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Table 1 The enrichment of the expression shifts between surface fish and cavefish in ASD-risk genes

From: The evolution of a series of behavioral traits is associated with autism-risk genes in cavefish

Human ASD-risk genes Cavefish genes
Risk category # of Listed Genes in Sfari.org % (#) human ASD-risk genes with cavefish orthologs % (#) of orthogroups that show significant age × morph interaction† % (#) of orthogroups that show significant expression difference between morphs at 72 hpf† % (#) of all paralogs that show significant age × morph interaction† % (#) of all paralogs that show significant expression difference between morphs at 72 hpf†
Category 1 19 94.7%
(18 of 19)
72.2%
(13 of 18)
94.4%
(17 of 18)
61.1%
(> 99.9 percentile)
(22 of 36)
75.0%
(> 99.9 percentile)
(27 of 36)
Category 2 43 93.0%
(40 of 43)
65.0%
(26 of 40)
67.5%
(27 of 40)
60.7%
(> 99.9 percentile)
(34 of 56)
64.3%
(> 99.9 percentile)
(36 of 56)
Category 3 139 95.0%
(132 of 139)
60.6%
(80 of 132)
70.5%
(93 of 132)
50.3%
(84.8 percentile)
(95 of 189)
58.2%
(> 99.9 percentile)
(110 of 189)
Category 4 244 89.8%
(219 of 244)
62.6%
(137 of 219)
63.0%
(138 of 219)
51.9%
(96.1 percentile)
(167 of 322)
52.5%
(94.4 percentile)
(169 of 322)
Category S (not already included among Cat 1–4 genes) 48 97.9%
(47 of 48)
57.4%
(27 of 47)
63.8%
(30 of 47)
44.2%
(4.7 percentile)
(34 of 77)
49.4%
(59.0 percentile)
(38 of 77)
Total 493 92.5%
(456 of 493 human genes)
62.1%
(283 of 456)
66.9%
(305 of 456)
53.8%
(352 of 654)
54.6%
(357 of 654)
Bootstrapping score: mean ± 95% confidence interval      48.0 ± 4.2% 49.0 ± 4.4%
  1. The 72 h post-fertilization (hpf) represents the stage in which fish have hatched, but have not yet developed a swim bladder and the jaw is underdeveloped, comparable to the late embryonic stage of mammals [111]. † P < 0.05 after Benjamini-Hochberg adjustment. Percentiles in the tables are from 9999-bootstrapped values. SF: surface fish. CF: Pachón cavefish. Hpf: hours post fertilization. We avoided testing the differences between morphs in each developmental time point (i.e. 10, 24 and 36 hpf) due to save statistical power. The number of genes are indicated in parentheses. See also Additional file 1 for each statistical test of age x morph and expression difference at 72 hpf