In silico tandem affinity purification refines an Oct4 interaction list

Cheong, Clara Yujing; Lon Ng, Patricia Miang; Ponnampalam, Rhonda; Tsai, Heng-Hang; Bourque, Guillaume; Lufkin, Thomas

doi:10.1186/scrt67

Stem Cell Research & Therapy

Table 2 Oct4-associated proteins using four different affinity tag approaches^a

From: In silico tandem affinity purification refines an Oct4 interaction list

Gene name	Entrez Gene ID	Description	Catalytic activity based on PANTHER	CBP	FLAG	HIS	S
Pou5f1	18999	POU domain, class 5, transcription factor 1		2.0	7.0	12.0	Exc
Cell cycle associated
Cdk1	12534	Cyclin-dependent kinase 1	Kinase	0.7	0.7	Exc	Exc
Smc2	14211	Structural maintenance of chromosome 2		0.8	Exc	Exc
Rad50	19360	RAD50 homolog (Saccharomyces cerevisiae)		Exc	Exc	1.3
Nup43	69912	Nucleoporin 43		Exc	Exc	1.2
Metabolic processing
Trip12	14897	Thyroid hormone receptor interactor 12		9.0	Exc	0.5
Ribonucleoprotein complex
Ddx1	104721	DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	Helicase, translation initiation	0.5	Exc	Exc
Dhx15	13204	DEAH (Asp-Glu-Ala-His) box polypeptide 15	Helicase	0.6	3.0	22.5
Nop56	67134	Nucleolar protein 5A			Exc		Exc
RNA and protein transport and localization
Kpna2	16647	Karyopherin (importin) α2		Exc	Exc
Nup93	71805	Nucleoporin 93		1.6	4.0	Exc
Nup85	445007	Nucleoporin 85	Transferase	3.5	Exc
Nop58	55989	Nucleolar protein 5		1.8	Exc		Exc
Nup107	103468	Nucleoporin 107		3.3	Exc	0.8
Rcc1	100088	Regulator of chromosome condensation 1	Ligase, small GTPase regulator, guanyl-nucleotide exchange factor	Exc	3.0
Thoc4	21681	THO complex 4			Exc		Exc
Lbr	98386	Lamin B receptor	Oxidoreductase		Exc	3.5
Nup153	218210	Nucleoporin 153		Exc	Exc
Nup155	170762	Nucleoporin 155		9.5	3.6	0.9
Tjp2	21873	Tight junction protein 2		2.0	Exc	0.5	Exc
Xpo1	103573	Exportin 1, CRM1 homolog (yeast)		3.0	Exc
RNA processing
Eftud2	20624	Elongation factor Tu GTP binding domain containing 2	Nucleotidyltransferase, GTPase, translation initiation and elongation	0.5	4.3	0.8	Exc
U2af2	22185	U2 small nuclear ribonucleoprotein auxiliary factor 2			Exc		Exc
Syncrip	56403	Synaptotagmin binding, cytoplasmic RNA interacting protein	RNA splicing factor, transesterification mechanism		5.0		3.0
Signal transduction
Cul4b	72584	Cullin 4B		Exc	Exc
Rsu1	20163	Ras suppressor protein 1		Exc		Exc
SWI/SNF Complex
Smarcd1	83797	SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily d, member 1		1.0	6.0	1.0	Exc
Transcriptional regulation
Fubp3	320267	Far upstream element (FUSE) binding protein 3		3.3	4.0		Exc
Fus	233908	Fusion, derived from t(12;16) malignant liposarcoma	RNA splicing factor, transesterification mechanism	Exc			Exc
Pelp1	75273	Proline, glutamic acid and leucine rich protein 1		Exc	Exc	0.6
Psip1	101739	PC4 and SFRS1 interacting protein 1		2.5	Exc		4.0
Tardbp	230908	TAR DNA binding protein	RNA splicing factor, transesterification mechanism	0.6	5.0	Exc	2.0
Top2a	21973	Topoisomerase (DNA) IIα		3.7	1.8	0.7	4.0
Translational regulation
Igf2bp1	140486	Insulin-like growth factor 2 mRNA binding protein 1	RNA splicing factor, transesterification mechanism		Exc		Exc

^aThe fold change of spectral counts of proteins from tag sample relative to wild-type sample is shown. Exc represents proteins that are seen exclusively in the tag sample.

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ISSN: 1757-6512

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