[Preprint]. 2023 Aug 30:rs.3.rs-3290462. [Version 1] doi: 10.21203/rs.3.rs-3290462/v1

Table 5.

Differential Expression Analysis of evx1;evx2 Mutant Group 3 V0v Spinal Interneurons.

Gene Symbol	Interneuron Marker	Interneuron Neurotransmitter Phenotype	Hurdle Model Statistical Data			ANOVA Statistical Data
			Least Squares Mean Reads		Fold-Change: Mutant 3 vs All Other Groups	Least Squares Mean Reads		Fold-Change: Mutant 3 vs All Other Groups
			Mutant Group 3	All Other Groups	Fold-Change: Mutant 3 vs All Other Groups	Mutant Group 3	All Other Groups	Fold-Change: Mutant 3 vs All Other Groups
gata2a	KA’, KA”, and V2b	Inhibitory	1.95	1.01	↑1.94 ^***	70.63	1.40	↑50.50 ^***
gata3	KA’, KA”, and V2b	Inhibitory	2.34	1.01	↑2.32 ^***	154.55	1.80	↑85.98 ^***
tal1	KA’, KA”, and V2b	Inhibitory	2.74	1.03	↑2.65 ^***	138.08	2.68	↑51.44 ^***
sst1.1	KA”	Inhibitory	N.C.	N.C.	N.C.	166.67	1.00	↑166.67 ^***
en1b	V1	Inhibitory	8.36	1.01	↑8.26 ^***	457.91	1.56	↑294.43 ^***
dmrt3a	dl6	Inhibitory	2.77	1.02	↑2.71 ^***	275.63	2.71	↑101.77 ^***
ibx1a	dI4, dI5, and dI6	Inhibitory (dI4, dI6) Excitatory (dI5)	1.93	1.01	↑1.91 ^***	59.87	1.72	↑34.78 ^***
islet1a	Motoneurons	Acetylcholinergic	1.29	1.01	↑1.28 ^***	21.25	1.69	↑12.58 ^***
islet2a	Motoneurons	Acetylcholinergic	1.46	1.01	↑1.45 ^***	54.58	1.56	↑35.06 ^***
islet2b	Motoneurons	Acetylcholinergic	1.21	1.00	↑1.21 ^***	18.15	1.32	↑13.73 ^***
mnx1	Motoneurons	Acetylcholinergic	1.42	1.00	↑1.42 ^***	36.21	1.16	↑31.19 ^***
mnx2a	Motoneurons	Acetylcholinergic	N.C.	N.C.	N.C.	15.16	1.00	↑15.16 ^***
mnx2b	Motoneurons	Acetylcholinergic	1.41	1.03	↑1.37 ^***	25.61	3.66	↑6.99 ^***
sim1a	V3	Excitatory	1.00	1.00	↓1.00	1.00	1.30	↓1.30
vsx2	V2a	Excitatory	1.12	1.02	↑1.10	15.06	3.26	↑4.62
tlx3b	dI3 and dI5	Excitatory	N.C.	N.C.	N.C.	2.11	1.00	↑2.11 ^**
foxp2	dI2	Excitatory	1.19	1.16	↑1.03	19.54	10.47	↑1.87
barhl2	dI1	Excitatory	N.C.	N.C.	N.C.	1.00	1.73	↓1.73

Gene-specific analyses of differential expression, created through Hurdle model (columns 4–6) and ANOVA (columns 7–9) statistical comparisons between distinct cell clusters in our 48 h evx1^i232/+;evx2^sa140/+ heterozygote incross single-cell atlas (see Fig 6A and also Methods for experimental details and rationale for using both statistical methods). For these comparisons, the ANOVA data is probably the most robust, as the number of cells in each sub-cluster is relatively small (see Methods for more information). We also include the Hurdle model data for completeness. Column 1 shows the gene symbol. Column 2 indicates the spinal neuron types that normally express the gene. Column 3 indicates the neurotransmitter phenotype for these neurons. Columns 4 and 7 show least squares mean read counts for cells in mutant group 3, and columns 5 and 8 show least squares mean read counts for cells in all the other clusters combined, respectively. Columns 6 and 9 show fold-change values. = fold-change increase, ^– = fold-change decrease in mutant group 3 (the antecedent (first) population) compared to all other populations combined (the consequent (second) population). Statistically significant (P<0.05) values are indicated in bold.

^***

P<0.001.

^**

P<0.01.

N.C. = Not Calculated. Hurdle model of differential expression analysis cannot be calculated, usually because expression was too low or not present in one of the groups being compared. Additional data for this comparison is available in Supp. Data Tables 2 (Hurdle model data) and 3 (ANOVA data).