Asexual Cell Cycle in P. falciparum

Sample description and normalization results (TXT file ).
Raw expression data, Affymetrix CEL files (gzip compressed).
The Scripps/GNF malaria array definition (probe-to-gene mapping, with probe sequence) (CSV file),
the complete array description (gzip tsv file, gzip file with probe sequence).
MOID analysis for each sample (TSV files)
(Sporozoite.tsv is the average of the two sporozite experiments)

Correlation coefficients between samples of two cell cycles (S & T) in both the linear scale (TXT file) and the log scale (TXT file).
(based only on cell-cycle regulated genes)
Correlation coefficients among samples in the log scale based on all P. falciparum genes (TXT files).
The correlation coefficients between replicates are 0.98 (log scale) and 0.99 (linear scale).

E-LogP analysis on the background control genes (PDF file).
The false positive rate is estimated to be 5+/-0.5% by the criterion: (E>10 & LogP<-0.5).
Present analysis results on all samples (CSV, all 16 stages).
Present analysis results on all cell cycles (S & T) (CSV): cell cycle S, CSV, cell cycle T, CSV, gametocyte & sporozoite).
The "cnt" column in the spreadsheet stores the number of samples where the gene is considered present. cnt=0 means the corresponding gene is absent in all the stages of the cell cycle. cnt=7 means the gene is always present in cell cycle S or T.
Results: 3864 genes are present in cell cycle S, 4026 genes are present in cell cycle T. Between them, 3614 are overlapped. 883 genes are absent in both cell cycles (S & T).
Download the list of genes that are present in both cell cycle S and T (TXT file).
Download the list of genes that are absent in both cell cycle S and T (TXT file).
Download the list of genes that are present in cell cycle S only (250) (TXT File).
Download the list of genes that are present in cell cycle T only (412) (TXT File).

Among the 3614 commonly expressed genes in both cell cycles,
1489+238 present genes are regulated (ANOVA P-value <= 0.05 & FC >= 1.5) in cell cycle S (CSV file),
1489+504 present genes are regulated (ANOVA P-value <= 0.05 & FC >= 1.5) in cell cycle T (CSV file),
1489 genes are regulated in both cell cycles (CSV file).
Download the list of genes that are regulated in cell cycle S only (238) (TXT file).
Download the list of genes that are regulated in cell cycle T only (504) (TXT file).
Download the list of genes that shows no regulation in both cell cycles (1383) (TXT file).
Download the list of genes that are cell cycle-regulated in both cell cycles (1489) (TXT file).
There are 746 genes that are not cell cycle-regulated in both methods (S & T), but show differential expression when both cell cycle data are compared to the add-on set (gametocyte and sporozoite).
(ANOVA P-value > 0.05 in cell cycle S and P-value > 0.05 in cell cycle T and (P-value <= 0.05 & FC >= 1.5) in cell cycle S + add-on and (P-value <= 0.05 & FC >= 1.5) in cell cycle T + add-on).
ANOVA results for testing on cell cycle S + the add-on set (CSV file).
ANOVA results for testing on cell cycle T + the add-on set (CSV file).
The list of 1489+746=2234 genes, that are used for final culstering analysis (CSV file).
Download the list of genes for the 746-gene set (TXT File).

(PDF file, PPT file).
Download all data that are used to compile the van diagram (XLS Excel file). (updated 4/17/03)

k= 10, 15, 20, 25, 30
Download all clusters (CSV file).
The results for k=15 is analyzed in our paper.

To visualize the results, please download and install the TreeView program from Eisen Lab (Eisen et al. (1998) PNAS 95:14863.).
Download .cdt & .gtr (gzip compressed).
We recommend you download the tar.gz files. If you download the individual .cdt and .gtr files, you must save the files with the exact extensions in order to use TreeView.
Choose "Load File" in TreeView to browse the .cdt files. Notice there are k sets of files, one for each of the k clusters.