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ABOUT
LinkedOmics is publicly available portal that includes multi-omics data from all 32 TCGA Cancer types. It also includes mass spectrometry-based proteomics data generated by the Clinical Proteomics Tumor Analysis Consortium (CPTAC) for TCGA breast, colorectal and ovarian tumors.

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,
    Vasaikar S., Straub P., Wang J., Zhang B. LinkedOmics: analyzing multi-omics data within and across 32 cancer types. Nucleic Acids Research, gkx1090, 2017 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).

For more information (Click here)
LinkedOmics Data Source
Cancer TypeCohort SourceCancer IDSamplesDeath EventsMedian OS (yrs)PermissionLinkData Download
Adrenocortical carcinomaTCGA ACC 92 33 NA Y TCGA, GDACDownload
Bladder urothelial carcinomaTCGA BLCA 412 178 2.84 Y TCGA, GDACDownload
Breast invasive carcinomaTCGA BRCA 1097 151 10.81 Y TCGA, GDAC
CPTAC
Download
Cervical and endocervical cancersTCGA CESC 307 71 8.48 Y TCGA, GDACDownload
CholangiocarcinomaTCGA CHOL 45 19 3.84 Y TCGA, GDACDownload
Colorectal adenocarcinomaTCGA COADREAD 629 124 6.94 Y TCGA, GDAC
CPTAC
Download
Lymphoid Neoplasm Diffuse Large B-cell LymphomaTCGA DLBC 48 9 17.6 Y TCGA, GDACDownload
Esophageal carcinomaTCGA ESCA 185 74 2.19 Y TCGA, GDACDownload
Glioblastoma multiformeTCGA GBM 595 472 1.21 Y TCGA, GDACDownload
GliomaTCGA GBMLGG 1110 595 2.05 Y TCGA, GDACDownload
Head and Neck squamous cell carcinomaTCGA HNSC 528 218 4.75 Y TCGA, GDACDownload
Kidney ChromophobeTCGA KICH 113 11 NA Y TCGA, GDACDownload
Pan-kidney cohortTCGA KIPAN 941 230 NA Y TCGA, GDACDownload
Kidney renal clear cell carcinomaTCGA KIRC 537 175 7.57 Y TCGA, GDACDownload
Kidney renal papillary cell carcinomaTCGA KIRP 291 44 NA Y TCGA, GDACDownload
Acute Myeloid LeukemiaTCGA LAML 200 109 1.34 Y TCGA, GDACDownload
Brain Lower Grade GliomaTCGA LGG 515 123 7.29 Y TCGA, GDACDownload
Liver hepatocellular carcinomaTCGA LIHC 377 125 4.91 Y TCGA, GDACDownload
Lung adenocarcinomaTCGA LUAD 522 179 4.11 Y TCGA, GDACDownload
Lung squamous cell carcinomaTCGA LUSC 504 203 4.64 Y TCGA, GDACDownload
MesotheliomaTCGA MESO 87 72 1.54 Y TCGA, GDACDownload
Ovarian serous cystadenocarcinomaTCGA OV 591 335 3.81 Y TCGA, GDAC
CPTAC
Download
Pancreatic adenocarcinomaTCGA PAAD 185 99 1.66 Y TCGA, GDACDownload
Pheochromocytoma and ParagangliomaTCGA PCPG 179 6 NA Y TCGA, GDACDownload
Prostate adenocarcinomaTCGA PRAD 499 10 NA Y TCGA, GDACDownload
SarcomaTCGA SARC 261 97 5.45 Y TCGA, GDACDownload
Skin Cutaneous MelanomaTCGA SKCM 470 221 6.58 Y TCGA, GDACDownload
Stomach adenocarcinomaTCGA STAD 443 162 2.86 Y TCGA, GDACDownload
Stomach and Esophageal carcinomaTCGA STES 628 236 2.58 Y TCGA, GDACDownload
Testicular Germ Cell TumorsTCGA TGCT 134 3 NA Y TCGA, GDACDownload
Thyroid carcinomaTCGA THCA 503 16 NA Y TCGA, GDACDownload
ThymomaTCGA THYM 124 9 NA Y TCGA, GDACDownload
Uterine Corpus Endometrial CarcinomaTCGA UCEC 548 91 NA Y TCGA, GDACDownload
Uterine CarcinosarcomaTCGA UCS 57 34 2.22 Y TCGA, GDACDownload
Uveal MelanomaTCGA UVM 80 23 3.82 Y TCGA, GDACDownload
CellLine Colorectal adenocarcinomaCL COADREAD 44-- N CL-COADREAD-
PDX - Breast CancerPDX BRCA 37-- N PDX-BRCA-
CPTAC - Colon AdenocarcinomaCPTACCOAD210--N-
CPTAC - Uterine Corpus Encometrial CarcinomaCPTACUCEC168--N-
Brain Metastatic Lung Cancer - Lung adenocarcinomaBMLCLUAD18--N-

Please Note:
  • COADREAD: colorectal, combines COAD + READ
  • GBMLGG: glioma, combines GBM + LGG
  • KIPAN: pan-kidney, combines KICH + KIRC + KIRP
  • STES: stomach-esophogeal, combines STAD + ESCA

(* We acknowledge usage of data from The cancer genome Atlas (TCGA), The Clinical Proteomic Tumor Analysis Consortium (CPTAC) and Broad GDAC)
Manual and Tutorial
News or Update
  • March 29, 2017 : First version of LinkedOmics portal is available to public.
  • Sept 29, 2017 : Workshop at Breast Cancer Center, Baylor College of Medicine. Workshop tutorial can be found here Workshop at BCM
  • May 2, 2018 : Workshop at CPTAC3 meeting NIH. Workshop tutorial can be found here Workshop at NIH
Share your Data
We are happy to integrate your data into LinkedOmics portal. Follow the instructions given in manual. Please contact admin to share your data (linkedomics.zhanglab@gmail.com).
Browser Compatibility
The tool best run with browser Chrome Version 56.0.2924.87+ (download). If you are using Safari then enable the hidden Develop menu in Safari: Pull down the “Safari” menu and choose “Preferences” Click on the “Advanced” tab. Check the box next to “Show Develop menu in menu bar”. Click Develop menu and select Chrome/Firefox as browser.