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Open Access Research article

In silico and biological survey of transcription-associated proteins implicated in the transcriptional machinery during the erythrocytic development of Plasmodium falciparum

Emmanuel Bischoff12 and Catherine Vaquero3

Author Affiliations

1 Institut Pasteur, Unité d'Immunologie Moléculaire des Parasites, CNRS URA 2581, 25-28 rue du Dr Roux, 75724, Paris cedex 15, France

2 Institut Pasteur, Unité de Génétique et Génomique des Insectes Vecteurs, CNRS URA 3012, 25-28 rue du Dr Roux, 75724, Paris cedex 15, France

3 UMRS 945, Inserm & Université Pierre et Marie Curie (UPMC Paris 6), 91 Bd de l'Hôpital, 75013 Paris, France

BMC Genomics 2010, 11:34  doi:10.1186/1471-2164-11-34

Published: 15 January 2010

Additional files

Additional file 1:

Detailed directory of Plasmodium AP with a non exhaustive list of molecular reports.

Format: XLS Size: 78KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Venn diagram of TAP data taken from Coulson, Callebaut and Balaji reports and compared to our data. Red circle represents the 202 TAP included in Table 1 to 5 and additional file 1 comprising the 104 TAP from Coulson, 10 from Callebaut, 27 ApiAP2 from Balaji, 27 from PlasmoDB and our 34 new annotations. Green circle represents the 129 annotated TAP from Coulson. Blue circle represents the 20 general TAP from Callebaut including the 10 already predicted by Coulson.

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Open Data

Additional file 3:

Overview of the Plasmodium IDC TAP transcriptome. A. A phaseogram of the IDC transcriptome was created as indicated in [6] by ordering the transcriptional profiles of all TAP within the 202 present in DeRisi's data and in the normalized Winzeler's data. Furthermore right to the phaseogram: first lane stands for class and subclass of TAP, followed by accession number, and if appropriate the corresponding protein complex and finally the functional annotation. This phaseogram was subdivided (from high to low) in seven sets of genes as indicated in the left of the figure. The green-red (low to high) representation of gene expression ratio is specified top of the figure. B. The hours of maximal expression reached throughout the IDC by every class of TAP are indicated: red: I. general transcription; green: II chromatin-related; blue: specific transcription factors and orange: IV TAP partners.

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Open Data

Additional file 4:

Clustering of Winzeler's data according to the deduced level of transcripts potential. The data using TIGR Mev 4.2. software were grouped in five clusters (left) from low to high expression levels. Colorimetric representation and the different stages of the IDC are as in figure 1 (top of the figure).

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Open Data

Additional file 5:

Potential interactions observed within the 202 TAP by in silico and yeast two hybrid approach. TAP candidates eliciting interactions from in silico [53] and Y2D data [54] were extracted from PlasmoDB and only the proteins inferring an interaction are presented. The two networks were merged and graphically represented using Cytoscape 2.6 http://www.cytoscape.org webcite. Red circle stands for general transcription factors, yellow for chromatin-related proteins, green for specific transcription factors and blue for partners. Grey lines represent the in silico and pink lines defined interactions proposed by the two-hybrid experiment.

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Open Data

Additional file 6:

List of 109 Pfam HMM profiles used for annotation of the 202 TAP.

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Open Data