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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)
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BMC Ecology and Evolution

ISSN: 2730-7182

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