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Table 2 Direction of gene expression (up- or down-regulated) in this and previously published studies (cavefish compared with surface fish, and cases compared with controls)

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

  # orthologs of SFARI Gene that express differently (up or down) Transcriptome from the cortices of ASD patients (Voineagu et al., 2011) Transcriptomes from multiple tissues of ASD patients (review: Ansel et al., 2017) Transcriptome from the cortices of ASD patients (Parikshak et al., 2016)
A. mexicanus
(Whole Embryo 10–72 hpf)
Reanalyzed in this study
335 of 409† (81.9%) 43‡ of 58 orthologs expressed differently between CF and SF
(74.1%)
51ठof 77 orthologs expressed differently between CF and SF
(66.2%)
2567‡ of 3442 orthologs expressed differently between CF and SF
(74.6%)
31 of 51‡ genes expressed in the same direction:
(60.7%)
27 of 45ठdirectionally expressed genes are in the same direction:
(60.0%)
1843 of 3152‡ directionally expressed genes are in the same direction:
(58.5%)
BTBR Mouse (Hippocampus)
Provenzano et al., 2016
30 of 493 (6.1%) 2 of 65 orthologs expressed differently in BTBR mouse
(3.0%)a
9§ of 105 orthologs expressed differently in BTBR mouse
(8.6%)b
216 of 4042 orthologs expressed differently in BTBR mouse
(5.3%)c
0 of 2 genes expressed in the same direction
(0.0%)
4 of 7§ directionally expressed genes are in the same direction
(57.1%)
109 of 216 directionally expressed genes are in the same direction
(50.5%)
ASD patients (Blood)
Pramparo et al., 2015
51 of 493 (10.3%) 11 of 65 human genes expressed differently in ASD patient’s blood
(16.7%)d
16§ of 107 human genes expressed differently in ASD patient’s blood
(14.8%)e
485 of 4425 human genes expressed differently in ASD patient’s blood
(11.0%)f
7 of 11 genes expressed in the same direction
(63.6%)
4 of 7§ directionally expressed genes are in the same direction
(57.1%)
179 of 485 directionally expressed genes are in the same direction
(36.9%)
Neural cells derived from iPS cell of ASD patient
Mariani et al., 2015
95 of 493
(19.3%)
18 of 65 of human genes expressed differently in neurons derived from iPS cells of ASD patients
(27.7%)g
21§ of 107 human genes expressed differently in neurons derived from iPS cells of ASD patients
(19.6%)h
527 of 4425 human genes expressed differently in neurons derived from iPS cells of ASD patients
(11.9%)i
0 of 18 human genes expressed in the same direction
(0%)
1 of 16§ directionally expressed genes are in the same direction
(6.3%)
163 of 527 directionally expressed genes are in the same direction
(30.9%)
  1. † 84 of 493 orthologs were not found in the Astyanax gene build at 2016 (Ensembl.org Assembly: AstMex102; Genebuild at Jul 2016)
  2. ‡ Some orthologs of human genes have multiple paralogs in A. mexianus (i.e. shank3a and shank3b)
  3. § We excluded genes that showed inconsistent expression directions between multiple reports (i.e. up-regulated in one paper but down-regulated in another [34])
  4. Χ2 tests for differentially expressed genes against total genes between A. mexicanus and BTBR Mouse (a: Χ2 = 30.2, P = 1.17 × 10− 7; b: Χ2 = 31.3, P = 6.57 × 10− 8; and c: Χ2 = 1785.6, P < 1.0 × 10− 10), between A. mexicanus and patients’ blood (d: Χ2 = 14.9, P = 3.48 × 10− 4; e: Χ2 = 21.7, P = 9.40 × 10− 6; and f: Χ2 = 1445.5, P < 1.0 × 10− 10), and between A. mexicanus and patients’ iPS cells (g: Χ2 = 8.1, P = 0.0136; h: Χ2 = 16.3, P = 1.66 × 10− 4; and i: Χ2 = 1377.2, P < 1.0 × 10− 10). All of these tests have df = 1. P-values were multiplied by the number of the tests (Bonferroni correction)