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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
    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 TypeCancer IDSamplesDeath EventsMedian OS (yrs)PermissionLink
Adrenocortical carcinoma ACC 92 33 NA Y TCGA-Link, GDAC-Link
Bladder urothelial carcinoma BLCA 412 178 2.84 Y TCGA-Link, GDAC-Link
Breast invasive carcinoma BRCA 1097 151 10.81 Y TCGA-Link, GDAC-Link
CPTAC-Link
Cervical and endocervical cancers CESC 307 71 8.48 Y TCGA-Link, GDAC-Link
Cholangiocarcinoma CHOL 45 19 3.84 Y TCGA-Link, GDAC-Link
Colorectal adenocarcinoma COADREAD 629 124 6.94 Y TCGA-Link, GDAC-Link
CPTAC-Link
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma DLBC 48 9 17.6 Y TCGA-Link, GDAC-Link
Esophageal carcinoma ESCA 185 74 2.19 Y TCGA-Link, GDAC-Link
Glioblastoma multiforme GBM 595 472 1.21 Y TCGA-Link, GDAC-Link
Glioma GBMLGG 1110 595 2.05 Y TCGA-Link, GDAC-Link
Head and Neck squamous cell carcinoma HNSC 528 218 4.75 Y TCGA-Link, GDAC-Link
Kidney Chromophobe KICH 113 11 NA Y TCGA-Link, GDAC-Link
Pan-kidney cohort KIPAN 941 230 NA Y TCGA-Link, GDAC-Link
Kidney renal clear cell carcinoma KIRC 537 175 7.57 Y TCGA-Link, GDAC-Link
Kidney renal papillary cell carcinoma KIRP 291 44 NA Y TCGA-Link, GDAC-Link
Acute Myeloid Leukemia LAML 200 109 1.34 Y TCGA-Link, GDAC-Link
Brain Lower Grade Glioma LGG 515 123 7.29 Y TCGA-Link, GDAC-Link
Liver hepatocellular carcinoma LIHC 377 125 4.91 Y TCGA-Link, GDAC-Link
Lung adenocarcinoma LUAD 522 179 4.11 Y TCGA-Link, GDAC-Link
Lung squamous cell carcinoma LUSC 504 203 4.64 Y TCGA-Link, GDAC-Link
Mesothelioma MESO 87 72 1.54 Y TCGA-Link, GDAC-Link
Ovarian serous cystadenocarcinoma OV 591 335 3.81 Y TCGA-Link, GDAC-Link
CPTAC-Link
Pancreatic adenocarcinoma PAAD 185 99 1.66 Y TCGA-Link, GDAC-Link
Pheochromocytoma and Paraganglioma PCPG 179 6 NA Y TCGA-Link, GDAC-Link
Prostate adenocarcinoma PRAD 499 10 NA Y TCGA-Link, GDAC-Link
Sarcoma SARC 261 97 5.45 Y TCGA-Link, GDAC-Link
Skin Cutaneous Melanoma SKCM 470 221 6.58 Y TCGA-Link, GDAC-Link
Stomach adenocarcinoma STAD 443 162 2.86 Y TCGA-Link, GDAC-Link
Stomach and Esophageal carcinoma STES 628 236 2.58 Y TCGA-Link, GDAC-Link
Testicular Germ Cell Tumors TGCT 134 3 NA Y TCGA-Link, GDAC-Link
Thyroid carcinoma THCA 503 16 NA Y TCGA-Link, GDAC-Link
Thymoma THYM 124 9 NA Y TCGA-Link, GDAC-Link
Uterine Corpus Endometrial Carcinoma UCEC 548 91 NA Y TCGA-Link, GDAC-Link
Uterine Carcinosarcoma UCS 57 34 2.22 Y TCGA-Link, GDAC-Link
Uveal Melanoma UVM 80 23 3.82 Y TCGA-Link, GDAC-Link
CellLine Colorectal adenocarcinoma CL_COADREAD 44-- N CL-COADREAD-Link
PDX - Breast Cancer PDX_BRCA 37-- N PDX-BRCA-Link

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
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.