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Table 2 Differential expression analysis of V0v candidate genes between WT and evx1;evx2 mutant cell groups

From: Molecular analyses of zebrafish V0v spinal interneurons and identification of transcriptional regulators downstream of Evx1 and Evx2 in these cells

A

Gene Symbol

Hurdle Model Fold-Change

Mutant 1 + 2 vs WT 1 + 2

Mutant 3 vs Mutant 1 + 2

Mutant 1 vs WT 1

Mutant 2 vs WT 2

Mutant 3 vs WT 1 + 2

WT 1 vs

WT 2

Mutant 1 vs Mutant 2

evx1

↓1.77***

↓2.45***

↓1.67*

↓1.86***

↓4.32***

↓1.03***

↑1.08

evx2

↓17.73***

↓1.50*

↓15.10***

↓20.31***

↓26.41***

↓1.61***

↓1.19**

slc17a6a

↓15.87***

↓1.04

↓14.50***

↓15.50***

↓16.51***

↑1.75***

↑1.87***

slc6a5

↑6.87***

↑28.60***

↑4.79***

↑8.39***

↑195.57***

↓1.91***

↓3.33***

slc6a1b

↑7.71***

↓1.54

↑201.72***

↑1.41***

↑5.01***

↑1.03

↑147.81***

gad1b

↑1.44***

↑1.50

↑3.72***

↑1.08**

↑2.17***

↓1.01

↑3.41***

skor1a

↓1.18**

↑1.17*

↓1.14

↓1.24*

↓1.00*

↓1.10*

N.C.

skor1b

↓1.09***

N.C.

N.C.

N.C.

↑1.05

↑1.37***

N.C.

skor2

↓43.94***

↓1.12

↓434.75***

↓3.12***

↓49.21***

↑90.90***

↓1.53***

ebf3a

↓4.24***

↓1.25

↓18.44***

↓1.18***

↓5.28***

↑9.15***

↓1.71**

uncx

↑3.94***

↓16.53***

↑2.56***

↑5.95***

↓4.21***

↑1.78***

↓1.31***

uncx4.1

↑1.10

↓1.02

↓1.05

↑1.18***

↑1.07

↑1.29***

↑1.04

nefma

↑7.23***

↑3.12***

↑10.66***

↑3.63***

↑22.47***

↑3.19***

↑9.34***

nefmb

↑1.27*

↑40.64***

↑1.96***

↑1.07

↑51.55***

↑1.98***

↑3.61***

neff1

↓8.12***

↑21.65***

↓22.08***

↓3.53***

↓2.68***

↑7.27***

↑1.16

inab

↓3.65***

↑1.25

↓6.43***

↓2.03***

↓2.92***

↓1.14***

↓3.61***

B

Gene Symbol

ANOVA Fold-Change

Mutant 1 + 2 vs WT 1 + 2

Mutant 3 vs Mutant 1 + 2

Mutant 1 vs WT 1

Mutant 2 vs WT 2

Mutant 3 vs WT 1 + 2

WT 1 vs

WT 2

Mutant 1 vs Mutant 2

evx1

↓1.07***

↓2.37***

↓1.24*

↑1.09**

↓2.54***

↑1.32

↓1.02

evx2

↓6.09***

↓2.39*

↓7.96***

↓4.98***

↓14.59***

↓1.05**

↓1.68

slc17a6a

↓5.33***

↑1.20

↓4.47***

↓7.53***

↓4.46***

↑1.52***

↑2.57***

slc6a5

↑5.39***

↑6.94***

↑6.21***

↑5.11***

↑37.44***

↓2.94***

↓2.42***

slc6a1b

↑138.60***

↓2.52***

↑186.10***

↑13.82***

↑54.94***

↑2.63

↑35.38***

gad1b

↑34.98***

↑1.17

↑74.42***

↑4.31*

↑41.08***

↓1.29

↑13.44***

skor1a

↓6.35***

↑9.00**

↓5.28*

↓7.44**

↑1.42

↓1.38

↑1.02

skor1b

↓12.24***

↑10.27***

↓22.80***

↓1.68

↓1.19

↑13.58***

N.C.

skor2

↓16.64***

↓10.94

↓141.98***

↓1.63***

↓182.04***

↑10.43***

↓8.35***

ebf3a

↓3.15***

↓2.16

↓8.64***

↑1.13

↓6.80***

↑4.03***

↓2.43**

uncx

↑2.25***

↓4.51***

↑1.63***

↑3.18***

↓2.00***

↑1.49***

↓1.31

uncx4.1

↑1.26

↑1.18

↓1.24

↑2.85*

↑1.49

↑3.51***

↓1.01

nefma

↑3.94***

↑2.06***

↑3.16***

↑11.32***

↑8.11***

↑9.38***

↑2.62***

nefmb

↑1.64***

↑18.45***

↑1.66***

↑1.42

↑30.22***

↑10.09***

↑11.80***

neff1

↓9.56***

↑19.31***

↓10.92***

↓6.68***

↑2.02***

↑3.46***

↑2.12

inab

↓1.43***

↑1.21

↓2.22***

↓1.02***

↓1.19***

↑1.13

↓1.92***

  1. Gene-specific analyses of differential expression, created through (A) Hurdle model and (B) ANOVA statistical comparisons between distinct cell clusters in our 48 h evx1i232/+;evx2sa140/+ heterozygote incross single-cell atlas (see Fig. 6A and also Methods for experimental details and rationale for using both statistical methods). The Hurdle model is generally the most statistically robust method for these analyses, if there are enough cells in each group. In contrast, ANOVA usually performs better when the numbers of cells being compared are very small (see Methods for more information). We are providing the data for both methods for completeness and comparison. Column 1 shows the gene symbol. Columns 2–8 show fold-change values. ↑ = fold-change increase, ↓ = fold-change decrease in the antecedent (first) population compared to the consequent (second) population in each comparison. Statistically significant (P < 0.05) values are indicated in bold. *** P < 0.001, ** P < 0.01, * P < 0.05. N.C. = Not Calculated. The differential expression analysis could not be calculated. In the case of skor1b, this is because there is no expression of this gene in some of the clusters. Mutant Groups 1 + 2 combined, Mutant Group 3, Mutant Group 1, Mutant Group 2, Mutant Group 3, WT Group 1, and Mutant Group 1 are the antecedent populations for columns 2, 3, 4, 5, 6, 7 and 8 respectively. WT Groups 1 + 2 combined, Mutant Groups 1 + 2 combined, WT Group 1, WT Group 2, WT Groups 1 + 2 combined, WT Group 2 and Mutant Group 2 are the consequent populations for columns 2, 3, 4, 5, 6, 7 and 8 respectively. Additional data for each comparison are available in Supp. Data Tables 2 (Hurdle model data) and 3 (ANOVA data)
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Neural Development

ISSN: 1749-8104