Table 2 Top candidate genes that have nonsynonymous amino acid changes between RH-ERP and GT1
From: Genetic basis for phenotypic differences between different Toxoplasma gondii type I strains
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 |