Summary of data of Chen Xin, et all 2002
paper
Last updated April 3, 2007 by
Nasser Abbasi
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
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)
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 |
|
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 |
|
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 |
|
SHAM |
Sample GSM79827 Primary tumor, Liver Sarcoma (SF26) GSM79868 Non-tumor tissue, Liver GSM79914 Non-tumor tissue, Liver GSM79916 Non-tumor tissue, Liver |
|
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 |
|
SHAO |
Samples GSM79786 Metastatic tumor, Liver GSM79787 Metastatic tumor, Liver GSM79788 Metastatic tumor, Liver GSM79789 Metastatic tumor, Liver GSM79878 Non-tumor tissue, Liver |
|
SHBJ |
Samples GSM79811 Non-tumor tissue, Liver |
|
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 |
|
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 |
|
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 |
|
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 |
|
SHQ |
Samples GSM79841 Cell-line, Liver GSM79873 Cell-line, Liver GSM79875 Cell-line, Liver GSM79876 Cell-line, Liver GSM79877 Cell-line, Liver |
|
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 |
http://genome-www.stanford.edu/hcc/
http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE3500