The data used

To produce the PlasmoDraft database, Gonna was applied to all P. falciparum publicly available postgenomic data sources we are aware of. 9 transcriptomic (microarray), 1 proteomic (mass-spectrometry), and 1 protein-protein interaction datasets were used. Below is a short description of each dataset, indexed by the name used in PlasmoDraft.

• LE03: KG Le Roch, Y Zhou, PL Blair, M Grainger, JK Moch, JD Haynes, P De La Vega, AA Holder, S Batalov, DJ Carucci, and EA Winzeler. Discovery of gene function by expression profiling of the malaria parasite life cycle. Science, 301(5639):1503-1508, Sep 12 2003. PubMed link
  A transcriptomic dataset that covers 9 stages of the entire cycle of strain 3D7: 6 asexual intraerythrocytic stages, plus the merozoite, gametocyte, and salivary gland sporozoite stages. Measurements for ~5100 genes.
• YO3D7: JA Young, QL Fivelman, PL Blair, P de la Vega, KG Le Roch, Y Zhou, DJ Carucci, DA Baker, and EA Winzeler. The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification. Mol. Biochem. Parasitol, 143(1):67-79, Sep 2005. PubMed link
  A transcriptomic dataset that covers the sexual developmental cycle (gametocytes) of strain 3D7. Measurements for ~5100 genes.
• YONF54: JA Young, QL Fivelman, PL Blair, P de la Vega, KG Le Roch, Y Zhou, DJ Carucci, DA Baker, and EA Winzeler.
  Same dataset as YO3D7, for strain NF54.
• LLHB3: Z Bozdech, M Llinas, BL Pulliam, ED Wong, J Zhu, and JL DeRisi. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol, 1(1), Oct 2003. PubMed link
  M Llinas, Z Bozdech, ED Wong, AT Adai, and JL DeRisi. Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Res, 34(4):1166-1173, 2006. PubMed link
  A transcriptomic dataset that covers 48 h of the intraerythrocytic developmental cycle of strain HB3. Measurements for ~4200 genes.
• LLDd2: M Llinas, Z Bozdech, ED Wong, AT Adai, and JL DeRisi. Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Res, 34(4):1166-1173, 2006. PubMed link
  Same dataset as LLHB3, for strain Dd2.
• LL3D7: M Llinas, Z Bozdech, ED Wong, AT Adai, and JL DeRisi. Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Res, 34(4):1166-1173, 2006. PubMed link
  Same dataset as LLHB3, for strain 3D7.
• DA06: EL Dahl, JL Shock, BR Shenai, J Gut, JL DeRisi, and PJ Rosenthal. Tetracyclines specifically target the apicoplast of the malaria parasite Plasmodium falciparum. Antimicrob Agents Chemother, 50(9):3124-3131, Sep 2006. PubMed link
  A transcriptomic dataset that covers two 48 h life cycles of doxycyclin treated parasites. Measurements for ~5300 genes.
• SH07: JL Shock, KF Fischer, and JL Derisi. Whole-genome analysis of mrna decay in Plasmodium falciparum reveals a global lengthening of mrna half-life during the intra-erythrocytic development cycle. Genome Biol, 8(7), Aug 7 2007. PubMed link
  A transcriptomic dataset analysing mRNA decay during the intraerythrocytic developmental cycle. Measurements for ~5300 genes.
• LE07: Series GSE4582 in the NCBI Gene Expression Omnibus.
  A transcriptomic dataset analysing the parasite response to choline analog T4 during the intraerythrocytic life cycle. Measurements for ~5100 genes.
• LE04: L Florens, MP Washburn, JD Raine, RM Anthony, M Grainger, JD Haynes, JK Moch, N Muster, JB Sacci, DL Tabb, AA Witney, D Wolters, Y Wu, MJ Gardner, AA Holder, RE Sinden, JR Yates, and DJ Carucci. A proteomic view of the Plasmodium falciparum life cycle. Nature, 419(6906):520-526, Oct 3 2002. PubMed link
  KG Le Roch, JR Johnson, L Florens, Y Zhou, A Santrosyan, M Grainger, SF Yan, KC Williamson, AA Holder, DJ Carucci, JR 3rd Yates, and EA Winzeler. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res, 14(11):2308-2318, Nov 2004. PubMed link
  A proteomic dataset that covers 7 stages of the entire cycle of strain 3D7: the ring, trophozoite, schizont, merozoite, gametocyte, gamete, and salivary gland sporozoite stages. Measurements for ~2900 genes.
• LA05: DJ LaCount, M Vignali, R Chettier, A Phansalkar, R Bell, JR Hesselberth, LW Schoenfeld, I Ota, S Sahasrabudhe, C Kurschner, S Fields, and RE Hughes. A protein interaction network of the malaria parasite Plasmodium falciparum. Nature, 438(7064):103-107, Nov 3 2005. PubMed link
  A protein-protein interaction dataset. Measurements for ~1300 genes.