PsyMuKB

PPI network (data source: BioGrid)

A gene is determined as “expressed” when its expression values are above the pre-determined cutoff, which is the mean normalized expression(base 2 log of (TPM+1)) +1 in all brain tissue from GTEx v7 or BrainSpan data.

A protein is determined as “expressed” when its expression values are above the pre-determined cutoff, which is the normalized expression (base 10 log of iBAQ intensity) ≥0.5 in at least one brain tissue from ProteomicsDB data. Otherwise, a gene or protein is determined as either with below-cutoff expressions or no available data.

	The queried gene/protein
	The interacting partner is expressed at mRNA-level
	The interacting partner is expressed at protein-level
	The interacting partner is expressed at both mRNA and protein level
	The interacting partner is with either below-cutoff expressions or no expression data at both mRNA and protein level
	The interacting partner is hit by coding DNMs
	Physical interaction between queried gene/protein and its partner
	Physical interaction between two interacting partners

Symbol A	GeneA coding DNM count	Symbol B	GeneB coding DNM count	Interaction detection method	Publication	Evidence
VCP	6	FAF1	1	affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, pull down, affinity chromatography technology, x-ray crystallography, x-ray crystallography, pull down, x-ray crystallography, affinity chromatography technology, pull down, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology	Alexandru G (2008), Alexandru G (2008), Haenzelmann P (2011), Song EJ (2005), Song EJ (2005), Shin HY (2010), Haenzelmann P (2011), Haenzelmann P (2011), Kang W (2011), Alexandru G (2012), Lee JJ (2013), Lee JJ (2013), Lee JJ (2013), Yu CC (2013), Baron Y (2014), Franz A (2016), Raman M (2015)	17
UBQLN1	1	APP	1	two hybrid, affinity chromatography technology, fluorescent resonance energy transfe	Stieren ES (2011), Stieren ES (2011), Hiltunen M (2006)	3
PTPRO	3	NGLY1	0	affinity chromatography technology	Li X (2016)	1
RAD23A	1	FAF1	1	affinity chromatography technology	Scanlon TC (2009)	1
RAD23B	1	UBQLN1	1	biochemical, biochemical	Havugimana PC (2012), Wan C (2015)	2
VCP	6	UBXN2B	2	affinity chromatography technology, two hybrid, affinity chromatography technology, pull down, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology	Alexandru G (2008), Rolland T (2014), Huttlin EL (2015), Zhang X (2015), Raman M (2015), Raman M (2015), Huttlin EL (2017)	7
DERL1	2	APP	1	pull down	Olah J (2011)	1
RAD23A	1	UBQLN1	1	x-ray crystallography, affinity chromatography technology, biochemical	Kang Y (2007), Kang Y (2007), Wan C (2015)	3
DERL1	2	EGFR	5	affinity chromatography technology, affinity chromatography technology	Dong QZ (2013), Dong QZ (2013)	2
NGLY1	0	GUCD1	0	two hybrid	Rolland T (2014)	1
NGLY1	0	RAD23B	1	x-ray crystallography, two hybrid, affinity chromatography technology, biochemical, affinity chromatography technology	Kamiya Y (2012), Rolland T (2014), Christianson JC (2012), Wan C (2015), Huttlin EL (2017)	5
NGLY1	0	RAD23A	1	x-ray crystallography, two hybrid	Kamiya Y (2012), Rolland T (2014)	2
RAD23A	1	TRIM54	1	two hybrid	Rolland T (2014)	1
FBXO6	0	NGLY1	0	affinity chromatography technology	Liu B (2012)	1
EGFR	5	FBXO6	0	affinity chromatography technology, affinity chromatography technology	Foerster S (2013), Liu B (2012)	2
PTPRO	3	VCP	6	affinity chromatography technology, affinity chromatography technology	Hsu SH (2013), Hsu SH (2013)	2
NGLY1	0	DERL1	2	affinity chromatography technology, affinity chromatography technology, biochemical, pull down, biochemical	Katiyar S (2005), Katiyar S (2005), Katiyar S (2005), Katiyar S (2005), Katiyar S (2005)	5
TMEM25	0	NGLY1	0	affinity chromatography technology, affinity chromatography technology	Huttlin EL (2015), Huttlin EL (2017)	2
NGLY1	0	UBXN2B	2	two hybrid	Rolland T (2014)	1
UBQLN1	1	VCP	6	pull down, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology	Lim PJ (2009), Yu CC (2013), Lim PJ (2009), Lim PJ (2009)	4
RAD23A	1	RAD23B	1	biochemical, affinity chromatography technology	van der Spek PJ (1996), Hsieh HC (2005)	2
VCP	6	APP	1	affinity chromatography technology	Jang JK (2017)	1
VCP	6	NGLY1	0	affinity chromatography technology, affinity chromatography technology, pull down, affinity chromatography technology, pull down	McNeill H (2004), Allen MD (2006), Allen MD (2006), Christianson JC (2012), McNeill H (2004)	5
TMEM25	0	EGFR	5	affinity chromatography technology	Huttlin EL (2015)	1
GUCD1	0	APP	1	pull down	Olah J (2011)	1
B4GALT4	0	NGLY1	0	affinity chromatography technology, affinity chromatography technology	Huttlin EL (2015), Huttlin EL (2017)	2
UBXN2B	2	FAF1	1	affinity chromatography technology	Raman M (2015)	1
SRPK2	1	NGLY1	0	enzymatic study	Varjosalo M (2013)	1
TRAFD1	2	NGLY1	0	two hybrid	Rolland T (2014)	1
EGFR	5	NGLY1	0	affinity chromatography technology	Tong J (2014)	1
ACP5	1	NGLY1	0	affinity chromatography technology	Li X (2016)	1
EGFR	5	TRAFD1	2	affinity chromatography technology	Yao Z (2017)	1
NGLY1	0	TRIM54	1	two hybrid	Rolland T (2014)	1
EGFR	5	APP	1	two hybrid, protein complementation assay	Kotlyar M (2015), Petschnigg J (2014)	2
NAGPA	2	NGLY1	0	affinity chromatography technology	Huttlin EL (2017)	1
UBQLN1	1	NGLY1	0	two hybrid	Rolland T (2014)	1
SRPK2	1	APP	1	pull down	Olah J (2011)	1
PTPRO	3	APP	1	pull down	Olah J (2011)	1
NSFL1C	1	FAF1	1	affinity chromatography technology	Raman M (2015)	1
RAD23A	1	VCP	6	affinity chromatography technology	Laco MN (2012)	1
NGLY1	0	NSFL1C	1	pull down	Allen MD (2006)	1
NGLY1	0	APP	1	pull down	Olah J (2011)	1
VCP	6	DERL1	2	affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, pull down, pull down, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, unspecified method, x-ray crystallography	Wang Q (2008), Ballar P (2007), Schulze A (2005), Schulze A (2005), Ye Y (2005), Lilley BN (2005), Greenblatt EJ (2011), Younger JM (2006), Christianson JC (2012), You H (2017), Lim JJ (2016), Lim JJ (2016)	12
VCP	6	NSFL1C	1	pull down, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, two hybrid, two hybrid, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, two hybrid, pull down, unspecified method, two hybrid, affinity chromatography technology, two hybrid, pull down, biochemical, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, pull down, affinity chromatography technology, affinity chromatography technology	Uchiyama K (2003), Uchiyama K (2003), Alexandru G (2008), Alexandru G (2008), Vinayagam A (2011), Madsen L (2011), Fernandez-Saiz V (2010), Noguchi M (2005), Uchiyama K (2002), Uchiyama K (2002), Uchiyama K (2002), Alexandru G (2012), Fogeron ML (2013), Grelle G (2006), Grelle G (2006), Grelle G (2006), Rolland T (2014), Besten Wd (2012), Madsen L (2014), Zhang X (2015), Wan C (2015), Hein MY (2015), Raman M (2015), Raman M (2015), Wang T (2016), Guo X (2017), Park ES (2017), Huttlin EL (2017)	28
NGLY1	0	FAF1	1	pull down	Allen MD (2006)	1
LINGO1	3	NGLY1	0	affinity chromatography technology	Huttlin EL (2017)	1
FBXO6	0	VCP	6	affinity chromatography technology, affinity chromatography technology	Yoshida Y (2005), Yoshida Y (2005)	2