Bcl-2-Ome - a database and interactive web service for dissecting the Bcl-2 interactome.
Ontology highlight
ABSTRACT:
SUBMITTER: Hantusch A
PROVIDER: S-EPMC5260498 | biostudies-literature | 2017 Jan
REPOSITORIES: biostudies-literature
Publications
Bcl-2-Ome - a database and interactive web service for dissecting the Bcl-2 interactome.
Hantusch Annika A Brunner Thomas T Frickey Tancred T Rehm Markus M
Cell death and differentiation 20161111 1
Similar Datasets
Project description:Unlabelled: We present ClicO Free Service, an online web-service based on Circos, which provides a user-friendly, interactive web-based interface with configurable features to generate Circos circular plots.Availability and implementationOnline web-service is freely available at http://clicofs.codoncloud.comContact: soonjoo.yap@codongenomics.comSupplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC4817113 | biostudies-literature
Project description:Analyzing mass spectrometry-based metabolomics data presents a major challenge to metabolism researchers, as it requires downloading and processing large data volumes through complex "pipelines", even in cases where only a single metabolite or peak is of interest. This presents a significant hurdle for data sharing, reanalysis, or meta-analysis of existing data sets, whether locally stored or available from public repositories. Here we introduce mzAccess, a software system that provides interactive, online access to primary mass spectrometry data in real-time via a Web service protocol, circumventing the need for bulk data processing. mzAccess allows querying instrument data for spectra, chromatograms, or two-dimensional MZ-RT areas in either profile or centroid modes through a simple, uniform interface that is independent of vendor or instrument type. Using a cache mechanism, mzAccess achieves response times in the millisecond range for typical liquid chromatography-mass spectrometry (LC-MS) peaks, enabling real-time browsing of large data sets with hundreds or even thousands of samples. By simplifying access to metabolite data, we hope that this system will help enable data sharing and reanalysis in the metabolomics field.
| S-EPMC5519509 | biostudies-literature
Project description:BackgroundPseudomonas putida KT2440 (P. putida KT2440) is a highly versatile saprophytic soil bacterium. It is a certified bio-safety host for transferring foreign genes. Therefore, the bacterium is used as a model organism for genetic and physiological studies and for the development of biotechnological applications. In order to provide a more systematic application of the organism, we have constructed a protein-protein interaction (PPI) network analysis system of P. putida KT2440.ResultsPutidaNET is a comprehensive interaction database and server of P. putida KT2440 which is generated from three protein-protein interaction (PPI) methods. We used PSIMAP (Protein Structural Interactome MAP), PEIMAP (Protein Experimental Interactome MAP), and Domain-domain interactions using iPfam. PutidaNET contains 3,254 proteins, and 82,019 possible interactions consisting of 61,011 (PSIMAP), 4,293 (PEIMAP), and 30,043 (iPfam) interaction pairs except for self interaction. Also, we performed a case study by integrating a protein interaction network and experimental 1-DE/MS-MS analysis data P. putida. We found that 1) major functional modules are involved in various metabolic pathways and ribosomes, and 2) existing PPI sub-networks that are specific to succinate or benzoate metabolism are not in the center as predicted.ConclusionWe introduce the PutidaNET which provides predicted interaction partners and functional analyses such as physicochemical properties, KEGG pathway assignment, and Gene Ontology mapping of P. putida KT2440 PutidaNET is freely available at http://sequenceome.kobic.kr/PutidaNET.
| S-EPMC2788370 | biostudies-literature
Project description:We present an intuitive and interactive web service for CARRIE (Computational Ascertainment of Regulatory Relationships Inferred from Expression). CARRIE is a computational method that analyzes microarray and promoter sequence data to infer a transcriptional regulatory network from the response to a specific stimulus. This service displays an interactive graph of the inferred network and provides easy access to the evidence for the involvement of each gene in the network. We provide functionality to include network data in KEGG XML (KGML) format in this graph. Our service also provides Gene Ontology annotation to aid the user in forming hypotheses about the role of each gene in the cellular response. The CARRIE web service is freely available at http://zlab.bu.edu/CARRIE-web.
| S-EPMC441540 | biostudies-literature
Project description:A major problem in structural biology is the recognition of errors in experimental and theoretical models of protein structures. The ProSA program (Protein Structure Analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures and in structure prediction and modeling. The analysis of protein structures is generally a difficult and cumbersome exercise. The new service presented here is a straightforward and easy to use extension of the classic ProSA program which exploits the advantages of interactive web-based applications for the display of scores and energy plots that highlight potential problems spotted in protein structures. In particular, the quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer. The service specifically addresses the needs encountered in the validation of protein structures obtained from X-ray analysis, NMR spectroscopy and theoretical calculations. ProSA-web is accessible at https://prosa.services.came.sbg.ac.at.
| S-EPMC1933241 | biostudies-literature
Project description:Our knowledge of the role of higher-order chromatin structures in transcription of microRNA genes (MIRs) is evolving rapidly. Here we investigate the effect of 3D architecture of chromatin on the transcriptional regulation of MIRs. We demonstrate that MIRs have transcriptional features that are similar to protein-coding genes. RNA polymerase II-associated ChIA-PET data reveal that many groups of MIRs and protein-coding genes are organized into functionally compartmentalized chromatin communities and undergo coordinated expression when their genomic loci are spatially colocated. We observe that MIRs display widespread communication in those transcriptionally active communities. Moreover, miRNA-target interactions are significantly enriched among communities with functional homogeneity while depleted from the same community from which they originated, suggesting MIRs coordinating function-related pathways at posttranscriptional level. Further investigation demonstrates the existence of spatial MIR-MIR chromatin interacting networks. We show that groups of spatially coordinated MIRs are frequently from the same family and involved in the same disease category. The spatial interaction network possesses both common and cell-specific subnetwork modules that result from the spatial organization of chromatin within different cell types. Together, our study unveils an entirely unexplored layer of MIR regulation throughout the human genome that links the spatial coordination of MIRs to their co-expression and function.
| S-EPMC3950692 | biostudies-literature
Project description:Commercially available histone antibodies were analyzed using peptide microarrays to assess specificity. For two H3K27me3 antibodies from different vendors, we performed ChIP-seq in WT and EED-null murine ES cells to assess specificity. Cell lines were generated from e3.5 blastocysts of EED fl/fl animals and transfected with plasmid CAG-CRE-ERT2. Null cells were generated by single cell clones from tamoxifen-treated parent cell line.
2015-06-21 | GSE66902 | GEO
Project description:The interactive chromatin modeling web server (ICM Web) is an interactive tool that allows users to rapidly assess nucleosome stability and fold sequences of DNA into putative chromatin templates. ICM Web takes a sequence composed of As, Cs, Gs, and Ts as input and generates (i) a nucleosome energy level diagram, (ii) coarse-grained representations of free DNA and chromatin and (iii) plots of the helical parameters (Tilt, Roll, Twist, Shift, Slide and Rise) as a function of position. The user can select from several different energy models, nucleosome structures and methods for placing nucleosomes in the energy landscape. Alternatively, if nucleosome footprints are known from experiment, ICM Web can use these positions to create a nucleosome array. The default energy model achieves a correlation coefficient of 0.7 with 100 experimentally determined values of stability and properly predicts the location of six positioned nucleosomes in the mouse mammary tumor virus (MMTV) promoter. ICM Web is suitable for interactively investigating nucleosome stability and chromatin folding for sequences up to tens of kilobases in length. No login is required to use ICM Web.
| S-EPMC2896153 | biostudies-literature
Project description:UnlabelledCytoscape Web is a web-based network visualization tool-modeled after Cytoscape-which is open source, interactive, customizable and easily integrated into web sites. Multiple file exchange formats can be used to load data into Cytoscape Web, including GraphML, XGMML and SIF.Availability and implementationCytoscape Web is implemented in Flex/ActionScript with a JavaScript API and is freely available at http://cytoscapeweb.cytoscape.org/.
| S-EPMC2935447 | biostudies-literature
Project description:Commercially available histone antibodies were analyzed using peptide microarrays to assess specificity. For two H3K27me3 antibodies from different vendors, we performed ChIP-seq in WT and EED-null murine ES cells to assess specificity. Cell lines were generated from e3.5 blastocysts of EED fl/fl animals and transfected with plasmid CAG-CRE-ERT2. Null cells were generated by single cell clones from tamoxifen-treated parent cell line. Analysis of the specificity of two H3K27me3 antibodies using WT and EED (Embryonic Ectoderm Develepment)-null (mutants lacking H3K27me3) ES cells. The goal was to compare WT and KO for each antibody with the expectation that if the antibodies were specific, there would remain few peaks and little signal in the knockout. We sequenced 2 replicates of each condition (3 for WT input) and after comparing replicates, we merged data, called peaks, and calculated signal in bins centered on the wild type H3K27me3 peaks. As little to no signal remained either by direct comparison of peaks or looking at 'metagenes' of the peaks, we concluded that the antibodies were specific. Antibodies: Abcam H3K27me3 (ab6002, lot# GR130002-1) Upstate H3K27me3 (07-449, lot# 2455635)
2015-06-21 | E-GEOD-66902 | biostudies-arrayexpress