Table 4

Statistics table

								Mean			Effect (Cohen’s d)					N
	Figure	Target	Group comparison	Data structure	Type of test	Shuffles	p value	Difference	95% CI lower	95% CI upper	Effect	95% CI lower	95% CI upper	Power	p < 0.05	UT	TTX
a		Gephyrin distance to synapsin1	Gephyrin positive synapses (UMAP 6 vs UMAP1-5)	Normal	Permutation t test	5000	0.002	−0.44	−0.46	−0.40	−16.60	−20.65	−12.49	1.0	*	6	5
	3A,F	Gephyrin integrated intensity	Gephyrin positive synapses (UMAP 6 vs UMAP1-5)	Normal	Permutation t test	5000	0.002	0.35	0.20	0.49	2.70	1.25	5.46	1.0	*	6	5
		PSD-95 distance to synapsin1	PSD-95 positive synapses (UMAP6 vs UMAP1-5)	Normal	Permutation t test	5000	0.003	−0.56	−0.70	−0.47	−5.67	−7.51	−4.11	1.0	*	6	5
	3A,F	PSD-95 integrated intensity	PSD-95 positive synapses (UMAP6 vs UMAP1-5)	Normal	Permutation t test	5000	0.007	−0.23	−0.31	−0.10	−2.56	−6.14	−0.69	1.0	*	6	5
	3A,F	Homer1-b/c integrated intensity	Homer1-b/c positive synapses (UMAP6 vs UMAP1)	Normal	Permutation t test	5000	0.003	−0.56	−0.67	−0.43	−5.08	−7.32	−3.58	1.0	*	6	5
b	4A	Excitatory synapse number	Untreated vs TTX	Normal	Permutation t test	5000	0.626	2.99	−7.40	15.23	0.29	−1.10	1.59	0.1		6	6
		Inhibitory synapse number	Untreated vs TTX	Normal	Permutation t test	5000	0.592	3.62	−7.56	16.24	0.33	−1.03	1.69	0.1		6	6
	4B	Excitatory:inhibitory synapse ratio	Untreated vs TTX	Normal	Permutation t test	5000	0.592	−0.86	−4.03	1.78	−0.32	−1.64	1.13	0.1		6	6
c	4C	vGlut1 integrated intensity	Untreated vs TTX (excitatory synapses)	Normal	Permutation t test	5000	0.006	0.17	0.10	0.24	2.82	1.17	5.03	1.0	*	6	5
		vGAT integrated intensity	Untreated vs TTX (inhibitory synapses)	Normal	Permutation t test	5000	0.001	0.60	0.44	0.75	4.31	2.84	6.50	1.0	*	6	5
		Synapsin1 integrated intensity	Untreated vs TTX (excitatory synapses)	Normal	Permutation t test	5000	0.110	0.10	−0.02	0.18	1.11	−0.52	4.00	0.4		6	5
		Synapsin1 integrated intensity	Untreated vs TTX (inhibitory synapses)	Normal	Permutation t test	5000	0.004	0.35	0.23	0.47	3.11	1.53	4.95	1.0	*	6	5
		Bassoon integrated intensity	Untreated vs TTX (excitatory synapses)	Normal	Permutation t test	5000	0.129	0.18	−0.04	0.38	1.02	−0.66	2.49	0.3		6	5
		Bassoon integrated intensity	Untreated vs TTX (inhibitory synapses)	Normal	Permutation t test	5000	0.360	0.11	−0.12	0.32	0.57	−0.98	2.07	0.1		6	5
		SHANK3 integrated intensity	Untreated vs TTX (excitatory synapses)	Normal	Permutation t test	5000	0.008	0.35	0.12	0.46	2.45	0.60	7.29	0.9	*	6	5
		Homer1-b/c integrated intensity	Untreated vs TTX (excitatory synapses)	Normal	Permutation t test	5000	0.037	0.15	0.02	0.26	1.54	−0.02	3.44	0.6	*	6	5
		PSD-95 integrated intensity	Untreated vs TTX (excitatory synapses)	Normal	Permutation t test	5000	0.017	0.15	0.06	0.24	1.93	0.71	3.31	0.8	*	6	5
		Gephyrin integrated intensity	Untreated vs TTX (inhibitory synapses)	Normal	Permutation t test	5000	0.610	0.07	−0.14	0.35	0.31	−1.24	1.72	0.1		6	5
		NR2B integrated intensity	Untreated vs TTX (excitatory synapses)	Normal	Permutation t test	5000	0.089	0.12	−0.02	0.22	1.18	−0.48	3.26	0.4		6	5
		Cortactin integrated intensity	Untreated vs TTX (excitatory synapses)	Normal	Permutation t test	5000	0.549	−0.09	−0.33	0.18	−0.39	−2.45	1.07	0.1		6	5
		Cortactin integrated intensity	Untreated vs TTX (inhibitory synapses)	Normal	Permutation t test	5000	0.589	−0.09	−0.41	0.24	−0.31	−1.87	1.14	0.1		6	5
		Actin integrated intensity	Untreated vs TTX (excitatory synapses)	Normal	Permutation t test	5000	0.475	−0.07	−0.26	0.04	−0.53	−1.80	1.06	0.1		6	5
		Actin integrated intensity	Untreated vs TTX (inhibitory synapses)	Normal	Permutation t test	5000	0.794	0.04	−0.22	0.38	0.17	−1.48	2.06	0.1		6	5
d	5C	Synapsin1 UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.202	0.13	−0.05	0.30	0.84	−0.72	2.49	0.2		5
		Synapsin1 UMAP2	Untreated vs TTX	Normal	Permutation t test	5000	0.479	−0.03	−0.12	0.03	−0.47	−1.83	1.09	0.1		6	5
		Synapsin1 UMAP3	Untreated vs TTX	Normal	Permutation t test	5000	0.569	0.03	−0.10	0.09	0.36	−1.23	3.70	0.1		6	5
		Synapsin1 UMAP4	Untreated vs TTX	Normal	Permutation t test	5000	0.237	−0.06	−0.17	0.03	−0.82	−2.54	1.03	0.2		6	5
		Synapsin1 UMAP5	Untreated vs TTX	Normal	Permutation t test	5000	0.099	−0.09	−0.18	0.01	−1.09	−2.63	0.48	0.4		6	5
		Synapsin1 UMAP6	Untreated vs TTX	Normal	Permutation t test	5000	0.005	0.37	0.24	0.49	3.09	1.64	4.75	1.0	*	6	5
		Gephyrin UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.464	0.02	−0.03	0.07	0.47	−0.92	1.96	0.1		6	5
		Gephyrin UMAP2	Untreated vs TTX	Normal	Permutation t test	5000	0.261	−0.03	−0.08	0.02	−0.68	−2.13	0.68	0.2		6	5
		Gephyrin UMAP3	Untreated vs TTX	Normal	Permutation t test	5000	0.345	−0.03	−0.08	0.02	−0.61	−1.96	0.76	0.1		6	5
		Gephyrin UMAP4	Untreated vs TTX	Normal	Permutation t test	5000	0.304	0.02	−0.02	0.06	0.69	−1.58	2.43	0.2		6	5
		Gephyrin UMAP5	Untreated vs TTX	Normal	Permutation t test	5000	0.647	0.02	−0.05	0.08	0.30	−1.82	2.69	0.1		6	5
		Gephyrin UMAP6	Untreated vs TTX	Normal	Permutation t test	5000	0.733	0.03	−0.12	0.25	0.20	−1.41	1.56	0.1		6	5
		Homer1-b/c UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.221	0.09	−0.05	0.23	0.81	−0.89	2.60	0.2		6	5
		Homer1-b/c UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.452	0.00	0.00	0.00	−0.81	−1.64	−0.40	0.2		6	5
		Homer1-b/c UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.438	0.05	−0.07	0.16	0.49	−1.17	2.16	0.1		6	5
		Homer1-b/c UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.660	0.01	−0.04	0.08	0.29	−1.70	2.07	0.1		6	5
		Homer1-b/c UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.474	0.02	−0.05	0.08	0.41	−1.23	2.01	0.1		6	5
		Homer1-b/c UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.031	0.19	0.07	0.29	1.80	0.48	4.20	0.8	*	6	5
		NR2B UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.144	0.10	−0.03	0.22	0.97	−0.48	2.77	0.3		6	5
		NR2B UMAP2	Untreated vs TTX	Normal	Permutation t test	5000	0.827	−0.02	−0.14	0.11	−0.15	−1.71	1.68	0.1		6	5
		NR2B UMAP3	Untreated vs TTX	Normal	Permutation t test	5000	0.312	0.07	−0.04	0.17	0.63	−0.95	2.41	0.2		6	5
		NR2B UMAP4	Untreated vs TTX	Normal	Permutation t test	5000	0.661	0.05	−0.18	0.28	0.26	−1.50	2.35	0.1		6	5
		NR2B UMAP5	Untreated vs TTX	Normal	Permutation t test	5000	0.744	−0.03	−0.20	0.12	−0.20	−1.80	1.34	0.1		6	5
		NR2B UMAP6	Untreated vs TTX	Normal	Permutation t test	5000	0.533	0.14	−0.33	0.54	0.37	−1.08	1.97	0.1		6	5
		PSD-95 UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.313	0.06	−0.04	0.17	0.65	−0.85	2.04	0.2		6	5
		PSD-95 UMAP2	Untreated vs TTX	Normal	Permutation t test	5000	0.053	0.06	0.01	0.11	1.43	−0.33	3.18	0.6		6	5
		PSD-95 UMAP3	Untreated vs TTX	Normal	Permutation t test	5000	0.778	0.02	−0.10	0.15	0.17	−1.28	1.56	0.1		6	5
		PSD-95 UMAP4	Untreated vs TTX	Normal	Permutation t test	5000	0.882	0.00	0.00	0.00	−0.12	−1.47	1.58	0.1		6	5
		PSD-95 UMAP5	Untreated vs TTX	Normal	Permutation t test	5000	0.184	0.00	0.00	0.01	0.86	0.40	1.50	0.2		6	5
		PSD-95 UMAP6	Untreated vs TTX	Normal	Permutation t test	5000	0.729	−0.01	−0.08	0.07	−0.21	−1.69	1.26	0.1		6	5
		SHANK3 UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.018	0.23	0.11	0.35	2.07	0.81	4.11	0.9	*	6	5
		SHANK3 UMAP2	Untreated vs TTX	Normal	Permutation t test	5000	0.011	0.10	0.04	0.15	1.94	0.55	3.24	0.8	*	6	5
		SHANK3 UMAP3	Untreated vs TTX	Normal	Permutation t test	5000	0.019	0.20	0.08	0.30	1.85	0.55	4.35	0.8	*	6	5
		SHANK3 UMAP4	Untreated vs TTX	Normal	Permutation t test	5000	0.186	0.06	−0.03	0.14	0.85	−0.62	2.44	0.2		6	5
		SHANK3 UMAP5	Untreated vs TTX	Normal	Permutation t test	5000	0.285	0.06	−0.04	0.16	0.67	−0.80	2.17	0.2		6	5
		SHANK3 UMAP6	Untreated vs TTX	Normal	Permutation t test	5000	0.360	0.07	−0.06	0.22	0.58	−0.84	2.15	0.1		6	5
		Actin UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.345	−0.10	−0.28	0.06	−0.60	−1.95	1.11	0.1		6	5
		Actin UMAP2	Untreated vs TTX	Normal	Permutation t test	5000	0.927	0.00	−0.05	0.06	−0.06	−1.54	1.59	0.1		6	5
		Actin UMAP3	Untreated vs TTX	Normal	Permutation t test	5000	0.407	−0.06	−0.18	0.06	−0.56	−2.01	1.13	0.1		6	5
		Actin UMAP4	Untreated vs TTX	Normal	Permutation t test	5000	0.721	−0.01	−0.07	0.05	−0.21	−1.70	1.26	0.1		6	5
		Actin UMAP5	Untreated vs TTX	Normal	Permutation t test	5000	0.923	−0.01	−0.18	0.07	−0.11	−1.72	2.14	0.1		6	5
		Actin UMAP6	Untreated vs TTX	Normal	Permutation t test	5000	0.876	0.01	−0.14	0.19	0.10	−1.31	1.65	0.1		6	5
		Bassoon UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.250	0.08	−0.04	0.21	0.74	−0.90	1.94	0.2		6	5
		Bassoon UMAP2	Untreated vs TTX	Normal	Permutation t test	5000	0.593	−0.02	−0.11	0.06	−0.33	−1.97	1.56	0.1		6	5
		Bassoon UMAP3	Untreated vs TTX	Normal	Permutation t test	5000	0.064	0.09	0.02	0.22	1.16	−0.33	2.12	0.4		6	5
		Bassoon UMAP4	Untreated vs TTX	Normal	Permutation t test	5000	0.877	0.01	−0.09	0.13	0.09	−2.47	3.45	0.1		6	5
		Bassoon UMAP5	Untreated vs TTX	Normal	Permutation t test	5000	0.569	0.02	−0.05	0.08	0.33	−1.26	2.33	0.1		6	5
		Bassoon UMAP6	Untreated vs TTX	Normal	Permutation t test	5000	0.281	0.07	−0.06	0.19	0.64	−0.83	2.20	0.2		6	5
		Cortactin UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.201	−0.09	−0.24	0.01	−0.84	−2.03	0.63	0.2		6	5
		Cortactin UMAP2	Untreated vs TTX	Normal	Permutation t test	5000	0.573	−0.02	−0.11	0.05	−0.34	−1.81	1.07	0.1		6	5
		Cortactin UMAP3	Untreated vs TTX	Normal	Permutation t test	5000	0.390	0.00	0.00	0.00	0.55	−0.98	2.37	0.1		6	5
		Cortactin UMAP4	Untreated vs TTX	Normal	Permutation t test	5000	0.867	0.00	0.00	0.00	0.11	−1.21	1.57	0.1		6	5
		Cortactin UMAP5	Untreated vs TTX	Normal	Permutation t test	5000	0.781	−0.02	−0.12	0.11	−0.16	−2.09	1.78	0.1		6	5
		Cortactin UMAP6	Untreated vs TTX	Normal	Permutation t test	5000	0.585	−0.06	−0.24	0.14	−0.33	−1.87	1.10	0.1		6	5
		vGlut1 UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.044	0.19	0.01	0.30	1.49	−0.25	3.75	0.6	*	6	5
		vGlut1 UMAP2	Untreated vs TTX	Normal	Permutation t test	5000	0.252	0.03	−0.02	0.08	0.78	−0.83	2.69	0.2		6	5
		vGlut1 UMAP3	Untreated vs TTX	Normal	Permutation t test	5000	0.045	0.08	0.01	0.16	1.38	−0.39	3.00	0.5	*	6	5
		vGlut1 UMAP4	Untreated vs TTX	Normal	Permutation t test	5000	0.231	0.03	−0.02	0.07	0.77	−0.83	2.44	0.2		6	5
		vGlut1 UMAP5	Untreated vs TTX	Normal	Permutation t test	5000	0.722	0.01	−0.05	0.09	0.21	−2.28	3.33	0.1		6	5
		vGlut1 UMAP6	Untreated vs TTX	Normal	Permutation t test	5000	0.358	−0.01	−0.02	0.01	−0.57	−2.24	1.05	0.1		6	5
		vGAT UMAP1	Untreated vs TTX	Normal	Permutation t test	5000	0.386	0.00	−0.01	0.00	−0.60	−1.69	1.01	0.1		6	5
		vGAT UMAP2	Untreated vs TTX	Normal	Permutation t test	5000	0.883	0.00	0.00	0.00	0.08	−1.41	1.55	0.1		6	5
		vGAT UMAP3	Untreated vs TTX	Normal	Permutation t test	5000	0.101	−0.01	−0.02	0.00	−1.03	−1.98	0.55	0.3		6	5
		vGAT UMAP4	Untreated vs TTX	Normal	Permutation t test	5000	0.861	0.00	0.00	0.01	0.06	−1.31	1.57	0.1		6	5
		vGAT UMAP5	Untreated vs TTX	Normal	Permutation t test	5000	0.101	−0.01	−0.01	0.00	−1.13	−2.16	−0.49	0.4		6	5
		vGAT UMAP6	Untreated vs TTX	Normal	Permutation t test	5000	0.002	0.86	0.61	1.08	3.99	2.55	6.30	1.0	*	6	5
e	5C	UMAP1 synapse number	Untreated vs TTX	Normal	Permutation t test	5000	0.117	0.11	0.01	0.22	1.09	−0.56	2.56	0.4		6	5
		UMAP2 synapse number	Untreated vs TTX	Normal	Permutation t test	5000	0.042	−0.27	−0.47	−0.04	−1.52	−3.59	0.15	0.6	*	6	5
		UMAP3 synapse number	Untreated vs TTX	Normal	Permutation t test	5000	0.092	0.23	0.07	0.53	1.17	0.10	2.19	0.4		6	5
		UMAP4 synapse number	Untreated vs TTX	Normal	Permutation t test	5000	0.091	−0.14	−0.28	0.03	−1.13	−3.51	0.56	0.4		6	5
		UMAP5 synapse number	Untreated vs TTX	Normal	Permutation t test	5000	0.002	−0.42	−0.60	−0.30	−3.12	−4.32	−1.96	1.0	*	6	5
		UMAP6 synapse number	Untreated vs TTX	Normal	Permutation t test	5000	0.428	0.12	−0.11	0.42	0.51	−0.84	1.85	0.1		6	5

Two-tailed permutation t tests, mean confidence intervals, and effect size were calculated the from 5000 reshuffles of the untreated (n = 6) and TTX-treated (n = 5) samples. The p values represent the likelihood of observing the reported effect size, if the null hypothesis of zero difference is true. Power analysis represents the probability of observing effect size if the null hypothesis of zero difference is true.