Malaria IDC Comparison Database

Step-by-step guide to this website:

Finding an Oligonucleotide:

As previously described, you can find an oligonucleotide or multiple oligonucleotides using the various query options. Once a specific oligonucleotide of interest has been identified, you will be sent to the appropriate oligonucleotide page.

Oligonucleotide page
The oligonucleotide page (shown below) contains four sections: oligonucleotide map, expression data, expression map, and the oligonucleotide idc/oligonucleotide-ORF data.

Oligonucleotide map
The Oligo map on the left side of the page displays the position of the ORF of interest. On top, the entire chromosome where this ORF maps to is displayed. The location of the ORF, plus the surrounding 100 kb is highlighted on the chromosome in red. In the second box, the ORF plus the surrounding 100 kb is displayed. The 10 kb surrounding the ORF is highlighed in a red box. The third box displays this 10 kb, centered around the ORF of interest. All unique oligonucleotides in this 10 kb region are displayed as black triangles. Finally, the bottom box displays the entire ORF. All unique oligonucleotides that map to the ORF are displayed as black triangles. Additionally, you can move along the chromosome to surrounding ORFs using the right and left arrows below this map.

Oligonucleotide expression graph
In the middle of the page, the expression data for the oligonucleotide of interest in the 3D7, Dd2, and HB3 strains is displayed as a graph of log ratio(cy5/cy3) versus time (top image). As you scroll your mouse arrow over the three oligo expression maps (described below), the graph changes to correspond to the strain that you are specifically in. For example, if you scroll over the 3D7 specific expression map, you will only see the 3D7 graph of expression data (bottom image). A black point represents a good data point. A white spot represents a bad data point. A red spot represents the average of multiple data for that point in the IDC.

Oligonucleotide expression maps
The oligonucleotide expression maps on the right side of the page displays the oligonucleotide's expression data as the log ratio(cy5/cy3) from -2 to 2. The oligonucleotide of interest is highlighted in a yellow box. Multiple oligonucleotides that hit the same ORF are highlighted by a black bar on the left side of each map. There is one map for each strain, 3D7, Dd2, and HB3, from right to left. The surrounding 20 oligonucleotides' expression data is also displayed.

Oligonucleotide IDC data and Oligo-ORF data
oligo data

This bottom table displays all IDC data associated with the oligonucleotide of interest: OligoID, uniqueness, hour of maximum and minimum relative expression, amplitude of expression, FFT score, phase, and CGH data. The oligo-orf data is at the bottom of this table. This portion of the table displays PlasmoDB ORF information, oligonucleotide sequence, and Automated prediction information associated with the oligonucleotide. Clicking on the PlasmoDB ID will send you back to the ORF page on this website. You can also BLAST the oligonucleotide sequence by clicking on the link: 'BLAST @ PlasmoDB'. Finally, clicking on any of the Automated predictions will link you to the appropriate page on PlasmoDB.org.

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