LinkedOmics: analyzing multi-omics data within and across 32 cancer types

Abstract

The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. To allow comprehensive analysis of these data, we developed three analysis modules in the LinkedOmics web application. The LinkFinder module allows flexible exploration of associations between a molecular or clinical attribute of interest and all other attributes, providing the opportunity to analyze and visualize associations between billions of attribute pairs for each cancer cohort. The LinkCompare module enables easy comparison of the associations identified by LinkFinder, which is particularly useful in multi-omics and pan-cancer analyses. The LinkInterpreter module transforms identified associations into biological understanding through pathway and network analysis. Using five case studies, we demonstrate that LinkedOmics provides a unique platform for biologists and clinicians to access, analyze and compare cancer multi-omics data within and across tumor types. LinkedOmics is freely available at http://www.linkedomics.org.

CCND1, NOP14 and DNMT3B are involved in miR‐502‐5p–mediated inhibition of cell migration and proliferation in bladder cancer

“…We initially analysed the effect of NOP14 on cell proliferation. The CCK8 assay showed a significant reduction in cell viabilities in the si-NOP14 group compared with the NC group at different concentration levels (25,50,75, 100 nmol/L; Figure 4A).…”

“…To identify direct targets of miR-502-5p, we initially used bioinformatics prediction websites (TargetScan, LinkedOmics and miRWalk) for primary screening analysis. [23][24][25] A total of 672 genes were found in all three databases ( Figure 3A). Furthermore, pathway analysis of the 672 genes was performed with KOBAS 3.0.…”

PYCR1 knockdown inhibits the proliferation, migration, and invasion by affecting JAK/STAT signaling pathway in lung adenocarcinoma

“…Indeed, a great range of lung cancer research was involved in this database, such as the prognostic roles of KIF23 in NSCLC 13 and the clinical significance of HOXA13 in LUAD 14 . LinkedOmics database (http://www.linkedomics.org) is a portal to analyze multiomics data and clinical data for 32 cancer types from The Cancer Genome Atlas (TCGA) project 15 . It contains three analysis modules, namely LinkFinder, LinkInterpreter, and LinkCompare.…”

HYAL‐1‐induced autophagy facilitates pancreatic fistula for patients who underwent pancreaticoduodenectomy

“…The Cancer Genome Atlas database consisted of 178 tissues samples of PDAC was downloaded from the updated TCGA database (https://cancergenome.nih.gov/). The RNA sequencing data were analyzed from LinkedOmics (http://www.linkedomics.org) …”

“…The RNA sequencing data were analyzed from LinkedOmics (http:// www.linke domics.org). 22 The correlated genes of HYAL-1 were evaluated with Pearson Correlation test in PDAC tissues and the Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and kinase targets were predicted. To gain insight into HYAL-1-mediated molecular and biological functions, Gene Set Enrichment Analysis (GSEA) was then assessed.…”