Table 2.
Top candidate genes that have nonsynonymous amino acid changes between RH-ERP and GT1
|
A. Candidate genes containing nonsynonymous SNPs between RH-ERP and GT1 | ||||
| ToxoDB GT1 ID |
ToxoDB annotation |
A.A. change (GT1 to RH-ERP) |
RH-ERP expression (Microarray) |
Possible involvement in Toxoplasma process |
| TGGT1_083030 |
28 kDa antigen, putative (GRA2) |
Gly to Ser |
13.8 |
Growth |
| TGGT1_113990 |
SRS29C |
Ser to Phe |
13.5 |
Invasion |
| TGGT1_114020 |
SRS29A |
Val to Met |
12.7 |
Invasion |
| TGGT1_069190 |
DEAD/DEAH box helicase, putative |
Ile to Asn |
11.9 |
Transcriptional control |
| TGGT1_030300 |
acid phosphatase, putative (GAP50) |
Ile to Asn |
11.4 |
Gliding motility |
| TGGT1_020630 |
conserved hypothetical protein (contains glycosyltransferase 17 family) |
Leu to Arg |
11.1 |
Growth |
| TGGT1_066370 |
hypothetical protein (eukaryotic initiation factor 3) |
Leu to Phe |
10.7 |
Translation |
| TGGT1_081400 |
ATP-dependent RNA helicase, putative |
Arg to Cys Ala to Asp |
9.6 |
Transcriptional control |
| TGGT1_069890 |
apoptosis-regulating basic protein, putative |
Leu to Phe |
8.8 |
Growth |
| TGGT1_118630 |
U2 small nuclear ribonucleoprotein, putative |
Thr to Ile |
8.7 |
Growth |
| TGGT1_098160 |
Coronin, putative |
Met to Val |
8.6 |
Gliding motility |
| TGGT1_086050 |
sushi domain-containing protein (RON1) |
Asp to Gly |
7.9 |
Invasion |
| TGGT1_009970 |
CCR4-NOT transcription complex subunit, putative |
Pro to Ser |
7.6 |
Transcriptional control |
|
B. Candidate extracellular viability genes containing nonsynonymous SNPs between RH-ERP and GT1 | ||||
| ToxoDB GT1 ID |
ToxoDB annotation |
A.A. change (GT1 to RH-ERP) |
Fold change between extracellular and intracellular tachyzoites |
|
| TGGT1_057870 |
conserved hypothetical protein (contains RNA recognition motif) |
Asp to His |
2.6 |
|
| TGGT1_021310 |
pinA, putative (contains forkhead associated domain) |
Phe to Leu |
2.0 |
|
| TGGT1_104520 |
conserved hypothetical protein |
Leu to Pro |
2.0 |
|
| TGGT1_016250 |
hypothetical protein (cyclic nucleotide-binding domain-containing protein) |
Ile to Asn |
2.0 |
|
| TGGT1_065470 |
conserved hypothetical protein (contains oligomerization domain) |
Ser to Cys |
-2.3 |
|
| TGGT1_098520 |
EF hand domain-containing protein, putative |
Val to Phe |
-2.6 |
|
| TGGT1_087130 |
apyrase, putative |
Pro to Leu |
-3.2 |
|
| TGGT1_026200 |
acylamino-acid-releasing enzyme, putative |
Trp to STOP |
-3.5 |
|
|
C. Candidate bradyzoite genes containing nonsynonymous SNPs between RH-ERP and GT1 | ||||
| ToxoDB GT1 ID |
ToxoDB annotation |
A.A. change (GT1 to RH-ERP) |
Fold change between 8 day M4 in vitro bradyzoites and 2 day M4 tachyzoites |
Fold change between 21 day M4 in vivo cysts and 2 day M4 tachyzoites |
| TGGT1_013440 |
conserved hypothetical protein |
Gly to Ser |
1.8 |
1.6 |
| TGGT1_020630 | conserved hypothetical protein (contains glycosyltransferase 17 family) | Leu to Arg | 2.3 | 1.5 |
(A) Candidate genes that have non-conservative, nonsynonymous amino acid changes between RH-ERP and GT1 and are expressed highly in RH-ERP as determined by Toxoplasma arrays. Toxoplasma array expression values are log2 transformed values, ranging from 6.5 (minimum) to 14.3 (maximum). (B) Candidate genes that are differentially expressed between intracellular and extracellular RH-ERP tachyzoites [44]. (C) Candidate genes that are differentially expressed between M4 in vitro tachyzoites, in vitro induced bradyzoites and in vivo cysts [46].