Data from Omics Studies in Liver Disease

Hepatocellular Carcinoma

Primary Biliary Cirrhosis

Primary Sclerosing Cholangitis

Non-Alcoholic SteatoHepatitis

Alcoholic Hepatitis

Cell Line

 

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Hepatocellular Carcinoma
Study Description Omics Link to Data
The Cancer Genome Atlas for human tumor/ adjacent tumor/ normal samples
  • Methylation
  • Copy number variation/ mutation/ structural variation/ SNP;
  • Transcriptome expression;
  • Non-coding RNA: micro RNA, long non-coding RNA, small non-coding RNA;
  • Protein expression
TCGA
Exosomal or serum miRNA in liver disease Non-coding RNA: micro RNA, long non-coding RNA, small non-coding RNA GSE85680
Non-coding RNA profiling from 100 HCC patients Non-coding RNA: micro RNA, long non-coding RNA, small non-coding RNA GSE28854
Tumor-adjacent liver tissues from 263 Japanese patients who underwent curative surgery for HCC Transcriptome expression GSE70297
Expression data from hepatocellular carcinoma PDX
  • Transcriptome expression;
  • Copy number variation/ mutation/ structural variation/ SNP
GSE90653
218 HCC, 10 Cirrhotic and 10 considered Normal patients + 12 liver cell lines Non-coding RNA: micro RNA, long non-coding RNA, small non-coding RNA GSE74618
Comparison of hepatocellular carcinoma with non-cancerous liver tissue. Transcriptome expression GSE364
801 primary HCC developed in 720 patients Transcriptome expression GSE129322
35 paired HCC and non-tumor tissues Transcriptome expression GSE124535
Gut microbiota analysis associated with hepatocellular carcinoma Microbiome 16s rRNA GSE108847
Comprehensive molecular characterization of liver cancer and inheritance of the phenotypic traits during tumor recurrence
  • Methylation
  • Transcriptome expression
GSE112791
Circulating microRNAs from HCC patients recruited in the Ph3 RESORCE trial Non-coding RNA: micro RNA, long non-coding RNA, small non-coding RNA GSE119221
Gene expression profiling of chronic hepatitis B induced HCC and adjacent-normal tissues Transcriptome expression GSE121248
Molecular predictors of prevention of recurrence in hepatocellular carcinoma with sorafenib as adjuvant treatment in the phase 3 STORM trial Transcriptome expression GSE109211
Integrative Epigenetic Analysis Reveals Therapeutic Targets to the DNA Methyltransferase Inhibitor SGI-110 in Hepatocellular Carcinoma Cells
  • Methylation
  • Transcriptome expression
GSE105067
MicroRNA and gene expression profile on 64 HCC tumor patients
  • Transcriptome expression
  • Non-coding RNA: micro RNA, long non-coding RNA, small non-coding RNA
GSE116182 and GSE116174
Single cell analysis reveals cancer cell heterogeneities in hepatocellular carcinoma Transcriptome expression GSE103591
Molecular Signature of Hepatitis D Virus-Associated Hepatocellular Carcinoma Transcriptome expression GSE107170
Molecular heterogeneity of multinodular hepatocellular carcinoma
  • Copy number variation/ mutation/ structural variation/ SNP
  • Transcriptome expression
GSE65373
Integrative genomic analysis in HCC samples
  • Copy number variation/ mutation/ structural variation/ SNP
  • Transcriptome expression
GSE109361
107 samples covering 9 stages of HCC Transcriptome expression GSE89377
mRNA profiling of 64 HCC and 30 non-tumor Transcriptome expression GSE87630
lncRNA profiling on 175 serum samples Non-coding RNA: micro RNA, long non-coding RNA, small non-coding RNA GSE78160
HCC and CCA from the Thailand Initiative in Genomics and Expression Research for Liver Cancer (TIGER-LC)
  • Copy number variation/ mutation/ structural variation/ SNP
  • Transcriptome expression
GSE76213
38 pairs of tumor tissues and adjacent non-tumor tissues from HCC patients
  • Transcriptome expression
  • Non-coding RNA: micro RNA, long non-coding RNA, small non-coding RNA
GSE84006
115 primary tumor tissue samples and 52 adjacent non-tumor tissues samples derived from 115 HCC patients Transcriptome expression GSE76427
The molecular landscape of HCC with portal vein tumor thrombosis
  • Methylation
  • Copy number variation/ mutation/ structural variation/ SNP
  • Transcriptome expression
  • Non-coding RNA: micro RNA, long non-coding RNA, small non-coding RNA
GSE77276
RNA-seq of 50 paired HCC Transcriptome expression GSE77314
60 biopsy pairs from HCC patients and 5 normal liver biopsies Transcriptome expression GSE64041
Single Cell triple omics sequencing reveals genetic and epigenetic heterogeneity in HCC Transcriptome expression GSE65364
Primary and adjacent non-malignant tissue samples of 100 HCC patients
  • Transcriptome expression
  • Non-coding RNA: micro RNA, long non-coding RNA, small non-coding RNA
GSE62044
Samples included 48 HBsAg carriers who developed HCC and 48 HBsAg carriers who did not during follow-up Methylation GSE78904
ctDNA methylation markers in diagnosis and prognosis of HCC (serum of 1221 HCC patients and from 970 healthy controls) Methylation GSE93203
37 paired genomic DNA from patients with hepatitis virus-related HCC Methylation GSE89852

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Primary Biliary Cirrhosis
Study Description Omics Link to Data
Whole blood samples from 90, 45, 95 and 93 patients with PBC, PSC, CD (Crohn’s disease), and UC (ulcerative colitis), respectively, and 47 healthy controls. Transcriptome expression GSE119600

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Primary Sclerosing Cholangitis
Study Description Omics Link to Data
Whole blood samples from 90, 45, 95 and 93 patients with PBC, PSC, CD (Crohn’s disease), and UC (ulcerative colitis), respectively, and 47 healthy controls. Transcriptome expression GSE119600

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Non-Alcoholic SteatoHepatitis
Study Description Omics Link to Data
Tumor-adjacent liver tissues from 263 Japanese patients who underwent curative surgery for HCC Transcriptome expression GSE70297
C (control=14), H (healthy obese=27), S (steatosis=14) and N (nash=18) Transcriptome expression GSE48452
Liver biopsies obtained from healthy normal weight (n=14) and obese (n=12) individuals, NAFL (n=15) and NASH (n=16) patients Transcriptome expression GSE126848
152 patients at baseline (44 no NASH, 104 NASH, 4 undefined) and 79 patients (54 no NASH, 22 NASH, 3 undefined) at 1 year follow-up (38 diet restriction [Diet], 41 bariatric surgery [BS]) Transcriptome expression GSE83452
63 participants (20 simple steatosis, 19 NASH, 24 healthy control) Transcriptome expression GSE89632
HCV 64 samples; HBV 4 samples; NASH 7 samples; healthy 12 Non-coding RNA: micro RNA, long non-coding RNA, small non-coding RNA GSE33857
35 mild NAFLD (33 unique samples) and 24 advanced NAFLD (23 unique sample) Methylation GSE49542

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Alcoholic Hepatitis
Study Description

Omics

Link to Data
Liver RNA-seq  (Hiseq2000, Illumina): 10 Normal liver, 18 severe AH (biopsies), 11 severe AH (explants), 12 Early Alcoholic Steatohepatitis (eASH), 10 HCV-related Cirrosis, 9 NAFLD, 9 HCV-chronic infection no cirrhosis; Liver DNA-methylomic chip (EPIC-infinium, Illumina): 5 normal livers, 6 severe AH Methylation

Transcriptome expression

dbGaP-AH
Severe alcoholic hepatitis treated with corticosteroids (array & nanostring) Transcriptome expression GSE94417

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Cell Line
Study Description Omics Link to Data
Cancer Cell Line Encyclopedia for liver cell lines Methylation

Copy number variation/ mutation/ structural variation/ SNP;

Transcriptome expression;

Non-coding RNA: micro RNA, long non-coding RNA, small non-coding RNA;

Protein expression

CCLE
Single cell analysis reveals cancer cell heterogeneities in hepatocellular carcinoma Transcriptome expression GSE103591
Integrative genomic analysis in HCC samples Copy number variation/ mutation/ structural variation/ SNP

Transcriptome expression

GSE109361
Single Cell triple omics sequencing reveals genetic and epigenetic heterogeneity in HCC Methylation

Transcriptome expression

GSE65364
11,215 tumors and 29 different tissues correlate with response to 265 compounds profiled in 1,001 cancer cell lines Methylation GSE68379
156 primary tissues and 25 cultured normal and HCC cell lines Methylation GSE60753

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