TDR Targets

[tcruzi] targets ranked by nucleotide diversity (TcSNP)

Posted by Fernan Aguero on 2012-07-03 17:06:05

List description

This is a prioritization exercise for the T. cruzi genome, where genetic polymorphism data (SNPs) has been used to increase the score of targets that are under apparent purifying selection, and at the same time penalize those that show more genetic diversity.

This query set represents the supplementary data for: Ackermann AA, Panunzi LG, Cosentino RO, Sanchez DO, and Aguero F (submitted).

Score for genes in query #49 (tcr expression epis-amas 1,5 fold 0.8 confidence): 12
Score for genes in query #50 (tcr expression trypos-amas 1,5 fold 0.8 confidence): 12
Score for genes in query #52 (tcr has ortholog in kinetoplastida): 9
Score for genes in query #55 (tcr doesn't have ortholog in mammals): 12
Score for genes in query #56 (Assayability - Assay Available): 7
Score for genes in query #57 (Assayability - Soluble): 7
Score for genes in query #58 (Pubmed): 12
Score for genes in query #59 (tcr MW < 100 kDa): 9
Score for genes in query #60 (has >= 1 TM domain): -3
Score for genes in query #61 (tcr > 2 paralogs): -18
Score for genes in query #62 (has GPI anchor signal): -3
Score for genes in query #63 (has Signal Peptide): -3
Score for genes in query #64 (has EC number): 9
Score for genes in query #67 (ortholog essential in E. coli): 12
Score for genes in query #68 (ortholog essential in M. tuberculosis): 12
Score for genes in query #69 (ortholog essential in S. cerevisiae): 12
Score for genes in query #70 (ortholog in C. elegans has 'embryonic arrest' RNAi phenotype): 12
Score for genes in query #71 (is enzyme): 15
Score for genes in query #72 (has 3D model(s)): 20
Score for genes in query #73 (has 3D structure(s)): 20
Score for genes in query #81 (nucleotide-diversity-normalized): var (function)

Click on the links below to browse the contents of each query. You can also use the checkboxes to select queries you would like to import into your history.
Import ranked queries into your history to redo the scoring strategy

tcr expression epis-amas 1,5 fold 0.8 confidence (855 records), 3
- Query: Uploaded list
- Unmatched identifiers: (Tc00.1047053509883.18)
tcr expression trypos-amas 1,5 fold 0.8 confidence (451 records), 3
- Query: Uploaded list
tcr has ortholog in kinetoplastida (9463 records), 3
- Species: tcr
- Phylogenetic distribution: IN tvi, IN lme, IN lif, IN lbz, IN tbg, IN lma, IN tbr
tcr doesn't have ortholog in mammals (20730 records), 3
- Phylogenetic distribution: NOT IN mmu, NOT IN hsa
- Species: tcr
- Imported: from "Prioritizing the Trypanosoma cruzi genome using SNPs", posted by Alejandro Ackermann
Assayability - Assay Available (334 records), 3
- Assay available: Yes
- Imported: from "Prioritizing the Trypanosoma cruzi genome using SNPs", posted by Alejandro Ackermann
- Species: tcr
Assayability - Soluble (205 records), 3
- Species: tcr
- Recombinant soluble protein: Yes
- Imported: from "Prioritizing the Trypanosoma cruzi genome using SNPs", posted by Alejandro Ackermann
Pubmed (460 records), 3
- Species: tcr
- Imported: from "Prioritizing the Trypanosoma cruzi genome using SNPs", posted by Alejandro Ackermann
- Pubmed: any
tcr MW < 100 kDa (22872 records), 3
- Species: tcr
- Molecular weight: < 100000
- Imported: from "Prioritizing the Trypanosoma cruzi genome using SNPs", posted by Alejandro Ackermann
has >= 1 TM domain (6065 records), 3
- Species: tcr
- Number of TM segments: > 0
- Imported: from "Prioritizing the Trypanosoma cruzi genome using SNPs", posted by Alejandro Ackermann
tcr > 2 paralogs (6333 records), 3
- Species: tcr
- Paralogs Number: > 2
- Imported: from "Prioritizing the Trypanosoma cruzi genome using SNPs", posted by Alejandro Ackermann
has GPI anchor signal (2131 records), 3
- Imported: from "Prioritizing the Trypanosoma cruzi genome using SNPs", posted by Alejandro Ackermann
- GPI Anchor: Y
- Species: tcr
has Signal Peptide (4347 records), 3
- Imported: from "Prioritizing the Trypanosoma cruzi genome using SNPs", posted by Alejandro Ackermann
- Species: tcr
- Signal Peptide: Y
has EC number (730 records), 3
- Species: tcr
- EC: any
- Imported: from "Prioritizing the Trypanosoma cruzi genome using SNPs", posted by Alejandro Ackermann
ortholog essential in E. coli (302 records), 3
- Essential: eco essential
- Species: tcr
ortholog essential in M. tuberculosis (308 records), 3
- Essential: mtu essential
- Species: tcr
ortholog essential in S. cerevisiae (981 records), 3
- Essential: sce inviable
- Species: tcr
ortholog in C. elegans has 'embryonic arrest' RNAi phenotype (1373 records), 3
- Species: tcr
- Essential: cel Embryonic Lethal/Arrest
is enzyme (4157 records), 3
- Is enzyme: Y
- Species: tcr
has 3D model(s) (7103 records), 3
- Structures: Modbase
- Species: tcr
has 3D structure(s) (73 records), 3
- Structures: PDB
- Species: tcr
nucleotide-diversity-normalized (6701 records), 3
- Query: Uploaded list
Union of (49, 50, 52, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 67, 68, 69, 70, 71, 72, 73, 81) (25010 records), 3
- Score for genes in query #57 (Assayability - Soluble): 7
- Score for genes in query #67 (ortholog essential in E. coli): 12
- Score for genes in query #69 (ortholog essential in S. cerevisiae): 12
- Score for genes in query #61 (tcr > 2 paralogs): -18
- Score for genes in query #58 (Pubmed): 12
- Score for genes in query #73 (has 3D structure(s)): 20
- Score for genes in query #81 (nucleotide-diversity-normalized): var
- Score for genes in query #55 (tcr doesn't have ortholog in mammals): 12
- Score for genes in query #50 (tcr expression trypos-amas 1,5 fold 0.8 confidence): 12
- Score for genes in query #71 (is enzyme): 15
- Score for genes in query #63 (has Signal Peptide): -3
- Score for genes in query #52 (tcr has ortholog in kinetoplastida): 9
- Score for genes in query #60 (has >= 1 TM domain): -3
- Score for genes in query #68 (ortholog essential in M. tuberculosis): 12
- Score for genes in query #49 ( tcr expression epis-amas 1,5 fold 0.8 confidence): 12
- Score for genes in query #72 (has 3D model(s)): 20
- Score for genes in query #56 (Assayability - Assay Available): 7
- Score for genes in query #70 (ortholog in C. elegans has 'embryonic arrest' RNAi phenotype): 12
- Score for genes in query #64 (has EC number): 9
- Score for genes in query #62 (has GPI anchor signal): -3
- Score for genes in query #59 (tcr MW < 100 kDa): 9