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Table 1 Transcripts differentially expressed between the procyclic and bloodstream forms of T. brucei.

From: The trypanosome transcriptome is remodelled during differentiation but displays limited responsiveness within life stages

A
Upregulated in the procyclic form
   PCF/BSF ratio  
Accession Name limma fspma RT-PCR Classification
*Tb10.6k15.0030 procyclin 22.3 34.6   Cell surface
*Tb927.6.450 procyclin 21.9 17.0   Cell surface
Tb927.7.6850 trans -sialidase 5.0 4.7   Cell surface
Tb10.6k15.3510 CRAM 3.8 3.8   Cell surface
*Tb09.244.2460 BARP 1.9 1.9 1.6 Cell surface
Tb11.01.8120 hypothetical ER chaperone 3.0 3.0 2.8 Chaperones
*Tb927.6.3740 Hsp70 mitochondrial 2.3 4.2   Chaperones
*Tb10.70.0280 Hsp60 chaperonin mitochondrial 2.0 2.1   Chaperones
Tb11.01.3110 Hsc70 1.6 2.8   Chaperones
*Tb927.8.1610 Gp63 (TbMSP-B) 3.3 5.6 3.8 Proteases
Tb11.02.1480 mitochondrial processing peptidase 5.6 5.1 5.6 Proteases
Tb09.211.4760 MCA5 metacaspase 2.2 2.1 1.3 Proteases
Tb10.61.0870 v-SNARE 2.9 2.8   SNAREs
Tb927.4.2020 AP3 mu 2.1 2.2   Vesicle coat
Tb927.4.4350 emp24 2.1 1.9 1.0 Vesicle coat
Tb927.3.4020 PI4K alpha 2.2 2.1 1.7 PI kinases
Tb10.6k15.2060 PI3K (FRAP1) 2.0 2.0   PI kinases
Tb11.01.7800 NDPK kinase (NME6) 2.7 4.4   Other kinases
Tb11.03.0090 ribokinase (RBSK) 2.7 3.4   Other kinases
Tb927.3.3190 NEK kinase (NEK2/6/7) 2.5 2.9   Other kinases
Tb10.389.0330 UGP2 2.4 2.2   Other kinases
Tb927.6.710 DPCK kinase 2.0 2.0   Other kinases
*Tb09.211.3540 glk1 (CARKL) 1.4 2.9   Other kinases
*Tb09.160.4560 AK 1.4 2.8   Other kinases
*Tb927.1.720 PGKA (PGK1) 1.9 2.4   Other kinases
Tb11.02.0580 Vps46 2.4 2.8   ESCRT
Tb927.2.4210 p60 glycosomal protein 9.9 7.4   Other trafficking
Tb11.01.7880 CAP17 4.5 3.3   Other trafficking
Tb927.4.3950 CAP5.5 4.1 3.2 8.0 Other trafficking
Tb927.7.2640 Sec34-like 8.3 7.9 3.7 Other trafficking
Tb11.01.2540 VHS domain-containing protein 2.6 2.8   Other trafficking
Tb11.47.0022 signal-peptide-containing protein 3.1 2.7   Other trafficking
Tb10.406.0240 dual specificity protein phosphatase 2.1 2.6   Other trafficking
Tb927.1.3110 Sec17/SNAP 1.8 2.5   Other trafficking
Tb09.160.3240 C2 domain-containing protein 2.0 1.9   Other trafficking
Tb927.7.3550 C2 domain-containing protein 1.8 2.5   Other trafficking
Tb10.100.0130 peroxin 14 2.1 1.9   Other trafficking
Tb09.211.2150 PABP2 2.7 2.4   Miscellaneous
Tb927.8.7120 farnesyltransferase 2.6 2.5   Miscellaneous
*Tb10.406.0330 histone H2B 2.5 2.8 1.0 Miscellaneous
*Tb927.3.1370 40S ribosomal protein S25 2.4 3.2 1.5 Miscellaneous
Tb11.02.5250 histone H2B, variant 2.3 1.7 0.9 Miscellaneous
*Tb927.1.2430 histone H3 2.2 2.9 1.1 Miscellaneous
*Tb927.1.2400 alpha tubulin 1.7 3.0 0.8 Miscellaneous
Tb927.8.4010 fla1 1.8 2.2   Miscellaneous
Tb11.01.1650 SRP54-like 2.0 2.3   Miscellaneous
Tb927.3.3020 actin-like 1.5 2.7   Miscellaneous
B
Upregulated in the bloodstream form
   BSF/PCF ratio  
Accession Name limma fspma RT-PCR Classification
*H25N7.15 ESAG6 52.0 27.7   Cell surface
*N19B2.155 ESAG7 27.7 22.8   Cell surface
*Tb927.5.1410 ISG65 14.8 9.6   Cell surface
*Tb927.2.3270 ISG65 7.2 4.8   Cell surface
*Tb927.2.3280 ISG65 7.0 5.5   Cell surface
*Tb927.2.3320 ISG65 6.4 3.9   Cell surface
*Tb927.5.390 ISG75 5.8 8.2   Cell surface
Tb11.47.0001 ISG65 2.4 1.7   Cell surface
*Tb09.244.2430 BARP 2.4 2.4   Cell surface
*Tb927.5.360 ISG75 2.3 2.4   Cell surface
Tb927.7.5790 PDI/ERp44 2.5 2.8   Chaperones
Tb11.01.2640 hypothetical ER chaperone 2.3 2.2 1.0 Chaperones
Tb927.3.3450 ARL3A 7.0 5.9 7.8 small GTPases
*Tb05.5K5.230 Rab1b 7.0 8.2   small GTPases
Tb927.4.2380 HSR1-related GTP-binding protein 3.9 3.4 5.2 small GTPases
*Tb927.5.4590 Rab1b 3.8 5.7   small GTPases
*Tb09.244.2070 Rab1b 3.5 2.4   small GTPases
Tb927.8.8140 TbRX3 2.8 2.4   small GTPases
Tb10.70.0590 TbRHP 2.3 2.1   small GTPases
Tb11.01.6670 RabX3 2.3 2.1 4.8 small GTPases
Tb927.8.4330 Rab11a 2.3 2.0 1.9 small GTPases
*Tb09.211.4460 TbARF1 2.0 2.0   small GTPases
Tb10.70.5290 Gp63 (TbMSP-C) 4.7 3.3 6.2 Proteases
Tb927.3.4230 Ser peptidase (sybtilisin-like) 5.6 7.5 3.3 Proteases
Tb09.211.0680 CAAX prenyl protease 1 2.5 2.3 2.7 Proteases
Tb11.02.1280 Ser peptidase (sybtilisin-like) 2.5 2.2 1.1 Proteases
*Tb927.6.930 MCA3 metacaspase 2.3 1.9 1.8 Proteases
Tb927.7.190 OPA Thimet oligopeptidase 2.1 2.0 1.2 Proteases
Tb09.160.2420 syntaxin 3.6 2.6   SNAREs
Tb927.7.6440 v-SNARE 2.9 3.5   SNAREs
Tb927.3.3720 t-SNARE (Bet1) 2.5 2.7   SNAREs
Tb09.211.3920 t-SNARE 2.5 1.8 1.8 SNAREs
Tb10.70.7410 VAMP (synaptobrevin) 1.8 2.5   SNAREs
Tb10.389.0480 Vps16 1.9 2.8   Tethers
Tb10.61.1910 CLL 3.1 2.5 4.2 Vesicle coat
Tb927.3.4000 AP1 sigma 6.0 7.0   Vesicle coat
Tb11.01.6880 emp24 2.1 2.2 1.7 Vesicle coat
*Tb11.50.0006 epsin-like protein 2.0 2.1 2.5 Vesicle coat
Tb11.01.6980 PI3K (FYVE domain) 7.5 10.3   PI kinases
Tb927.8.7110 Ser/Thr kinase NEK7-like (PH domain) 2.6 2.1   PI kinases
Tb10.70.2440 PIK5KII 2.1 2.6   PI kinases
*Tb927.4.5310 Ser/Thr kinase A (PH domain) 1.9 1.7   PI kinases
*Tb10.70.5800 hexokinase (GCK/HK) 3.8 3.8   Other kinases
Tb927.6.1780 MAP kinase (MAPK8/9) 2.9 2.3   Other kinases
Tb927.4.3770 calcium-dependent protein kinase (CAMK4) 2.5 3.2   Other kinases
Tb10.61.2680 pyruvate kinase (PKLR) 2.2 1.8   Other kinases
Tb10.61.2490 MAP kinase kinase kinase (MAP3K8) 2.2 2.0   Other kinases
Tb10.70.1130 two UIM domain-containing protein 8.8 5.9   Ubiquitin sorting
Tb11.46.0014 Doa4 (Ubiquitin C-term hydrolase) 2.7 2.9   Ubiquitin sorting
Tb09.211.3610 UBA2/E1 2.3 2.4 2.5 Ubiquitin sorting
Tb927.6.2370 Ubiquitin-protein ligase 2.2 2.2   Ubiquitin sorting
Tb927.4.2710 E2 1.6 2.5 1.6 Ubiquitin sorting
Tb927.2.6000 GPI-PLC 8.7 8.0   Other trafficking
Tb11.01.3805 CAP15 4.3 4.8   Other trafficking
Tb09.211.4240 sorting nexin 2 (PX domain) 3.4 4.8   Other trafficking
Tb10.70.4620 gamma SNAP 2.7 2.5   Other trafficking
Tb927.4.2070 giantin 3.1 1.8   Other trafficking
Tb927.6.3500 RME-8 endosome trafficking 2.8 2.2 2.3 Other trafficking
Tb11.01.4460 scavenger receptor 3.0 2.8   Other trafficking
Tb927.5.4520 Uso1p-like (spectrin repeat) 2.7 1.8   Other trafficking
Tb927.5.3220 Sec11 2.4 3.4   Other trafficking
Tb11.01.6260 Sec63 2.3 2.3   Other trafficking
Tb927.1.1560 NSF 2.2 1.7   Other trafficking
Tb10.70.5100 lysosomal alpha-mannosidase 2.2 1.8   Other trafficking
Tb11.02.1370 katanin/Ser peptidase 1.7 1.7   Other trafficking
Tb927.4.2080 C2 domain-containing protein 1.9 1.8   Other trafficking
*Tb927.5.420 ISG65-like 3.5 5.1   Miscellaneous
Tb927.5.310 ISG-like 3.3 3.2   Miscellaneous
*Tb927.8.4060 fla2 (fla1-like) 3.5 2.6   Miscellaneous
Tb10.61.1090 H3 variant 2.3 2.9 1.8 Miscellaneous
Tb10.406.0320 ARPC5 2.2 2.5   Miscellaneous
Tb927.5.630 ISG65-like 2.2 2.4   Miscellaneous
Tb927.5.430 ISG65-like 2.2 2.1   Miscellaneous
  1. ORFs represented by oligonucleotides on the array which gave a PCF to BSF expression ratio (panel A) or BSF to PCF expression (panel B) greater than two by limma or fpmsa analysis, or which had a value of over one for the B statistic in limma are shown. Limma ratios which correspond to a B value of >1 are given in bold. For candidates validated by qRT-PCR, the resulting qRT-PCR ratio is also given. Ratios below two may not be significant. The names of well-characterised genes which can be used as controls to validate the array results are in bold. Asterisk indicates oligonucleotides that hybridise with mRNA derived from more than one ORF [see Additional file 2].
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