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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 carcinoma TCGA ACC 92 33 NA Y TCGA, GDAC Download
Bladder urothelial carcinoma TCGA BLCA 412 178 2.84 Y TCGA, GDAC Download
Breast invasive carcinoma TCGA BRCA 1097 151 10.81 Y TCGA, GDAC, CPTAC Download
Cervical and endocervical cancers TCGA CESC 307 71 8.48 Y TCGA, GDAC Download
Cholangiocarcinoma TCGA CHOL 45 19 3.84 Y TCGA, GDAC Download
Colorectal adenocarcinoma TCGA COADREAD 629 124 6.94 Y GDAC, CPTAC Download
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma TCGA DLBC 48 9 17.60 Y TCGA, GDAC Download
Esophageal carcinoma TCGA ESCA 185 74 2.19 Y TCGA, GDAC Download
Glioblastoma multiforme TCGA GBM 595 472 1.21 Y TCGA, GDAC Download
Glioma TCGA GBMLGG 1110 595 2.05 Y TCGA, GDAC Download
Head and Neck squamous cell carcinoma TCGA HNSC 528 218 4.75 Y TCGA, GDAC Download
Kidney Chromophobe TCGA KICH 113 11 NA Y TCGA, GDAC Download
Pan-kidney cohort TCGA KIPAN 941 230 NA Y TCGA, GDAC Download
Kidney renal clear cell carcinoma TCGA KIRC 537 175 7.57 Y TCGA, GDAC Download
Kidney renal papillary cell carcinoma TCGA KIRP 291 44 NA Y TCGA, GDAC Download
Acute Myeloid Leukemia TCGA LAML 200 109 1.34 Y TCGA, GDAC Download
Brain Lower Grade Glioma TCGA LGG 515 123 7.29 Y TCGA, GDAC Download
Liver hepatocellular carcinoma TCGA LIHC 377 125 4.91 Y TCGA, GDAC Download
Lung adenocarcinoma TCGA LUAD 522 179 4.11 Y TCGA, GDAC Download
Lung squamous cell carcinoma TCGA LUSC 504 203 4.64 Y TCGA, GDAC Download
Mesothelioma TCGA MESO 87 72 1.54 Y TCGA, GDAC Download
Ovarian serous cystadenocarcinoma TCGA OV 591 335 3.81 Y TCGA, GDAC, CPTAC Download
Pancreatic adenocarcinoma TCGA PAAD 185 99 1.66 Y TCGA, GDAC Download
Pheochromocytoma and Paraganglioma TCGA PCPG 179 6 NA Y TCGA, GDAC Download
Prostate adenocarcinoma TCGA PRAD 499 10 NA Y TCGA, GDAC Download
Sarcoma TCGA SARC 261 97 5.45 Y TCGA, GDAC Download
Skin Cutaneous Melanoma TCGA SKCM 470 221 6.58 Y TCGA, GDAC Download
Stomach adenocarcinoma TCGA STAD 443 162 2.86 Y TCGA, GDAC Download
Stomach and Esophageal carcinoma TCGA STES 628 236 2.58 Y TCGA, GDAC Download
Testicular Germ Cell Tumors TCGA TGCT 134 3 NA Y TCGA, GDAC Download
Thyroid carcinoma TCGA THCA 503 16 NA Y TCGA, GDAC Download
Thymoma TCGA THYM 124 9 NA Y TCGA, GDAC Download
Uterine Corpus Endometrial Carcinoma TCGA UCEC 548 91 NA Y TCGA, GDAC Download
Uterine Carcinosarcoma TCGA UCS 57 34 2.22 Y TCGA, GDAC Download
Uveal Melanoma TCGA UVM 80 23 3.82 Y TCGA, GDAC Download
CellLine Colorectal adenocarcinoma CL COADREAD 44 - - N - -
PDX - Breast Cancer PDX BRCA 37 - - N - -
Brain Metastatic Lung Cancer - Lung adenocarcinoma BMLC LUAD 18 - - N - -
CPTAC - Colon Adenocarcinoma CPTAC COAD 210 - - N - -
CPTAC - Uterine Corpus Encometrial Carcinoma CPTAC UCEC 168 - - N - -
CPTAC - Breast invasive carcinoma CPTAC BRCA 17 - - N - -
PDX - Breast Cancer (TW) PDX BRCA 16 - - 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
  • Oct 8, 2018 : WikiPathways summit demo. Workshop tutorial can be found here Summit at UCSF, Gladstone Institute
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.