Summary of data of Chen Xin, et all 2002 paper

Last updated April 3, 2007 by Nasser Abbasi

 

Introduction. 1

Data tables. 2

Reference. 8

 

Introduction

This is a review of the data used by Chen Xin, et all 2002 paper:  PubMed ID 12058060, 15154008

http://genome-www.stanford.edu/hcc/

The purpose of this note is to get more familiar with the content of the data before we start the PCA and ICA analysis using this data.

The data contains a total of 207 samples. 74 of these are non-tumor, 102 are primary liver tumor, 74 are Metastatic tumor, Liver (Tumor that primary in another part of the body but has spread to the liver), and 3 are Adenoma (benign lesions), 4 are benign tumor, and 10 are liver cell lines (which I need to understand more what this means).

This table summarizes this:

Description

No. of Samples

Adenoma

3

FNH

4

HCC (Primary)

105

Metastatic

9

Non-tumor liver

76

Liver cancer cell lines

10

 

The data that will be used in the PCA and ICA analysis will use the GEO database from NCBI. The data will be downloaded in the form of SOFT file (560 MB in size). Matlab bioinformatics toolbox 2.5 will be used to read the data initially.

The data can be found at this link below:

http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE3500
 


 

Data tables

I have compiled this long table below which shows each sample name/reference, the type of sample, and the platform the sample was build on. This table will be used as a reference when the analysis part starts.

The dataset (called series, GSE) is GSE3500, it contains 13 platforms, and 207 samples.  The dataset can be seen at the following URL

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3500

It contains 13 platforms. (GPL), platforms contains samples (GSM files)

GPL2648

SHX

Samples

GSM79795 Metastatic tumor, Liver

GSM79796 Primary tumor, Liver

GSM79797 Primary tumor, Liver

GSM79798 Non-tumor tissue, Liver

GSM79814 Non-tumor tissue, Liver

GSM79821 Metastatic tumor, Liver Met. Colon Cancer (SF10)

GSM79904 Primary tumor, Liver

GSM79905 Primary tumor, Liver

GSM79906 Non-tumor tissue, Liver

GSM79925 Primary tumor, Liver

GSM79926 Non-tumor tissue, Liver

GSM79932 Non-tumor tissue, Liver

GSM79933 Primary tumor, Liver

GSM79934 Non-tumor tissue, Liver

GSM79971 Non-tumor tissue, Liver

GSM79973 Primary tumor, Liver

GSM79975 Non-tumor tissue, Liver

GSM79980Primary tumor, Liver

GSM79981 Non-tumor tissue, Liver

GSM79982Primary tumor, Liver

GSM79983 Primary tumor, Liver

GSM79984 Primary tumor, Liver

GPL2649

SHT

Samples

GSM79785 Primary tumor, Liver HCC (HCV+, SF30)

GSM79818 Primary tumor, Liver

GSM79924 Non-tumor tissue, Liver

GSM79986 Non-tumor tissue, Liver

GSM79989 Non-tumor tissue, Liver

GPL2831

SHR

Samples

GSM79790 Primary tumor, Liver

GSM79801 Cell-line, Liver

GSM79809 Non-tumor tissue, Liver

GSM79813 Primary tumor, Liver

GSM79822 Non-tumor tissue, Liver

GSM79828 Metastatic tumor, Liver

GSM79862 Cell-line, Liver

GSM79872 Cell-line, Liver

GSM79899 Primary tumor, Liver

GSM79900 Primary tumor, Liver

GSM79902 Non-tumor tissue, Liver

GSM79903 Non-tumor tissue, Liver

GSM79923 Primary tumor, Liver

GSM79927 Primary tumor, Liver

GSM79930 Primary tumor, Liver

GSM79931 Primary tumor, Liver

GSM79945 Cell-line, Liver

GSM79948 Non-tumor tissue, Liver

GSM79953 Primary tumor, Liver

GSM79955 Primary tumor, Liver

GSM79956 Non-tumor tissue, Liver

GSM79959 Non-tumor tissue, Liver

GSM79960 Non-tumor tissue, Liver

GSM79962 Primary tumor, Liver

GSM79965 Primary tumor, Liver

GSM79967Primary tumor, Liver

GPL2868

SHAM

Sample

GSM79827 Primary tumor, Liver Sarcoma (SF26)

GSM79868 Non-tumor tissue, Liver

GSM79914 Non-tumor tissue, Liver

GSM79916 Non-tumor tissue, Liver

GPL2906

SHAK

Samples

GSM79802 Primary tumor, Liver

GSM79806 Adenoma, Liver

GSM79825 Primary tumor, Liver

GSM79843 Non-tumor tissue, Liver

GSM79850 Primary tumor, Liver

GSM79851 Primary tumor, Liver

GSM79867 Primary tumor, Liver

GSM79869 Primary tumor, Liver

GSM79870 Non-tumor tissue, Liver

GSM79879 Primary tumor, Liver

GSM79890 Primary tumor, Liver

GSM79896 Primary tumor, Liver

GSM79897 Primary tumor, Liver

GSM79898 Non-tumor tissue, Liver

GSM79901 Primary tumor, Liver

GSM79908 Primary tumor, Liver

GSM79912 Primary tumor, Liver

GSM79913 Primary tumor, Liver

GSM79915 Primary tumor, Liver

GSM79951 Non-tumor tissue, Liver

GSM79952Non-tumor tissue, Liver

GSM79964 Primary tumor, Liver

GSM79987 Non-tumor tissue, Liver

GSM79988Non-tumor tissue, Liver

GPL2935

SHAO

Samples

GSM79786 Metastatic tumor, Liver

GSM79787 Metastatic tumor, Liver

GSM79788 Metastatic tumor, Liver

GSM79789 Metastatic tumor, Liver

GSM79878 Non-tumor tissue, Liver

GPL2938

SHBJ

Samples

GSM79811 Non-tumor tissue, Liver

GPL2948

SHAD

Samples

GSM79792 Non-tumor tissue, Liver

GSM79829 Non-tumor tissue, Liver

GSM79835 Non-tumor tissue, Liver

GSM79839 Primary tumor, Liver

GSM79853 Metastatic tumor, Liver, Met. Colon Carcinoid (SF11)

GSM79858 Non-tumor tissue, Liver

GSM79863 Primary tumor, Liver

GSM79884 Non-tumor tissue, Liver

GSM79917 Non-tumor tissue, Liver

GSM79918 Primary tumor, Liver

GSM79919 Non-tumor tissue, Liver

GSM79920 Primary tumor, Liver

GSM79922 Non-tumor tissue, Liver

GSM79929 Primary tumor, Liver

GSM79946 Primary tumor, Liver

GSM79947 Primary tumor, Liver

GSM79949Primary tumor, Liver

GSM79963 Primary tumor, Liver

GSM79977 Primary tumor, Liver

GPL3007

SHAB

Samples

GSM79936 Non-tumor tissue, Liver

GSM79937 Primary tumor, Liver

GSM79939 Non-tumor tissue, Liver

GSM79941Primary tumor, Liver

GSM79943 Non-tumor tissue, Liver

GSM79944 Primary tumor, Liver

GSM79968 Non-tumor tissue, Liver

GSM79969Metastatic tumor, Liver,Undifferentiated Carcinoma (HK17)

GSM79972 Non-tumor tissue, Liver

GSM79974 Primary tumor, Liver

GSM79976Non-tumor tissue, Liver

GSM79978Primary tumor, Liver

GPL3008

SHW

Samples

GSM79791 Non-tumor tissue, Liver

GSM79793 Primary tumor, Liver

GSM79794 Non-tumor tissue, Liver

GSM79817 Cell-line, Liver

GSM79938 Primary tumor, Liver

GSM79942 Primary tumor, Liver

GSM79966 Non-tumor tissue, Liver

GPL3009

SHAG

Samples:

GSM79784 Non-tumor tissue, Liver

GSM79800 Non-tumor tissue, Liver

GSM79812 Primary tumor, Liver

GSM79815 Non-tumor tissue, Liver

GSM79816 Primary tumor, Liver

GSM79819 Primary tumor, Liver

GSM79820 Non-tumor tissue, Liver

GSM79837 Primary tumor, Liver

GSM79838 Primary tumor, Liver

GSM79840 Primary tumor, Liver

GSM79845 Primary tumor, Liver

GSM79849 Primary tumor, Liver

GSM79880 Primary tumor, Liver

GSM79881 Primary tumor, Liver

GSM79882 Primary tumor, Liver

GSM79883 Primary tumor, Liver

GSM79885 Primary tumor, Liver

GSM79886 Primary tumor, Liver

GSM79893 Primary tumor, Liver

GSM79928 Non-tumor tissue, Liver

GSM79950 Non-tumor tissue, Liver

GSM79954Non-tumor tissue, Liver

GSM79957 FNH, Liver

GSM79958 Non-tumor tissue, Liver

GSM79961 FNH, Liver

GSM79970 Non-tumor tissue, Liver

GSM79985 Non-tumor tissue, Liver

GSM79990 Primary tumor, Liver

GPL3010

SHQ

Samples

GSM79841 Cell-line, Liver

GSM79873 Cell-line, Liver

GSM79875 Cell-line, Liver

GSM79876 Cell-line, Liver

GSM79877 Cell-line, Liver

GPL3011

SHAN

Samples

GSM79799 Primary tumor, Liver

GSM79803 Non-tumor tissue, Liver

GSM79804 Primary tumor, Liver

GSM79805 Primary tumor, Liver

GSM79807 Primary tumor, Liver

GSM79808 Non-tumor tissue, Liver

GSM79810 Non-tumor tissue, Liver

GSM79823 Primary tumor, Liver

GSM79824 Primary tumor, Liver

GSM79826 Primary tumor, Liver

GSM79830 Primary tumor, Liver

GSM79831 Non-tumor tissue, Liver

GSM79832 Primary tumor, Liver

GSM79833 Non-tumor tissue, Liver

GSM79834 Primary tumor, Liver

GSM79836 Primary tumor, Liver

GSM79842 FNH, Liver

GSM79844 FNH, Liver

GSM79846 Adenoma, Liver

GSM79847 Primary tumor, Liver

GSM79848 Non-tumor tissue, Liver

GSM79852 Non-tumor tissue, Liver

GSM79854 Non-tumor tissue, Liver

GSM79855 Non-tumor tissue, Liver

GSM79856 Non-tumor tissue, Liver

GSM79857 Primary tumor, Liver

GSM79859 Primary tumor, Liver

GSM79860 Non-tumor tissue, Liver

GSM79861 Non-tumor tissue, Liver

GSM79864 Primary tumor, Liver

GSM79865 Primary tumor, Liver

GSM79866 Non-tumor tissue, Liver

GSM79871 Adenoma, Liver

GSM79874 Primary tumor, Liver

GSM79887 Primary tumor, Liver

GSM79888 Primary tumor, Liver

GSM79889 Primary tumor, Liver

GSM79891 Primary tumor, Liver

GSM79892 Primary tumor, Liver

GSM79894 Primary tumor, Liver

GSM79895 Primary tumor, Liver

GSM79907 Non-tumor tissue, Liver

GSM79909 Primary tumor, Liver

GSM79910 Primary tumor, Liver

GSM79911 Primary tumor, Liver

GSM79921 Non-tumor tissue, Liver

GSM79935 Non-tumor tissue, Liver

GSM79940 Non-tumor tissue, Liver

GSM79979Primary tumor, Liver

 

Reference

http://genome-www.stanford.edu/hcc/

http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE3500