[tcruzi] targets ranked by nucleotide diversity (TcSNP)

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

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)

Queries in this set

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  tcr expression epis-amas 1,5 fold 0.8 confidence (855 records). Show parameters.

  tcr expression trypos-amas 1,5 fold 0.8 confidence (451 records). Show parameters.

  tcr has ortholog in kinetoplastida (9463 records). Show parameters.

  tcr doesn't have ortholog in mammals (20730 records). Show parameters.

  Assayability - Assay Available (334 records). Show parameters.

  Assayability - Soluble (205 records). Show parameters.

  Pubmed (460 records). Show parameters.

  tcr MW < 100 kDa (22872 records). Show parameters.

  has >= 1 TM domain (6065 records). Show parameters.

  tcr > 2 paralogs (6333 records). Show parameters.

  has GPI anchor signal (2131 records). Show parameters.

  has Signal Peptide (4347 records). Show parameters.

  has EC number (730 records). Show parameters.

  ortholog essential in E. coli (302 records). Show parameters.

  ortholog essential in M. tuberculosis (308 records). Show parameters.

  ortholog essential in S. cerevisiae (981 records). Show parameters.

  ortholog in C. elegans has 'embryonic arrest' RNAi phenotype (1373 records). Show parameters.

  is enzyme (4157 records). Show parameters.

  has 3D model(s) (7103 records). Show parameters.

  has 3D structure(s) (73 records). Show parameters.

  nucleotide-diversity-normalized (6701 records). Show parameters.

  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). Show parameters.