Malaria IDC Database

This is an OLD SITE
(5/2006)

GO TO THE UPDATED SITE with all three strains: HB3, 3D7, and Dd2 and all the same search functions.

PRIMARY AND SUPPLEMENTAL DATA:

Datasets:
All arrays in these datasets have been normalized by a linear scalar (global normalization) to set the total sum of Cy3 intensity equal to the total sum of Cy5 intensity across the entire array. To calculate these sums, only array spots with an R-squared value (coefficient of determination) greater than or equal to 0.75 were included. Timepoints for which there were more than one array first were normalized and then averaged.
These datasets have not been log-transformed or mean-centered as in our expression profile figures.

Complete set (3.6 MB)
The complete dataset as a tab-delimited text file. This file includes all raw data for every oligonucleotide at each time point.

QC set (3.0 MB)
The set of oligonucleotides that passed all quality control filters. This is a tab-delimited text file.

Overview set (2.2 MB)
The dataset used to generate the IDC phaseogram as described in Fig. 2. This is a tab-delimited text file.

Primary Data:
To analyze data which has not been normalized or averaged, you will need to reconstruct the timecourse from these files. The gpr files are the output of analysis of the tiff files using GenePixPro 3.0 and contain all information regarding each individual array.

All HB3 gpr files (29 MB)
All GenePix 3.0 results files (gpr) for each microarray used in this study. These files have been compressed into a .ZIP file.

All HB3 JPEG files (159 MB)
Images in JPEG format of all microarrays used in this study. These files have been compressed into a .ZIP file.

All HB3 tiff files (450 MB)
The raw scans as .TIFF files of all microarrays used in this study. These files have been compressed into a .ZIP file.

Supplemental Data:

Table S1. Pearson correlations for ORFs represented by multiple oligonucleotides
(Tab-delimited text file - 44 KB).

Table S2. P. falciparum functional gene groups
(Tab-delimited text file - 291 KB).

Table S3. Coregulation along the chromosomes of P. falciparum
(Tab-delimited text file - 7 KB).

Table S4. 3D7 v. HB3 comparative genomic hybridization
(Tab-delimited text file - 417 KB).

Table S5. Putative apicoplast targeted genes and expression profiles
(Tab-delimited text file - 151 KB).

Table S6. Putative P. falciparum proteases and their expression data
(Tab-delimited text file - 59 KB).

Table S7. Vaccine candidate correlation table
(Tab-delimited text file - 205 KB).

Figure S1. Histogram of percent power at peak frequencies for the yeast cell cycle data.

Also available in Portable Document Format (PDF-148 KB)

Figure S2. Pearson correlation maps for the P. falciparum chromosomes.

Pearson maps and data for individual chromosomes.
Examine and download datasets used to examine coregulation of gene expression along each chromosome. Also included are graphs of the Pearson correlations of genes along each chromosome, a histogram of Pearson correlations, and a tab-delimited text file of the results. All data can be downloaded in a single .ZIP file.

Figure S3a-n. Comparative genomic hybridization of 3D7 versus HB3 for all chromosomes
Download and examine CGH data along individual chromosomes or all data.

Figure S4. Distribution of Euclidean distances between expression profiles of the IDC genes and seven vaccine candidates.

Also available in Portable Document Format (PDF-154 KB)

Expression mapped along chromosomes (802 KB)
IDC expression of unique oligonucleotides along all 14 P. falciparum chromosomes as tab-delimited PCL files for viewing in TreeView. Files have been compressed into a single .ZIP file.