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Table 1 Distribution of genes associated with hotspot regions, minimum of 5 candidates on the arrays

From: Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization

Gene Name # Genome Occurrences1 #Array Occurrences2 # Array Candidates3 # Sig CNV4 % Sig of Candidates
mucin TcMUCII 728 506 164 121 73.7
serine carboxypeptidase 7 7 6 4 66.6
tryptophanyl-tRNA synthetase 23 8 6 4 66.6
mucin-associated surface 1377 948 437 243 55.6
retrotransposon hot 753 419 82 41 50
ATP-dependent chaperone 5 5 5 2 40
beta galactofuranosyl 66 47 10 4 40
mitogen-activated protein kinase 11 11 10 4 40
Sialidase 3209 789 135 51 37.7
clathrin coat 7 7 7 2 28.5
surface protease 425 258 88 25 28.4
myosin heavy 19 19 17 3 17.6
PIF1 helicase-like 12 12 12 2 16.6
mismatch repair 13 13 13 2 15.3
ATP-dependent DEAD/H 106 88 66 10 15.1
leucine-rich repeat 17 16 16 2 12.5
DNA topoisomerase 9 9 9 1 11.1
protein tyrosine 10 10 9 1 11.1
cytochrome c 20 18 13 1 7.6
protein transport 16 16 14 1 7.1
elongation factor 203 65 15 1 6.6
ABC transporter 33 33 33 2 6
ubiquitin-conjugating enzyme 24 24 23 1 4.3
serine/threonine protein 80 78 78 3 3.8
60S ribosomal 106 106 93 3 3.2
DNA repair 37 36 35 1 2.8
RNA-binding protein 80 72 71 2 2.8
hypothetical protein 11812 10489 9735 122 1.2
protein kinase 311 277 270 1 0.3
  1. 1. # genome occurrences = number of instances for the annotation in the genome.
  2. 2. # array occurrences = number of annotated genes with probes on the arrays.
  3. 3. # array candidates = number of annotated genes represented by probes on the arrays and which had probe density of 5 unique probes per 500 bp. Genes could have insufficient probe density due to repeat regions or they could have too few probes due to length of the gene (minimum of 5 probes).
  4. 4. # sig CNV = CNV with a minimum log2 ratio difference of +/- 0.5, for a minimum of 5 probes over a segment size of 500 bp in at least 5 test strains.