All data has been taken from the article: U. Alon, N. Barkai, D. A. Notterman, K. Gish, S. Ybarra, D. Mack, and A. J. Levine "Broad patterns of gene expression revealed by clustering of tumor and normal colon tissues probed by oligonucleotide arrays", Proc. Natl. Acad. Sci. USA, 96 (12), 6745-6750 (1999) [ MEDLINE abstract; PNAS full text ].
Data contain the measured expression levels for 2000 human cDNAs and ESTs (including the sequences that are homologous to some known eukaryotic genes) in colon adenocarcinomas from several patients. For some patients, the expression of these RNAs was also measured in normal colon tissues. Totally, the table contains expression measurements for 40 tumorous and 22 normal colon tissues. These data are combined in appropriate groups: "Tumor" and "Normal".
Original data has been taken from the site Microarray Databases (November 2002 ) Data pertaining to the article ‘Broad patterns of gene expression revealed by clustering of tumor and normal colon tissues probed by oligonucleotide arrays’ page. Expression data are taken from the I2000.html, file, displayed on this page. The order and numeration correspond to data from the tissues.html, file with '-' symbol. Names of normal tissues begin with letter "N". Sequences' identifiers have been taken from the names.html, file also displayed on this page (the order of IDs corresponds to that in the I2000.html file). On formation of SELTAG data, the columns 1 and 2 of the file were interchanged. The resulting file of data in SELTAG format (alon1999_set.txt) has been formed by direct integration of sequences' descriptors (fields F1-F6) and data on expression (fields F7-F68).
The SELTAG software was used for hierarchical clustering of experiments form the "alon1999_set" by means of various agglomerative approaches. The results are represented in the alon1999_set.doc file are in accordance with that in the article Alon et al (1999).
Complete list of files for "alon1999_set" data that are on Softberry server:
| File | Size | Description |
| alon1999_set.txt | 1,471 kb | Data in SELTAG format |
| alon1999_set.descr | 191 kb | Links for genes Unigene (sorted by their GenBank AC, field F1 "SequenceId" from file alon1999_set.txt) |
| alon1999_set.seq | 2,999kb | Genes' sequences in FASTA format |
| alon1999_set_example.pdf | 523 kb | Example of data analysis by mean of SELTAG (pdf) |
| alon1999_set_example.html | 31 kb | Example of data analysis by mean of SELTAG (html) |
| alon1999_set_I2000_ori.txt | 1,806 kb | Original "I2000" file with data on genes expression |
| alon1999_set_names_ori.txt | 531 kb | Original "names" file with sequences' descriptors |
| alon1999_set_tissues_ori.txt | 1 kb | Original "tissues" file with tissues marking |
| alon1999_set_descr_ori.txt | 3 kb | Description of original data |
| alon1999_set_paper.pdf | 732 kb | Original article Alon et al (1999) |