Abstract
In 2017, we released GEPIA (Gene Expression Profiling Interactive Analysis) webserver to facilitate the widely used analyses based on the bulk gene expression datasets in the TCGA and the ...GTEx projects, providing the biologists and clinicians with a handy tool to perform comprehensive and complex data mining tasks. Recently, the deconvolution tools have led to revolutionary trends to resolve bulk RNA datasets at cell type-level resolution, interrogating the characteristics of different cell types in cancer and controlled cohorts became an important strategy to investigate the biological questions. Thus, we present GEPIA2021, a standalone extension of GEPIA, allowing users to perform multiple interactive analysis based on the deconvolution results, including cell type-level proportion comparison, correlation analysis, differential expression, and survival analysis. With GEPIA2021, experimental biologists could easily explore the large TCGA and GTEx datasets and validate their hypotheses in an enhanced resolution. GEPIA2021 is publicly accessible at http://gepia2021.cancer-pku.cn/.
Graphical Abstract
Graphical Abstract
GEPIA2021 applied CIBERSORT/EPIC/quanTIseq to deconvolute the TCGA/GTEx bulk samples with the gene signature matrix of multiple cell types. Based on the cell proportions inferred, users can perform further analysis such as proportion comparison, proportion correlation, cell type-level differential expression and survival analysis.
The PharmMapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database. The ...original version of PharmMapper includes more than 7000 target pharmacophores derived from complex crystal structures with corresponding protein target annotations. In this article, we present a new version of the PharmMapper web server, of which the backend pharmacophore database is six times larger than the earlier one, with a total of 23 236 proteins covering 16 159 druggable pharmacophore models and 51 431 ligandable pharmacophore models. The expanded target data cover 450 indications and 4800 molecular functions compared to 110 indications and 349 molecular functions in our last update. In addition, the new web server is united with the statistically meaningful ranking of the identified drug targets, which is achieved through the use of standard scores. It also features an improved user interface. The proposed web server is freely available at http://lilab.ecust.edu.cn/pharmmapper/.
Functional enrichment analysis has played a key role in the biological interpretation of high-throughput omics data. As a long-standing and widely used web application for functional enrichment ...analysis, WebGestalt has been constantly updated to satisfy the needs of biologists from different research areas. WebGestalt 2017 supports 12 organisms, 324 gene identifiers from various databases and technology platforms, and 150 937 functional categories from public databases and computational analyses. Omics data with gene identifiers not supported by WebGestalt and functional categories not included in the WebGestalt database can also be uploaded for enrichment analysis. In addition to the Over-Representation Analysis in the previous versions, Gene Set Enrichment Analysis and Network Topology-based Analysis have been added to WebGestalt 2017, providing complementary approaches to the interpretation of high-throughput omics data. The new user-friendly output interface and the GOView tool allow interactive and efficient exploration and comparison of enrichment results. Thus, WebGestalt 2017 enables more comprehensive, powerful, flexible and interactive functional enrichment analysis. It is freely available at http://www.webgestalt.org.
With advances in next-generation sequencing technologies, numerous novel transcripts in a large number of organisms have been identified. With the goal of fast, accurate assessment of the coding ...ability of RNA transcripts, we upgraded the coding potential calculator CPC1 to CPC2. CPC2 runs ∼1000 times faster than CPC1 and exhibits superior accuracy compared with CPC1, especially for long non-coding transcripts. Moreover, the model of CPC2 is species-neutral, making it feasible for ever-growing non-model organism transcriptomes. A mobile-friendly web server, as well as a downloadable standalone package, is freely available at http://cpc2.cbi.pku.edu.cn.
Mobile-edge computing (MEC) is an emerging paradigm that provides a capillary distribution of cloud computing capabilities to the edge of the wireless access network, enabling rich services and ...applications in close proximity to the end users. In this paper, an MEC enabled multi-cell wireless network is considered where each base station (BS) is equipped with a MEC server that assists mobile users in executing computation-intensive tasks via task offloading. The problem of joint task offloading and resource allocation is studied in order to maximize the users' task offloading gains, which is measured by a weighted sum of reductions in task completion time and energy consumption. The considered problem is formulated as a mixed integer nonlinear program (MINLP) that involves jointly optimizing the task offloading decision, uplink transmission power of mobile users, and computing resource allocation at the MEC servers. Due to the combinatorial nature of this problem, solving for optimal solution is difficult and impractical for a large-scale network. To overcome this drawback, we propose to decompose the original problem into a resource allocation (RA) problem with fixed task offloading decision and a task offloading (TO) problem that optimizes the optimal-value function corresponding to the RA problem. We address the RA problem using convex and quasi-convex optimization techniques, and propose a novel heuristic algorithm to the TO problem that achieves a suboptimal solution in polynomial time. Simulation results show that our algorithm performs closely to the optimal solution and that it significantly improves the users' offloading utility over traditional approaches.
•The relationship among server inlet temperature, utilization, and heat generation is analyzed.•Variable airflow server model is proposed for data center cooling energy simulation.•Annual cooling ...energy simulation is conducted in a modular data center with air-side economizer.•Server airflow variation shows significant impact on data center cooling energy prediction.
This paper proposes a server model that can be applied to simulating the annual cooling energy consumption of data centers and an analysis of its impact. Recently, aisle containment architecture and the variable air volume system have been widely adopted in the data center industry because of their superior indoor thermal management and cooling energy savings. However, the current simulation method, which fixes the server heat generation and the supply and return air temperature difference of the computer room air handler (CRAH), does not correctly reflect current cooling systems. In this study, a server model was developed that accounts for server thermal characteristics – including server power, fan airflow, and exhaust temperature – according to the given CPU utilization and temperature. After the proposed server model was validated, the annual cooling energy consumption was simulated for modular data centers with an air-side economizer and high ambient temperature. Unlike the conventional method, the proposed model showed that the cooling energy consumption increased when the CRAH supply air temperature was higher than 19°C because of the increase in fan energy consumption.
Abstract
Intrinsically disordered proteins and protein regions (IDPs/IDRs) exist without a single well-defined conformation. They carry out important biological functions with multifaceted roles ...which is also reflected in their evolutionary behavior. Computational methods play important roles in the characterization of IDRs. One of the commonly used disorder prediction methods is IUPred, which relies on an energy estimation approach. The IUPred web server takes an amino acid sequence or a Uniprot ID/accession as an input and predicts the tendency for each amino acid to be in a disordered region with an option to also predict context-dependent disordered regions. In this new iteration of IUPred, we added multiple novel features to enhance the prediction capabilities of the server. First, learning from the latest evaluation of disorder prediction methods we introduced multiple new smoothing functions to the prediction that decreases noise and increases the performance of the predictions. We constructed a dataset consisting of experimentally verified ordered/disordered regions with unambiguous annotations which were added to the prediction. We also introduced a novel tool that enables the exploration of the evolutionary conservation of protein disorder coupled to sequence conservation in model organisms. The web server is freely available to users and accessible at https://iupred3.elte.hu.
Graphical Abstract
Graphical Abstract
IUPred3 disorder conservation tool can help hypothesis generation.
Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular ...docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein-protein and protein-DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10-20 min for a docking run. Tested on the cases with weakly homologous complexes of <30% sequence identity from five docking benchmarks, the HDOCK pipeline tied with template-based modeling on the protein-protein and protein-DNA benchmarks and performed better than template-based modeling on the three protein-RNA benchmarks when the top 10 predictions were considered. The performance of HDOCK became better when more predictions were considered. Combining the results of HDOCK and template-based modeling by ranking first of the template-based model further improved the predictive power of the server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/.
The COFACTOR web server is a unified platform for structure-based multiple-level protein function predictions. By structurally threading low-resolution structural models through the BioLiP library, ...the COFACTOR server infers three categories of protein functions including gene ontology, enzyme commission and ligand-binding sites from various analogous and homologous function templates. Here, we report recent improvements of the COFACTOR server in the development of new pipelines to infer functional insights from sequence profile alignments and protein-protein interaction networks. Large-scale benchmark tests show that the new hybrid COFACTOR approach significantly improves the function annotation accuracy of the former structure-based pipeline and other state-of-the-art functional annotation methods, particularly for targets that have no close homology templates. The updated COFACTOR server and the template libraries are available at http://zhanglab.ccmb.med.umich.edu/COFACTOR/.
The IntaRNA algorithm enables fast and accurate prediction of RNA-RNA hybrids by incorporating seed constraints and interaction site accessibility. Here, we introduce IntaRNAv2, which enables ...enhanced parameterization as well as fully customizable control over the prediction modes and output formats. Based on up to date benchmark data, the enhanced predictive quality is shown and further improvements due to more restrictive seed constraints are highlighted. The extended web interface provides visualizations of the new minimal energy profiles for RNA-RNA interactions. These allow a detailed investigation of interaction alternatives and can reveal potential interaction site multiplicity. IntaRNAv2 is freely available (source and binary), and distributed via the conda package manager. Furthermore, it has been included into the Galaxy workflow framework and its already established web interface enables ad hoc usage.
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