SLIDE – a web-based tool for interactive visualization of large-scale – omics data

Ghosh, Soumita; Datta, Abhik; Tan, Kai Sen; Choi, Hyungwon

doi:10.1093/bioinformatics/bty534

Cited by 8 publications

(9 citation statements)

References 8 publications

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“…In addition, prior to multiSLIDE visualization of matching mRNAs and proteins for 1237 genes, the mRNA data was separately inspected in the context of the whole transcriptome (16,704 genes) using a related single-omics data visualization tool SLIDE 39 (see Methods and Supplementary Fig. S2 ).…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, it may not be particularly well suited for the unrestricted exploration of whole multi-omics datasets. Such global exploration can be done using other tools such as multiSLIDE’s sister tool SLIDE 39 . As an alternative querying mechanism, multiSLIDE provides the option to detect differentially expressed genes and perform enrichment analysis to identify key pathways and GO terms enriched in the user’s data.…”

Section: Discussionmentioning

confidence: 99%

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multiSLIDE is a web server for exploring connected elements of biological pathways in multi-omics data

2021

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Quantitative multi-omics data are difficult to interpret and visualize due to large volume of data, complexity among data features, and heterogeneity of information represented by different omics platforms. Here, we present multiSLIDE, a web-based interactive tool for the simultaneous visualization of interconnected molecular features in heatmaps of multi-omics data sets. multiSLIDE visualizes biologically connected molecular features by keyword search of pathways or genes, offering convenient functionalities to query, rearrange, filter, and cluster data on a web browser in real time. Various querying mechanisms make it adaptable to diverse omics types, and visualizations are customizable. We demonstrate the versatility of multiSLIDE through three examples, showcasing its applicability to a wide range of multi-omics data sets, by allowing users to visualize established links between molecules from different omics data, as well as incorporate custom inter-molecular relationship information into the visualization. Online and stand-alone versions of multiSLIDE are available at https://github.com/soumitag/multiSLIDE.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

multiSLIDE is a web server for exploring connected elements of biological pathways in multi-omics data

2021

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“…Before we explore this multi-omics data, we first visualize the entire data sets separately using the SLIDE tool, another related tool that we had previously developed for full-scale single-omics data visualization (41). We applied hierarchical clustering with Euclidean distance and complete linkage to the whole transcriptome data comprising of 16,704 genes in SLIDE ( Supplementary Figure S3A ).…”

Section: Resultsmentioning

confidence: 99%

“…Moreover, such architectures facilitate highly parallel communication. Similar to SLIDE, a tool we had developed for online visualization of single -omics data (41), multiSLIDE is available online and can also be used as a standalone software. Due to its modular design, multiSLIDE can also easily scale to distributed multi-node environments.…”

Section: Methodsmentioning

confidence: 99%

multiSLIDE: a web server for exploring connected elements of biological pathways in multi-omics data

Ghosh

Datta

Choi

2019

Preprint

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We present multiSLIDE, an open-source tool for query-driven visualization of quantitative single- or multiomics data. Using pathways and networks as the basis for data linkage, multiSLIDE provides an interactive platform for querying the multi-omics data by genes, pathways, and intermolecular relationships. Representing individual -omics levels as separate heatmaps, multiSLIDE visualizes quantitative data for selected genes at all omics levels in a single snapshot. The tool also provides functionalities to arrange data both ways, by their phenotypic characteristics and by their molecular interactions or co-membership to common pathways. Built-in statistical tests and clustering methods provide display subsets of interesting genes or rearrange the genes based on expression patterns. All visualization panels are fully customizable, and both the graphics and the analysis workspace can be saved and shared between collaborating parties. We demonstrate the utility of multiSLIDE through two example studies. First, with a time-course data of HeLa cells, subjected to dithiothreitol induced endoplasmic reticulum stress, we visualized different stages of unfolded protein response and identified temporal patterns of gene expression response at the mRNA and protein levels. Second, through joint visualization of mRNA and protein expression of TCGA/CPTAC Invasive Breast Carcinoma data, we explored the estrogen receptor α regulon and prioritized clusters of genes associated with PAM50 basal-like subtype.

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“…In addition to the aforementioned list of tools/methods that help in integration of multi-omics data sets to derive meaningful and actionable insights, there are a wide array of portals/ platforms that help in exploration, visualization, analysis, and interpretation of multi-omics data. There are a multitude of tools like GENEASE, 79 CGDV 80 and SLIDE 81 that provide ease of visualization and interpretation of large biological data sets. However, these tools help in analysis and visualization of single omic data set at a time.…”

Section: Portals For Visualization and Interpretation Of Multi-omics Data Setsmentioning

confidence: 99%

Multi-omics Data Integration, Interpretation, and Its Application

Subramanian

Verma

Kumar

et al. 2020

Bioinform Biol Insights

814

611

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To study complex biological processes holistically, it is imperative to take an integrative approach that combines multi-omics data to highlight the interrelationships of the involved biomolecules and their functions. With the advent of high-throughput techniques and availability of multi-omics data generated from a large set of samples, several promising tools and methods have been developed for data integration and interpretation. In this review, we collected the tools and methods that adopt integrative approach to analyze multiple omics data and summarized their ability to address applications such as disease subtyping, biomarker prediction, and deriving insights into the data. We provide the methodology, use-cases, and limitations of these tools; brief account of multi-omics data repositories and visualization portals; and challenges associated with multi-omics data integration.

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SLIDE – a web-based tool for interactive visualization of large-scale – omics data

Abstract: Supplementary Information are available at Bioinformatics online.

Cited by 8 publications

References 8 publications

multiSLIDE is a web server for exploring connected elements of biological pathways in multi-omics data

multiSLIDE is a web server for exploring connected elements of biological pathways in multi-omics data

multiSLIDE: a web server for exploring connected elements of biological pathways in multi-omics data

Multi-omics Data Integration, Interpretation, and Its Application

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