Linkouts
The NG-CHM Viewer includes in its architecture a mechanism to supports link outs to other websites and tools. The linkots are configured to pass data to the other websites to enable searching for selected data in those websites and tools either in a new browser tab and/or in some cases inside a Linkout Panel inside the NG-CHM panels area. These features can enable acces to tools that can help to better understand and explain the data in the NG-CHMs.
NGCHM Linkouts for Bioinformatics Researchers
You can enhance your NGCHM experience by leveraging a range of plugins that provide seamless integration with various genomic and bioinformatics databases.
The various linkouts that are available for a particular NG-CHM will vary dependent on the type of data the NG-CHM is defined to contain. i.e. If one of the axes is defined to be genes, then the gene related linkouts will be available for the rows of genes selected in the NG-CHM.
Here’s a brief explanation of each of the NG-CHM linkouts:
Amigo Gene Ontology Database
Linking to Amigo allows you to explore gene ontology information directly from your heatmap, providing insights into gene functions, biological processes, and molecular functions relevant to your data.
BioGPS Gene Annotation Portal
BioGPS annotations help you quickly obtain gene-related information such as expression profiles, functional annotations, and pathway data, making your heatmap more informative and context-rich.
Cancer Digital Slide Archive - TCGA Digital Slide Images
This plugin enables you to view digital pathology slides from TCGA directly linked to your heatmap data, facilitating a visual correlation between genomic alterations and histopathological features.
cBioPortal - Cancer Genomics
Integrate cBioPortal data to access comprehensive cancer genomics datasets. This allows for in-depth analysis of genetic mutations, expression changes, and other genomic features directly from your heatmap.
CIViC Mutation Database
Linking to CIViC provides clinically relevant information on cancer mutations, enhancing your ability to understand the clinical impact and relevance of genetic variations observed in your heatmap.
COSMIC - Catalogue of Somatic Mutations in Cancer
The COSMIC plugin allows you to explore somatic mutation data within your heatmap, helping you identify known cancer-associated mutations and their implications.
Decipher Database
Accessing the Decipher database through your heatmap helps you investigate genomic variants and their clinical significance, providing a deeper understanding of genetic aberrations in your data.
DepMap Portal
Integrate DepMap data to study cancer dependencies and vulnerabilities. This can aid in identifying potential therapeutic targets based on the dependencies highlighted in your heatmap.
Ensembl Genome Browser
Linking to Ensembl allows you to explore detailed genomic annotations and comparative genomics, enriching your heatmap data with extensive genomic context.
FireBrowse Portal
FireBrowse integration enables you to access and visualize TCGA data, making it easier to correlate your heatmap findings with publicly available cancer genomics data.
GDC Data Portal
The GDC plugin facilitates access to the Genomic Data Commons, allowing you to incorporate extensive cancer genomics datasets into your heatmap analysis.
GeneCards - Human Gene Card Database
GeneCards integration provides comprehensive gene annotations, including functional information, expression data, and disease associations, directly within your heatmap.
Google Scholar
Quickly search for literature related to specific genes or findings in your heatmap, facilitating a connection between your data and the broader scientific research.
GTEx Portal
Integrating GTEx data allows you to analyze tissue-specific gene expression patterns, helping you understand the biological context of your heatmap findings across different tissues.
Ideogram Viewer - Interactive Ideogram
Visualize sets of genes and miRNAs on an ideogram, providing a chromosomal context to your heatmap data and helping identify genomic regions of interest.
LinkedOmics Database
Linking to LinkedOmics allows you to explore multidimensional cancer data, integrating clinical and molecular data to gain comprehensive insights from your heatmap.
MaveDB Variant Effects Database
Accessing MaveDB helps you investigate the functional effects of genetic variants observed in your heatmap, providing a deeper understanding of their biological impact.
miRBase
Linking to miRBase allows you to explore microRNA data, enhancing your heatmap with information on miRNA functions and interactions.
MSigDB Pathways Database
Integrate MSigDB data to analyze curated pathways and gene sets, helping you interpret the biological pathways involved in your heatmap findings.
MuPIT Interactive
MuPIT integration allows you to visualize protein interaction networks, providing insights into the molecular interactions underlying your heatmap data.
MWannotation - Metabolomics Name
Accessing MWannotation helps you annotate metabolites in your heatmap, linking your data to comprehensive metabolomics resources.
NCBI Resources
The NCBI plugin provides access to a wide range of NCBI resources, including gene sequences, protein information, and bibliographic data, enriching your heatmap analysis.
NDEx IQuery
Integrate NDEx IQuery to explore network data, providing a systems biology perspective to your heatmap findings.
OLSVis Ontology Lookup Service
Linking to OLSVis allows you to access ontology terms and definitions, helping you annotate and interpret the functional aspects of your heatmap data.
MD Anderson Pathways Browser
Accessing the Pathways Browser facilitates pathway analysis, helping you identify pathway memberships and interactions relevant to your heatmap.
PeptideAtlas
Integrate PeptideAtlas data to access peptide and protein identification data, enriching your heatmap with proteomics information.
PubMed Portal
Quickly access relevant research articles from PubMed, providing a bibliographic context to the findings in your heatmap.
QuickGO Gene Ontology Browser
Link to QuickGO to explore gene ontology annotations, helping you understand the biological processes, cellular components, and molecular functions associated with your heatmap data.
Antibody RRID
Access antibody identification data, ensuring the reproducibility and accuracy of your experimental results linked to your heatmap.
TCGA - The Cancer Genome Atlas
Enhance your heatmap with comprehensive cancer genomics data from TCGA, providing a rich dataset for exploring cancer biology.
TumorPortal
Linking to TumorPortal helps you explore somatic mutations in cancer, aiding in the identification of key genetic alterations in your heatmap data.
UCSC Genome Browser
Integrate UCSC Genome Browser data to access a wide range of genomic annotations, enhancing the contextual information available in your heatmap.
UniProt Protein Database
Access comprehensive protein information from UniProt, providing detailed annotations and functional information relevant to your heatmap.
Vega Genome Browser
Link to the Vega genome browser for detailed gene annotations, adding depth to your genomic analysis.
Pathways Toolbox - Analyze Gene Labels for Pathway Membership
Use the Pathways Toolbox to analyze gene labels for pathway memberships, helping you identify and understand the pathways involved in your heatmap data.