Table 2. NEK7 Interacting Proteins Identified by IP-LC–MS/MS^a.

proteinb	gene	Uniprot accession	fold change TICc	FLAG-control total spectra	FLAG-NEK7 total spectra
Serine/threonine-protein kinase Nek7	NEK7	Q8TDX7	9.10 × 109		1291
cDNA FLJ60124, highly similar to Mitochondrial dicarboxylate carrier	SLC25A10	Q9UBX3	2.60 × 108		68
Importin-9	IPO9	Q96P70	1.00 × 108		88
ATPase family AAA domain-containing protein 3A isoform 3	ATAD3A	Q9NVI7	9.90 × 107		94
Protein RCC2	RCC2	Q9P258	4.90 × 107		80
Isoform 3 of Apoptosis-inducing factor 1, mitochondrial	AIFM1	O95831	3.80 × 107		43
Ubiquitin-40S ribosomal protein S27a	RPS27A	P62979	3.50 × 107		36
Isoform 1 of AP-2 complex subunit beta	AP2B1	P63010	3.30 × 107		22
Isoform 1 of Structural maintenance of chromosomes protein 2	SMC2	O95347	2.80 × 107		35
Isoform 1 of Caprin-1	CAPRIN1	Q14444	2.80 × 107		37
Isoform 1 of Structural maintenance of chromosomes protein 4	SMC4	Q9NTJ3	2.70 × 107		69
Isoform 1 of CLIP-associating protein 1	CLASP1	Q7Z460	2.50 × 107		89
Isoform 1 of CLIP-associating protein 2	CLASP2	O75122	1.60 × 107		20
Ras-related protein Rab-32	RAB32	Q13637	1.50 × 107		25
Isoform 1 of Centrosomal protein of 170 kDa	CEP170	Q5SW79	1.20 × 107		33
Isoform 1 of Rho guanine nucleotide exchange factor 2	ARHGEF2	Q92974	1.20 × 107		24
Structural maintenance of chromosomes protein 1A	SMC1A	Q14683	1.20 × 107		18
Isoform 1 of Microtubule-associated protein 2	MAP2	P11137	1.10 × 107		17
Zinc finger protein 622	ZNF622	Q969S3	6600000		32
Isoform 1 of Cyclin-dependent kinase 13	CDK13	Q14004	6300000		17
Isoform 2 of Nuclear mitotic apparatus protein 1	NUMA1	Q14980	5600000		23
Structural maintenance of chromosomes protein 3	SMC3	Q9UQE7	5600000		24
Isoform 1 of Dedicator of cytokinesis protein 4	DOCK4	Q8N1I0	5400000		11
Isoform 1 of MAP7 domain-containing protein 1	MAP7D1	Q3KQU3	5000000		17
Condensin complex subunit 1	NCAPD2	Q15021	4700000		28
Condensin-2 complex subunit D3	NCAPD3	P42695	3300000		31
Serine/threonine-protein kinase PLK1	PLK1	P53350	3000000		13
Kinesin-like protein KIF20A	KIF20A	O95235	2900000		9
Isoform 1 of Cyclin-dependent kinase 12	CDK12	Q9NYV4	2700000		92
Isoform 1 of DNA repair protein RAD50	RAD50	Q92878	2100000		10
Isoform B of AP-2 complex subunit alpha-1	AP2A1	O95782	2000000		15
cDNA FLJ54776, highly similar to Cell division control protein 42 homologue	CDC42	P60953	1700000		17
Condensin complex subunit 3	NCAPG	Q9BPX3	830000		6
40S ribosomal protein S4, X isoform	RPS4X	P62701	1,9	115	236
40S ribosomal protein S6	RPS6	P62753	1,4	71	149
Tu translation elongation factor, mitochondrial precursor	TUFM	P49411	1,1	54	114
Similar to Elongation factor 1-alpha 1	EEF1A1	P68104	0,8	44	63

^aThe proteins that co-immunoprecipitated with NEK7-FLAG but not FLAG-control and that were not deposited in the CRAPome or the proteins that overlapped with Y2H are listed.

^bThe overlapping proteins found by mass spectrometry (this table) and by yeast two-hybrid (Table 1) are underlined.

^cFold change, as determined by the Scaffold program;²⁵ TIC = total ion count.