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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).

For more information (Click here)
LinkedOmics Data Source
Cancer TypeCohort SourceCancer IDSamplesPermissionLinkData Download
Pheochromocytoma and Paraganglioma TCGA PCPG 179 Y TCGA, GDAC Download
Prostate adenocarcinoma TCGA PRAD 499 Y TCGA, GDAC Download
Sarcoma TCGA SARC 261 Y TCGA, GDAC Download
Pancreatic adenocarcinoma TCGA PAAD 185 Y TCGA, GDAC Download
Ovarian serous cystadenocarcinoma TCGA OV 591 Y TCGA, GDAC, CPTAC Download
Lung squamous cell carcinoma TCGA LUSC 504 Y TCGA, GDAC Download
Mesothelioma TCGA MESO 87 Y TCGA, GDAC Download
Skin Cutaneous Melanoma TCGA SKCM 470 Y TCGA, GDAC Download
Stomach adenocarcinoma TCGA STAD 443 Y TCGA, GDAC Download
Adrenocortical carcinoma TCGA ACC 92 Y TCGA, GDAC Download
Uterine Carcinosarcoma TCGA UCS 57 Y TCGA, GDAC Download
Uveal Melanoma TCGA UVM 80 Y TCGA, GDAC Download
Thymoma TCGA THYM 124 Y TCGA, GDAC Download
Thyroid carcinoma TCGA THCA 503 Y TCGA, GDAC Download
Stomach and Esophageal carcinoma TCGA STES 628 Y TCGA, GDAC Download
Testicular Germ Cell Tumors TCGA TGCT 134 Y TCGA, GDAC Download
Lung adenocarcinoma TCGA LUAD 522 Y TCGA, GDAC Download
Uterine Corpus Endometrial Carcinoma TCGA UCEC 548 Y TCGA, GDAC Download
Cholangiocarcinoma TCGA CHOL 45 Y TCGA, GDAC Download
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma TCGA DLBC 48 Y TCGA, GDAC Download
Esophageal carcinoma TCGA ESCA 185 Y TCGA, GDAC Download
Cervical and endocervical cancers TCGA CESC 307 Y TCGA, GDAC Download
Breast invasive carcinoma TCGA BRCA 1097 Y TCGA, GDAC, CPTAC Download
Liver hepatocellular carcinoma TCGA LIHC 377 Y TCGA, GDAC Download
Bladder urothelial carcinoma TCGA BLCA 412 Y TCGA, GDAC Download
Glioblastoma multiforme TCGA GBM 595 Y TCGA, GDAC Download
Colorectal adenocarcinoma TCGA COADREAD 629 Y GDAC, CPTAC Download
Kidney renal papillary cell carcinoma TCGA KIRP 291 Y TCGA, GDAC Download
Glioma TCGA GBMLGG 1110 Y TCGA, GDAC Download
Brain Lower Grade Glioma TCGA LGG 515 Y TCGA, GDAC Download
Kidney renal clear cell carcinoma TCGA KIRC 537 Y TCGA, GDAC Download
Acute Myeloid Leukemia TCGA LAML 200 Y TCGA, GDAC Download
Pan-kidney cohort TCGA KIPAN 941 Y TCGA, GDAC Download
Head and Neck squamous cell carcinoma TCGA HNSC 528 Y TCGA, GDAC Download
Kidney Chromophobe TCGA KICH 113 Y TCGA, GDAC Download
CPTAC - Lung squamous cell carcinoma CPTAC LSCC 108 Y Download
CPTAC - Glioblastoma CPTAC GBM 99 Y CPTAC Download
CPTAC - Ovarian Cancer Confirmatory Study CPTAC OV 83 Y CPTAC Download
CPTAC - Pancreatic Ductal Adenocarcinoma Discovery Study CPTAC PDAC 140 Y CPTAC Download
CPTAC - Head-and-neck squamous cell carcinoma CPTAC HNSCC 110 Y CPTAC Download
CPTAC-ICPC - Combined Lung Adenocarcinoma Cohorts CPTAC LUAD 402 N - -
CPTAC - Lung Adenocarcinoma Confirmatory Study CPTAC LUAD 123 N - -
CPTAC - Clear Cell Renal Cell Carcinoma Discovery Cohort CPTAC CCRCC 110 Y CPTAC Download
CPTAC - Colon Adenocarcinoma CPTAC COAD 210 Y CPTAC Download
CPTAC - Lung adenocarcinoma CPTAC LUAD 110 Y CPTAC Download
CPTAC Gastric Cancer Discover Study CPTAC GC 189 N - -
CPTAC - Uterine Corpus Endometrial Carcinoma CPTAC UCEC 95 Y CPTAC Download
CPTAC - Uterine Corpus Endometrial Carcinoma Confirmatory Study CPTAC UCEC 138 Y Publication Download
CPTAC - Breast cancer prospective cohort CPTAC BRCA 122 Y CPTAC Download
CPTAC pancan - Head-and-neck squamous cell carcinoma CPTAC-pancan HNSCC 108 Y CPTAC, PDC Download
CPTAC pancan - Glioblastoma CPTAC-pancan GBM 98 Y CPTAC, PDC Download
CPTAC pancan - Lung squamous cell carcinoma CPTAC-pancan LSCC 108 Y CPTAC, PDC Download
CPTAC pancan - Lung adenocarcinoma CPTAC-pancan LUAD 110 Y CPTAC, PDC Download
CPTAC pancan - Colon Adenocarcinoma cohort CPTAC-pancan COAD 109 Y CPTAC, PDC Download
CPTAC pancan - Breast cancer prospective cohort CPTAC-pancan BRCA 122 Y CPTAC, PDC Download
CPTAC pancan - Pancreatic Ductal Adenocarcinoma CPTAC-pancan PDAC 105 Y CPTAC, PDC Download
CPTAC pancan - Clear Cell Renal Cell Carcinoma CPTAC-pancan CCRCC 103 Y CPTAC, PDC Download
CPTAC pancan - Uterine Corpus Endometrial Carcinoma CPTAC-pancan UCEC 94 Y CPTAC, PDC Download
CPTAC pancan - Ovarian Cancer CPTAC-pancan OV 83 Y CPTAC, PDC Download
Breast cancer ER+ PDX PDX BRCA 22 N - -
PDX - Breast Cancer (TW) PDX BRCA 16 N - -
PDX - Breast Cancer PDX BRCA 37 N - -
PDX Breast Cancer (BCM_PDX_BRCA 2021) PDX BRCA 94 N - -
CellLine Colorectal adenocarcinoma CL COADREAD 44 N - -
Brain Metastatic Lung Cancer - Lung adenocarcinoma BMLC LUAD 18 N - -
Liverpool - Non-Small Cell Lung Cancer Liverpool NSCLC 194 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.