Summary of Study ST000230

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000186. The data can be accessed directly via it's Project DOI: 10.21228/M87303 This work is supported by NIH grant, U2C- DK119886.


Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files
Study IDST000230
Study TitleComprehensive analysis of transcriptome and metabolome in Intrahepatic Cholangiocarcinoma and Hepatocellular Carcinoma
Study Typetissue type comparison
Study SummaryCholangiocarcinoma tissue, surrounded non-tumor tissue, Hepatocellular Carcinoma tissue, and surrounded non-tumor tissue were compared via metabolomic analysis.
Osaka City University
DepartmentDepartment of Hepatology
Last NameMurakami
First NameYoshiki
Address1-4-3, asahimachi, Abeno-ku, Osaka 545-8585, Osaka Japan
Submit Date2015-07-11
Num Groups4
Total Subjects24 samples
Raw Data AvailableNo
Analysis Type DetailLC-MS
Release Date2015-08-03
Release Version1
Yoshiki Murakami Yoshiki Murakami application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR000186
Project DOI:doi: 10.21228/M87303
Project Title:Comprehensive analysis of transcriptome and metabolome analysis in Intrahepatic Cholangiocarcinoma and Hepatocellular Carcinoma
Project Type:Population Genetics for comparison between cholangiocarcinoma and hepatocellular carcinoma
Project Summary:Intrahepatic cholangiocarcinoma (ICC) and hepatocellular carcinoma (HCC) are liver originated malignant tumors. The prognosis of ICC is generally worse than that of HCC because there is lack of early diagnostic marker for ICC and the carcinogenic mechanism of ICC is not fully understood. So our aim was to perform metabolome and transcriptome analysis to reveal the carcinogenetic mechanism and to detect an early diagnostic marker for ICC Ten ICC and 6 HCC which were resected surgically, were enrolled. miRNA and mRNA expression analysis were performed by microarray on ICC and HCC and their corresponding non-tumor tissues (ICC_NT and HCC_NT). Compound analysis was performed using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS). Principle component analysis (PCA) revealed that our four sample groups (ICC, ICC_NT, HCC, and HCC_NT) have 14 compounds, 62 mRNAs and 17 miRNAs with distinct expressive patterns. There were two distinct patterns among the 4 groups; one is tumor and non-tumor, the other is ICC and non-ICC. To clarify the biological significance of individual genes and compounds, we performed pathway analysis. ICC formation was related to RNA synthesis, amino acid synthesis, and glucose-lipid synthesis pathway. ICC was classified by distinct pattern of compounds with high accuracy (84.38%). PCA revealed that several pathways were associated with the development of ICC and distinguished ICC from other diseases. These findings are a promising step towards establishing novel biomarkers that can be clinically applicable.
Institute:Osaka City University
Department:Department of Hepatology
Last Name:Murakami
First Name:Yoshiki
Address:1-4-3, asahimachi, Abeno-ku, Osaka 545-8585, Osaka Japan


Subject ID:SU000249
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human


Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Tissue Type
SA01084419HCC (Hepatocellular carcinoma)
SA01084523HCC (Hepatocellular carcinoma)
SA01084610HCC (Hepatocellular carcinoma)
SA01084713HCC (Hepatocellular carcinoma)
SA01084815HCC (Hepatocellular carcinoma)
SA01084917HCC (Hepatocellular carcinoma)
SA01085020HCC-NT (surrounded non tumor of HCC)
SA01085112HCC-NT (surrounded non tumor of HCC)
SA01085214HCC-NT (surrounded non tumor of HCC)
SA01085316HCC-NT (surrounded non tumor of HCC)
SA01085418HCC-NT (surrounded non tumor of HCC)
SA01085524HCC-NT (surrounded non tumor of HCC)
SA01085621ICC (Intrahepatic cholangiocarcinoma)
SA0108571ICC (Intrahepatic cholangiocarcinoma)
SA0108583ICC (Intrahepatic cholangiocarcinoma)
SA0108595ICC (Intrahepatic cholangiocarcinoma)
SA0108607ICC (Intrahepatic cholangiocarcinoma)
SA0108619ICC (Intrahepatic cholangiocarcinoma)
SA01086222ICC-NT (surrounded non tumor of ICC)
SA0108632ICC-NT (surrounded non tumor of ICC)
SA0108644ICC-NT (surrounded non tumor of ICC)
SA0108656ICC-NT (surrounded non tumor of ICC)
SA0108668ICC-NT (surrounded non tumor of ICC)
SA01086711ICC-NT (surrounded non tumor of ICC)
Showing results 1 to 24 of 24


Collection ID:CO000239
Collection Summary:-
Sample Type:Liver


Treatment ID:TR000259

Sample Preparation:

Sampleprep ID:SP000253
Sampleprep Summary:-

Combined analysis:

Analysis ID AN000343 AN000344
Analysis type MS MS
Chromatography type
Chromatography system
MS instrument type TOF TOF
MS instrument name Agilent 6220 TOF Agilent 6220 TOF
Units Peak area Peak area


Chromatography ID:CH000257


MS ID:MS000289
Analysis ID:AN000343
Instrument Name:Agilent 6220 TOF
Instrument Type:TOF
Tube Lens Voltage:ANION (NEGATIVE)
MS ID:MS000290
Analysis ID:AN000344
Instrument Name:Agilent 6220 TOF
Instrument Type:TOF
Tube Lens Voltage:CATION (POSITIVE)