GEO DataSets

(Submitter supplied) Background and aims: Primary liver cancers (LCs), including HCC and intrahepatic cholangiocarcinoma (iCCA), are derived from a common developmental lineage, conferring a molecular spectrum between them. To elucidate the molecular spectrum, we performed an integrative analysis of transcriptome profiles associated with patients' radiopathologic features. Approach and results: We identified four LC subtypes (LC1-LC4) from RNA-sequencing profiles, revealing intermediate subtypes between HCC and iCCA. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

137 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: TSV, XLS

(Submitter supplied) The two oncogenes Myc and Kras cooperate to drive tumorigenesis and tumor suppressive pathways, to regulate the tumor microenvironment and to respond to immuno-therapies in different types of cancer. However, the interactions between Myc and Kras in cancer plasticity remain largely unknown. Primary liver cancer (PLC) comprises hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC), two tumor subtypes which are morphologically and clinically different, and cell intrinsic molecular mechanisms that lead to the onset of HCC or ICC remain elusive. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: TSV

(Submitter supplied) The two oncogenes Myc and Kras cooperate to drive tumorigenesis and tumor suppressive pathways, to regulate the tumor microenvironment and to respond to immuno-therapies in different types of cancer. However, the interactions between Myc and Kras in cancer plasticity remain largely unknown. Primary liver cancer (PLC) comprises hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC), two tumor subtypes which are morphologically and clinically different, and cell intrinsic molecular mechanisms that lead to the onset of HCC or ICC remain elusive. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: XLS

(Submitter supplied) 11 CCC and 5 HCC patients' tumor and non-tumor parts tissues are extracted. Then total RNA are purified from tissues and mRNA and miRNA profiles are measured using agilent one color microarrays designed for mRNA or microRNA expression profiles.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL18044 GPL16699

64 Samples

Download data: TXT

(Submitter supplied) Genome wide chromatin profiling of 16 primary liver cancer patients was performed using scATAC-seq. The aim of this study was to assess transcription factor activity in malignant and microenviornment component cells of human primary liver cancers. scATAC-seq profiles reveal similar microenvironment composition, yet malignant cells have high levels of heterogeneity in TF activation within and between patients. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

16 Samples

Download data: CSV, MTX, TBI, TSV

(Submitter supplied) Hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC) are the major primary liver cancers in adults. It has been shown the phenotypic overlap between HCC and CC, comprising continuous liver cancer spectrum. As a proof of concept, a recent study has demonstrated a genomic subtype of HCC expressing CC-like gene expression trait, i.e. CC-like HCC, which has revealed common genomic trait of stem cell-like property and aggressive clinical outcome. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

26 Samples

Download data: TXT

(Submitter supplied) Background & Aims: Intrahepatic cholangiocarcinoma (ICC) is known to heterogeneous with diverse etiology, morphology, and clinical outcomes. Recently, cholangiolar differentiation of ICC has been suggested to associate with prognostic outcomes, however, its molecular patho-biological features and clinical significances were not evaluated extensively. Methods:Integrative analysis was performed using transcriptomic profiles (n=27) and tissue microarrays (n=142) from ICC specimens. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

27 Samples

Download data: TXT

(Submitter supplied) Intrahepatic cholangiocarcinoma (iCCA) is the second most common primary liver cancer. It is defined by cholangiocytic differentiation and has poor prognosis. Recently, epigenetic processes have been shown to play an important role in cholangiocarcinogenesis. We performed an integrative analysis on 52 iCCAs using both genetic and epigenetic data with a specific focus on DNA methylation components. We identified four major iCCA subgroups with widespread genomic and epigenomic differences and prognostic implications. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

64 Samples

Download data: IDAT

(Submitter supplied) Purpose: The aim of this study is to investigate mechanisms driving tumor-promoting mechanisms in cholangiocarcinoma while focusing on transitions from normal cholangiocytes to precancer lesions and from precancer lesion to invasive carcinoma. An original mouse model of intrahepatic cholangiocarcinoma was developed, based on induction of a KrasG12D mutation in cholangiocytes combined with chronic inflammation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL6244 GPL14732

72 Samples

Download data: CEL, RCC

(Submitter supplied) We compared transcriptomic profiles of ICC tumor specimens to hepatocellular carcinoma (HCC) specimens using Affymetrix mRNA array and the miRNA array platforms to search for unique gene signatures linked to patient prognosis. ICC and HCC share common stem-like molecular characteristics and stem-like tumor features associated with poor prognosis.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL14732

35 Samples

Download data: RCC

(Submitter supplied) We compared transcriptomic profiles of 23 ICC tumor specimens to hepatocellular carcinoma (HCC) specimens using Affymetrix mRNA array and the miRNA array platforms to search for unique gene signatures linked to patient prognosis. ICC and HCC share common stem-like molecular characteristics and stem-like tumor features associated with poor prognosis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

37 Samples

Download data: CEL

(Submitter supplied) Intrahepatic cholangiocarcioma has two molecular classification of intrahepatic CCA with distinct clinical, pathological, biological and prognostic differences

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

57 Samples

Download data: TXT

(Submitter supplied) Introduction: Combined hepatocellular-cholangiocarcinoma (cHCC-CCA) is a mixed-type tumor of hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), which is classified into classical type (i.e., c-CHC) and intermediate cell type (i.e., i-CHC). c-CHC harbors both HCC and iCCA cells, whereas i-CHC is comprised of intermediate cell types lacking classical regions of HCC or iCCA cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

25 Samples

Download data: TXT