This directory contains the primary data from the publication

"Genes Periodically Expressed in the Human Cell Cycle and Their
Expression in Tumors."  by Whitfield, M. et al. (2002) Mol. Biol. Cell.

NOTICE: Many of the data files are simply TEXT, and can be displayed
within your web browser.  They can be saved to your hard drive after
loading, or if you prefer to download the data to your PC directly, it
is possible to retrieve them using HTTP in an equivalent manner to
FTP.  In order to download the figures without displaying them in the
browser, do the following: If using a PC, right click on each link
using your mouse and then choose "Save Target As".  If using MacOS,
"option-clicking" is the equivalent command.

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The cell cycle dataset is quite large, and so is organized in
contextual sets, named by experiment set ID (as they appear in the
Stanford Microarray Database,
http://genome-www.stanford.edu/microarray).


-exptsetno_901.tar.gz	Cell Cycle - HeLa S3, Double Thymidine Block, Experiment 1
-exptsetno_902.tar.gz	Cell Cycle - HeLa S3, Double Thymidine Block, Experiment 2
-exptsetno_903.tar.gz	Cell Cycle - HeLa S3, Double Thymidine Block, Experiment 3
-exptsetno_904.tar.gz	Cell Cycle - HeLa S3, Thymidine-Nocodazole Block
-exptsetno_905.tar.gz	Cell Cycle - HeLa S3, Mitotic Selection, Experiment 1

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- additional data from the full analysis, as visualized in the
figures, is in the following files:

dataplusscores_all5.txt		complete data and scores for all clones in all five experiments.

CellCycleGeneList_1134.txt	complete genelist and annotations for all 1134 cell cycle regulated clones.

markergenes.pcl			complete data shown in Figure 2.

top1134_all5_final_Annot.cdt	complete data table from Figures 3B and 9B
top1134_all5_final_Annot.gtr	gene tree data from from Figures 3B and 9B
top1134_all5_final_Annot.pcl	pre-clustered data from ordered as in Figure 3A and 9A.

top1134_breast_cc.cdt		complete data table from Figures 5 and 11
top1134_breast_cc.gtr		gene tree data from Figures 5 and 11
top1134_breast_cc.pcl		pre-clustered data from Figures 5 and 11

table2_knowngenes.txt		known genes from Table2 as a tab delimited text file.




-The comparisons between the 1134 clones identified in this study,
Whitfield et al.(2002) and the genes identified as cell cycle
regulated by Cho et al.(2001) Nature Genetics are in the following
files:

1134_and_Cho.txt	UNIGENE clusters identified as cell cycle regulated in this study, Whitfield et al.(2002) AND by Cho et al.(2001) Nature Genetics.
1134_not_Cho.txt	UNIGENE clusters identified as cell cycle regulated in this study but NOT by Cho et al.(2001).
cho_not_1134.txt	UNIGENE clusters identified as cell cycle reuglated by Cho et al.(2001) but NOT in this study.