. 2017 Dec 4;6:e24192. doi: 10.7554/eLife.24192

Table 1. Shisa7 is a native interactor of hippocampal AMPARs.

Shisa7 complexes were immunoprecipitated from the hippocampi of Shisa7 WT and KO animals (DDM-extracted crude synaptic membranes; n = 3 IPs per genotype) and subjected to mass spectrometric analysis. The following protein categories were indicated: Shisa7, AMPAR subunits, established non-PDZ AMPAR-interacting proteins (Schwenk et al., 2012), PDZ domain-containing interactors. Percent coverage, percent of the database protein sequence covered by all matching peptides. Values of statistical significance upon performing a Student’s t-test with permutation-based FDR analysis (S0 = 1, FDR < 0.05 (bold)) are indicated. Note the identification of a peptide specific for exon 4 containing Shisa7 (NLYNTMKPSNLDwNLHYNVNSPK; diamond indicates exon3-exon4 boundary). The full list of identified protein groups is reported in Table 1—source data 1, and the statistical analysis is provided in Table 1—source data 2, which includes a volcano-plot of differentially IP-ed proteins.

Table 1—source data 1. Maxquant analysis of hippocampal Shisa7 immunoprecipitation experiments, as detailed in the Materials and methods section.

The Maxquant ‘proteinGroups.txt’ output file was supplemented with ‘LFQ intensity _ Average KO’, ‘LFQ intensity _ Average WT’, and the ‘KO/WT’ and ‘WT/KO’ ratios thereof.

elife-24192-table1-data1.xlsx^{(260.7KB, xlsx)}

DOI: 10.7554/eLife.24192.008

Table 1—source data 2. Statistical analysis of hippocampal Shisa7 immunoprecipitation data, as detailed in the Materials and methods section.

Tab 1: In summary, the Maxquant ‘proteinGroups.txt’ output file was imported into Perseus, and processed in the following manner: (1) Removal of ‘Reverse’, ‘Potential contaminant’, and ‘Only identified by site’ protein groups; (2) Log(2) transformation of all LFQ intensity values; (3) Removal of protein groups with less than three valid ‘Log(2) LFQ intensity’ values in either the WT or KO groups; (4) Imputation of missing values (8.6% of the population) from a normal distribution (width 0.3, down shift 1.8, whole matrix); (5) Performing a Student's t-test followed by permutation-based FDR analysis (S0 = 1, FDR = 0.01, 2500 permutations). Tab 2: Visualization of the data by means of Histogram and Vulcanoplot is presented in the additional sheets. Tab 3: Distribution of LFQ intensities after replacing missing values from a normal distribution. The imputed value distribution is depicted in red.

elife-24192-table1-data2.xlsx^{(765.5KB, xlsx)}

DOI: 10.7554/eLife.24192.009

Gene name	Uniprot recommendedprotein name(s)	Uniprot ID	PDZ-domains	Number of unique peptides						LFQ intensity						Average KO LFQ intensity	Average WT LFQ intensity	Average KO/WT LFQ intensity	Average WT/KO LFQ intensity	T-test significant FDR0.01 = ++ DR0.05 = +	T-test q-value	Percent cover-age
Gene name	Uniprot recommendedprotein name(s)	Uniprot ID	PDZ-domains	KO1	KO2	KO3	WT1	WT2	WT3	KO1	KO2	KO3	WT1	WT2	WT3	Average KO LFQ intensity	Average WT LFQ intensity	Average KO/WT LFQ intensity	Average WT/KO LFQ intensity	T-test significant FDR0.01 = ++ DR0.05 = +	T-test q-value	Percent cover-age
Shisa7	Protein Shisa-7	Q8C3Q5	0	1	1	2	17	18	16	865	873	1750	319820	305190	346730	1163	323913	0.4%	278.58	++	0.0000	39.2
Shisa7	Protein Shisa-7:Exon4-specificpeptideNLYNTMKPSNLDNLHYNVNSPK	-	-	0	0	0	1	0	0	-	-	-	-	-	-	-	-	-	-	-	-	-
Gria1	Glutamatereceptor 1	P23818	0	0	0	0	10	12	12	5921	0	3217	17828	52304	54212	4569	41448	11.0%	9.07	++	0.0000	22.8
Gria2	Glutamatereceptor 2	P23819	0	2	1	0	17	17	17	2743	0	0	104860	101430	93097	2743	99796	2.7%	36.39	++	0.0000	36.4
Gria3	Glutamatereceptor 3	Q9Z2W9	0	0	0	0	4	4	5	0	0	0	6529	7068	10102	0	7900	0.0%	NaN	++	0.0000	17.7
Cacng8	Voltage-dependentcalciumchannelgamma-8subunit;TARPgamma-8	Q8VHW2	0	2	2	1	2	1	5	4023	0	0	0	0	3962	4023	3962	101.5%	0.98	-	N/A	30.5
Olfm1	Noelin	O88998	0	1	1	0	0	2	2	0	1076	0	0	1004	779	1076	892	120.6%	0.83	-	N/A	7.0
Prrt1	Proline-richtransmem-braneprotein 1;SynDIG4	O35449	0	0	0	0	1	1	0	0	0	0	969	0	0	0	969	0.0%	NaN	-	N/A	7.2
Prrt2	Proline-richtransmem-braneprotein 2	E9PUL5	0	0	1	0	1	1	1	0	333	0	318	0	202	333	260	127.9%	0.78	-	N/A	3.8
Rap2b	Ras-relatedproteinRap-2b	P61226	0	0	1	1	1	0	0	0	0	2588	0	0	0	2588	0	NaN	0.00	-	N/A	12.0
Shisa6	Proteinshisa-6homolog	Q3UH99	0	1	0	0	3	3	1	0	0	0	2666	3580	2136	0	2794	0.0%	NaN	+	0.0306	9.9
Dlg1	Disks largehomolog 1;SAP97	Q811D0	3	0	1	1	3	0	0	0	0	0	2126	0	0	0	2126	0.0%	NaN	-	N/A	4.4
Dlg3	Disks largehomolog 3;SAP102	P70175	3	0	0	0	0	2	2	0	0	0	0	2441	0	0	2441	0.0%	NaN	-	N/A	4.8
Dlg4	Disks largehomolog 4;PSD95	Q62108	3	0	0	0	9	8	7	0	0	0	11835	13410	9284	0	11510	0.0%	NaN	++	0.0000	21.7
Magi2	Membrane-associatedguanylatekinase,WW and PDZdomain-containingprotein 2	Q9WVQ1	6	0	0	0	1	1	0	0	0	0	0	1558	0	0	1558	0.0%	NaN	-	N/A	1.6