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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].