Omics Data - Liver Diseases

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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