BMC Genomics 2008, 9:298 http://www.biomedcentral.com/1471-2164/9/298 Table 3: Expression changes associated with in vivo versus in vitro culture of T. brucei. MiTat vs SMB up in SMB Gene DHH1 procyclin PRA1 procyclin CSNK1D (casein kinase) CAP5.5 Rab1a SNF1-like kinase cofilin (ADF) NEK2/6/7 kinase PI3K (FYVE) Trs20/sedlin Ser peptidase (Bem46-like) Ubiquitin conjugating AP4 sigma ARPC5 FYVE Zn finger containing protein ARPC4 GSK3B kinase IFT88 RabGAP nuclear transport factor 2 ISG65-like two UIM domains t-SNARE Rab7 CBL-interacting protein kinase 9 VHS domain containing protein GTP1/OBG/Hsr1 Hsr1/GTP-binding MAPK8 kinase PABP2 calreticulin (lectin) RanGEF ARL3A p67 polyUb RanGEF Gene CAP5.5 Sec34-like Accession Tb10.70.3290 Tb927.6.450 Tb10.389.1550 Tb10.6k15.0030 Tb927.5.800 Tb927.4.3950 Tb927.8.890 Tb10.70.1760 Tb927.3.5180 Tb927.3.3190 Tb11.01.6980 Tb927.8.5900 Tb09.211.2310 Tb11.02.0815 Tb10.61.2530 Tb10.406.0320 Tb927.4.3380 Tb927.2.2900 Tb927.7.2420 Tb11.55.0006 Tb10.6k15.1770 Tb10.70.5500 Tb927.5.410 Tb10.70.1130 Tb11.03.0965 Tb09.211.2330 Tb927.8.870 Tb11.01.2540 Tb927.2.4240 Tb927.7.2630 Tb10.70.2070 Tb09.211.2150 Tb927.4.5010 Tb927.8.7290 Tb927.3.3450 Tb927.5.1810 Tb11.01.1680 Tb10.6k15.3150 Accession Tb927.4.3950 Tb927.7.2640 Fold difference 6.2 5.0 4.1 3.8 3.6 3.5 3.5 3.5 3.1 3.0 2.8 2.7 2.7 2.6 2.6 2.6 2.5 2.5 2.5 2.3 2.3 2.3 2.3 2.2 2.2 2.2 2.2 2.2 2.1 2.1 2.1 2.1 2.0 2.0 2.0 2.0 2.0 2.9 2.3 2.0 Fold difference up in MiTat1.1 SMB 4°C vs SMB up in 4°C Significantly differentially expressed transcripts for in vivo MITat1.1 bloodstream culture vs in vitro SMB culture, and for SMB treated at 4°C for one hour. Ratios are given on a linear scale. Only ORFs which show at least a two-fold change are shown. Ratios which correspond to a value >1 for the B-statistic in limma analysis are shown in bold. ESAG6/7 transferrin receptor mRNAs and protein pro- vides a potential example of signal-mediated changes to mRNA abundance [45,65,105]. Analysis of a large gene cohort indicates that the transferrin receptor is a special case, and we were unable to find compelling evidence for alterations to levels of most mRNAs. The transferrin recep- tor genes are located in an RNA Pol I-transcribed subtelo- meric array [126] and thus may be regulated differentially from most genes that are transcribed by RNA Pol II [127]. We also observed mRNA level alterations in a further Pol I-derived transcript, procyclin, in response to several chal- lenges, but we note that procyclin expression is unusually sensitive to many factors (for example [128]). Regardless of these exceptions, our data indicate that the vast major- Page 19 of 28 (page number not for citation purposes)