AMP for both types of evaluation were more positive than opinions on the ALP. This observation was statistically significant (P < .005). When evaluations with photos and video transcripts were compared, no significant differences in terms of participant opinions were observed (P < .005).ConclusionsAMP use may be a valuable tool for assistant and postgraduate education, as it offers a more suitable view angle for ACL reconstruction.Level of evidenceLevel V, survey study.
| S-EPMC8220608 | biostudies-literature
Project description:Background & objectiveGenome-wide profiles of tumors obtained using functional genomics platforms are being deposited to the public repositories at an astronomical scale, as a result of focused efforts by individual laboratories and large projects such as the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium. Consequently, there is an urgent need for reliable tools that integrate and interpret these data in light of current knowledge and disseminate results to biomedical researchers in a user-friendly manner. We have built the canEvolve web portal to meet this need.ResultscanEvolve query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. canEvolve stores gene, microRNA (miRNA) and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information. canEvolve allows querying of results of primary analysis, integrative analysis and network analysis of oncogenomics data. The querying for primary analysis includes differential gene and miRNA expression as well as changes in gene copy number measured with SNP microarrays. canEvolve provides results of integrative analysis of gene expression profiles with copy number alterations and with miRNA profiles as well as generalized integrative analysis using gene set enrichment analysis. The network analysis capability includes storage and visualization of gene co-expression, inferred gene regulatory networks and protein-protein interaction information. Finally, canEvolve provides correlations between gene expression and clinical outcomes in terms of univariate survival analysis.ConclusionAt present canEvolve provides different types of information extracted from 90 cancer genomics studies comprising of more than 10,000 patients. The presence of multiple data types, novel integrative analysis for identifying regulators of oncogenesis, network analysis and ability to query gene lists/pathways are distinctive features of canEvolve. canEvolve will facilitate integrative and meta-analysis of oncogenomics datasets.AvailabilityThe canEvolve web portal is available at http://www.canevolve.org/.
| S-EPMC3572035 | biostudies-literature