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ABOUT
LinkedOmics is publicly available portal that includes multi-omics data from all 32 TCGA Cancer types and 10 Clinical Proteomics Tumor Analysis Consortium (CPTAC) cancer cohorts.

The web application has three analytical modules: LinkFinder, LinkInterpreter and LinkCompare. LinkFinder allows users to search for attributes that are associated with a query attribute, such as mRNA or protein expression signatures of genomic alterations, candidate biomarkers of clinical attributes, and candidate target genes of transcriptional factors, microRNAs, or protein kinases. Analysis results can be visualized by scatter plots, box plots, or Kaplan-Meier plots. To derive biological insights from the association results, the LinkInterpreter module performs enrichment analysis based on Gene Ontology, biological pathways, network modules, among other functional categories. The LinkCompare module uses visualization functions (interactive venn diagram, scatter plot, and sortable heat map) and meta-analysis to compare and integrate association results generated by the LinkFinder module, which supports multi-omics analysis in a cancer type or pan-cancer analysis.


LinkedOmics provides a unique platform for biologists and clinicians to access, analyze and compare cancer multi-omics data within and across tumor types.
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Citation
Please cite this article as,
    Suhas V Vasaikar, Peter Straub, Jing Wang, Bing Zhang, LinkedOmics: analyzing multi-omics data within and across 32 cancer types, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D956–D963.https://doi.org/10.1093/nar/gkx1090
LinkedOmics "OMICS" Datatype
  • Clinical Data : It inculdes attributes like age, overall survival, phological stage (I, II, III, IV), TNM staging, Clinical subtype, Molecular Subtype, number of lymph nodes, radiation therapy.
  • Copy Number (Level: Focal, Gene) : Normalized copy number (SNPs) ans Copy number alterations for aggregated/segmented regions, per sample
  • miRNA (Leve: Gene, Isoform) : Normalized signals per probe or probe set for each participant's tumor sample
  • Mutation (Level: Site, Gene) : Mutation calls for each participant
  • Methylation (Level: Gene) : Calculated beta values mapped to genome, per sample
  • RNAseq (Level: Gene) : The normalized expression signal of individual Gene (transcripts), per sample
  • RPPA (Level: Analyte, Gene) : Normalized protein expression for each gene, per sample
  • Proteomics (Level: Gene) : Average log-ratio of sample reporter-ion to common reference of peptide ions associated with the gene in acquisitions from a specific biological Sample (Unshared Log Ratio-Average log-ratio of sample reporter-ion to common reference of peptide ions of unshared peptides only associated with the gene in acquisitions from a specific biological sample).
  • Phospho-Proteomics (Level: Site) : Average log-ratio of sample reporter-ion to common reference of peptide ions associated with phosphorylated site combinations in acquisitions from a specific biological sample (CDAP Protein Report).
  • Glyco-Proteomics (Level: Site) : Average log-ratio of sample reporter-ion to common reference of peptide ions associated with deglycosylated N-glycosylation site combinations in acquisitions from a specific biological sample (CDAP Protein Report).

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LinkedOmics Data Source
Cancer TypeCohort SourceCancer IDSamplesPermissionLinkData Download