Overview of Q-fever studies eligible for the integrative data analysis.

Biological data analysis is the key to new discoveries in disease biology and drug discovery. The rapid proliferation of high-throughput ‘omics’ data has necessitated a need for tools and platforms that allow the researchers to combine and analyse different types of biological data and obtain biologically relevant knowledge. We had previously developed TargetMine, an integrative data analysis platform for target prioritisation and broad-based biological knowledge discovery. Here, we describe the newly modelled biological data types and the enhanced visual and analytical features of TargetMine. These enhancements have included: an enhanced coverage of gene–gene relations, small molecule metabolite to pathway mappings, an improved literature survey feature, and in silico prediction of gene functional associations such as protein–protein interactions and global gene co-expression. We have also described two usage examples on trans-omics data analysis and extraction of gene-disease associations using MeSH term descriptors. These examples have demonstrated how the newer enhancements in TargetMine have contributed to a more expansive coverage of the biological data space and can help interpret genotype–phenotype relations. TargetMine with its auxiliary toolkit is available at https://targetmine.mizuguchilab.org. The TargetMine source code is available at https://github.com/chenyian-nibio/targetmine-gradle.

This dataset contains the latent variable READ_THETA that was estimated across 5 different projects using integrated data analysis

Additional file 20: Table S1. Comparison of the performances in detecting simulated metadata between envfit, adonis, ANOSIM and tmap.

This dataset contains p-values and statistical significance data derived from analyzing various metabolic and dietary states in mice. The data supports research investigating the effects of diet and metabolic conditions on localized variables in specific regions of mice. The files included are:

1. PValues_and_Significance_Fasted.xlsx: P-values for variables under a fasted metabolic state.
2. PValues_and_Significance_CTRL.xlsx: P-values for variables under a control dietary state.
3. PValues_and_Significance_Western.xlsx: P-values for variables under a western dietary state.
4. PValues_and_Significance_Interdietary.xlsx: P-values comparing variables between different dietary states.

Data Collection Methods The data was collected by analyzing correlations between variables within localized regions of the mice. These variables were consistent within individuals but showed variation dependent on dietary or metabolic states. Data collection involved the following steps: 1. Selection of experimental groups based on dietary and metabolic conditions. 2. Quantitative measurement of specific variables in localized regions of mice. 3. Statistical analysis to determine the significance of correlations across the groups.

Data Generation and Processing 1. Generation: Measurements were obtained through laboratory analysis using standardized protocols for each dietary/metabolic condition. 2. Processing: - Statistical tests were performed to identify significant correlations (e.g., t-tests, ANOVA). - P-values were computed to quantify the significance of the relationships observed. - Data was compiled into Excel sheets for organization and clarity. Technical and Non-Technical Information - Technical Details: Each file contains tabular data with headers indicating the variable pairs analyzed, their respective p-values, and the significance level (e.g., p<0.05, p<0.01).

Additional file 21: Table S2. Detection of host covariates significantly associated with the FGFP microbiomes using envfit, adonis, ANOSIM and tmap.

Additional file 24: Table S5. Comparison of the stratification of the AGP microbiomes between tmap and PAM based clustering.

Hepatocellular organic anion transporting polypeptides (OATP1B1, OATP1B3, and OATP2B1) are important for proper liver function and the regulation of the drug elimination process. Understanding their roles in different conditions of liver toxicity and cancer requires an in-depth investigation of hepatic OATP–ligand interactions and selectivity. However, such studies are impeded by the lack of crystal structures, the promiscuous nature of these transporters, and the limited availability of reliable bioactivity data, which are spread over different data sources in the open domain. To this end, we integrated ligand bioactivity data for hepatic OATPs from five open data sources (ChEMBL, the UCSF–FDA TransPortal database, DrugBank, Metrabase, and IUPHAR) in a semiautomatic KNIME workflow. Highly curated data sets were analyzed with respect to enriched scaffolds, and their activity profiles and interesting scaffold series providing indication for selective, dual-, or pan-inhibitory activity toward hepatic OATPs could be extracted. In addition, a sequential binary modeling approach revealed common and distinctive ligand features for inhibitory activity toward the individual transporters. The workflows designed for integrating data from open sources, data curation, and subsequent substructure analyses are freely available and fully adaptable. The new data sets for inhibitors and substrates of hepatic OATPs as well as the insights provided by the feature and substructure analyses will guide future structure-based studies on hepatic OATP–ligand interactions and selectivity.

Cross-linking mass spectrometry data for integrative structural analyses of the Smc5/6 holo-complex from budding yeast. Electron microscopy, crosslinking mass spectrometry, and computational modeling reveal that while the complex shares an overall organization with other SMC complexes, it possesses several strikingly different features.

Additional file 22: Table S3. Co-enrichment subnetworks of pet past 3 months and its co-enriched features of the FGFP microbiomes.

Web based gene expression database and analysis platform. Used for integrative data mining of genotype and phenotype data, with optimized workflows.

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 6/12/25. ITTACA is a database created for Integrated Tumor Transcriptome Array and Clinical data Analysis. ITTACA centralizes public datasets containing both gene expression and clinical data and currently focuses on the types of cancer that are of particular interest to the Institut Curie: breast carcinoma, bladder carcinoma, and uveal melanoma. ITTACA is developed by the Institut Curie Bioinformatics group and the Molecular Oncology group of UMR144 CNRS/Institut Curie. A web interface allows users to carry out different class comparison analyses, including comparison of expression distribution profiles, tests for differential expression, patient survival analyses, and users can define their own patient groups according to clinical data or gene expression levels. The different functionalities implemented in ITTACA are: - To test if one or more gene, of your choice, is differentially expressed between two groups of samples exhibiting distinct phenotypes (Student and Wilcoxon tests). - The detection of genes differentially expressed (Significance Analysis of Microarrays) between two groups of samples. - The creation of histograms which represent the expression level according to a clinical parameter for each sample. - The computation of Kaplan Meier survival curves for each group. ITTACA has been developed to be a useful tool for comparing personal results to the existing results in the field of transcriptome studies with microarrays.

Various types of genomic data (e.g., SNPs and mRNA transcripts) have been employed to identify risk genes for complex diseases. However, the analysis of these data has largely been performed in isolation. Combining these multiple data for integrative analysis can take advantage of complementary information and thus can have higher power to identify genes (and/or their functions) that would otherwise be impossible with individual data analysis. Due to the different nature, structure, and format of diverse sets of genomic data, multiple genomic data integration is challenging. Here we address the problem by developing a sparse representation based clustering (SRC) method for integrative data analysis. As an example, we applied the SRC method to the integrative analysis of 376821 SNPs in 200 subjects (100 cases and 100 controls) and expression data for 22283 genes in 80 subjects (40 cases and 40 controls) to identify significant genes for osteoporosis (OP). Comparing our results with previous studies, we identified some genes known related to OP risk (e.g., ‘THSD4’, ‘CRHR1’, ‘HSD11B1’, ‘THSD7A’, ‘BMPR1B’ ‘ADCY10’, ‘PRL’, ‘CA8’,’ESRRA’, ‘CALM1’, ‘CALM1’, ‘SPARC’, and ‘LRP1’). Moreover, we uncovered novel osteoporosis susceptible genes (‘DICER1’, ‘PTMA’, etc.) that were not found previously but play functionally important roles in osteoporosis etiology from existing studies. In addition, the SRC method identified genes can lead to higher accuracy for the diagnosis/classification of osteoporosis subjects when compared with the traditional T-test and Fisher-exact test, which further validates the proposed SRC approach for integrative analysis.

The objective of the fourth Technical Meeting on Fusion Data Processing, Validation and Analysis was to provide a platform during which a set of topics relevant to fusion data processing, validation and analysis are discussed with the view of extrapolating needs to next step fusion devices such as ITER. The validation and analysis of experimental data obtained from diagnostics used to characterize fusion plasmas are crucial for a knowledge-based understanding of the physical processes governing the dynamics of these plasmas. This paper presents the recent progress and achievements in the domain of plasma diagnostics and synthetic diagnostics data analysis (including image processing, regression analysis, inverse problems, deep learning, machine learning, big data and physics-based models for control) reported at the meeting. The progress in these areas highlight trends observed in current major fusion confinement devices. A special focus is dedicated on data analysis requirements for ITER and DEMO with a particular attention paid to Artificial Intelligence for automatization and improving reliability of control processes.

The global integrated data visualization tools market is anticipated to reach a value of XXX million by 2033, expanding at a CAGR of XX% during the forecast period (2025-2033). The market growth is attributed to the increasing adoption of data visualization tools by organizations to gain insights from complex data, make informed decisions, and improve operational efficiency. Furthermore, the growing demand for cloud-based data visualization solutions and the rising adoption of mobile devices for data visualization are also contributing to the market growth. North America is expected to dominate the integrated data visualization tools market throughout the forecast period. The region is home to leading technology companies that offer innovative data visualization solutions. Additionally, the presence of a large number of enterprises and government organizations in North America is driving the demand for data visualization tools. The Asia Pacific region is anticipated to witness the fastest growth rate during the forecast period due to the increasing adoption of data visualization tools in emerging economies such as China and India.

The size of the Cloud Network Integrated Data Center market was valued at USD XXX million in 2024 and is projected to reach USD XXX million by 2033, with an expected CAGR of XX % during the forecast period.

Integrative analysis between methylation and expression data in PTC samples. Legend. FGD functional genomic distribution, CHR chromosome, DMR differential methylation region, RDMR reprogramming-specific differentially methylated region, CDMR cancer-specific differentially methylated region, NA not available, NS not significant, FC fold change, FDR false discovery rate, R inverse correlation. (XLSX 122 kb)

The purpose of this data collection is to provide an official public record of the business of the federal courts. The data originate from district and appellate court offices throughout the United States. Information was obtained at two points in the life of appellate and civil cases: filing and termination. The termination data (archived in this data collection) contain information on both filing and terminations, while the pending data (archived as a separate data collection) contain only filing information on the most recent pending cases. The unit of analysis for the appellate and civil terminations data is the case. This collection also contains data on criminal cases in federal courts. However, the unit of analysis for the criminal data is the defendant, and a defendant can be included in several cases.

Applying differentially expressed genes (DEGs) to identify feasible biomarkers in diseases can be a hard task when working with heterogeneous datasets. Expression data are strongly influenced by technology, sample preparation processes, and/or labeling methods. The proliferation of different microarray platforms for measuring gene expression increases the need to develop models able to compare their results, especially when different technologies can lead to signal values that vary greatly. Integrative meta-analysis can significantly improve the reliability and robustness of DEG detection. The objective of this work was to develop an integrative approach for identifying potential cancer biomarkers by integrating gene expression data from two different platforms. Pancreatic ductal adenocarcinoma (PDAC), where there is an urgent need to find new biomarkers due its late diagnosis, is an ideal candidate for testing this technology. Expression data from two different datasets, namely Affymetrix and Illumina (18 and 36 PDAC patients, respectively), as well as from 18 healthy controls, was used for this study. A meta-analysis based on an empirical Bayesian methodology (ComBat) was then proposed to integrate these datasets. DEGs were finally identified from the integrated data by using the statistical programming language R. After our integrative meta-analysis, 5 genes were commonly identified within the individual analyses of the independent datasets. Also, 28 novel genes that were not reported by the individual analyses (‘gained’ genes) were also discovered. Several of these gained genes have been already related to other gastroenterological tumors. The proposed integrative meta-analysis has revealed novel DEGs that may play an important role in PDAC and could be potential biomarkers for diagnosing the disease.