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
FOXJ1	0	RFX1	3	affinity chromatography technology, affinity chromatography technology	Li X (2015), Huttlin EL (2017)	2
XYLT2	3	FOXJ1	0	affinity chromatography technology	Boldt K (2016)	1
SOX2	4	NFIB	2	affinity chromatography technology	Engelen E (2011)	1
TADA3	0	HSPA8	4	two hybrid	Stelzl U (2005)	1
RFX1	3	XYLT2	3	affinity chromatography technology	Boldt K (2016)	1
NFIX	8	HDAC1	4	affinity chromatography technology	Singh J (2002)	1
RFX1	3	HSPA8	4	affinity chromatography technology	Guo Y (2016)	1
SMAD4	9	SMAD9	0	two hybrid, affinity chromatography technology, affinity chromatography technology	Rual JF (2005), Nishita M (1999), Li X (2015)	3
STUB1	4	ABL1	9	enzymatic study, affinity chromatography technology	Tsukahara F (2010), Huang H (2017)	2
INPP5K	6	RFX1	3	affinity chromatography technology	Huttlin EL (2017)	1
SMAD1	0	RFX1	3	two hybrid	Colland F (2004)	1
SMAD1	0	STUB1	4	affinity chromatography technology, x-ray crystallography, enzymatic study, two hybrid, pull down, affinity chromatography technology, affinity chromatography technology, pull down, enzymatic study	Wang L (2011), Wang L (2011), Wang L (2011), Li L (2004), Li L (2004), Li L (2004), Li L (2004), Shimamoto S (2013), Shimamoto S (2013)	9
RFX1	3	NFIX	8	affinity chromatography technology	Norquay LD (2003)	1
RFX1	3	NFIC	5	affinity chromatography technology	Norquay LD (2003)	1
STUB1	4	RFX1	3	affinity chromatography technology, affinity chromatography technology	Guo Y (2016), Guo Y (2016)	2
FOXJ1	0	RFX3	7	affinity chromatography technology, affinity chromatography technology, affinity chromatography technology	Li X (2015), Huttlin EL (2017), Boldt K (2016)	3
RFX1	3	NFIB	2	affinity chromatography technology	Norquay LD (2003)	1
SMAD4	9	NFIX	8	affinity chromatography technology	Li X (2015)	1
ARRB2	5	STUB1	4	affinity chromatography technology	Zhang Z (2009)	1
NOTCH1	25	RFX1	3	affinity chromatography technology	Yatim A (2012)	1
FBXL3	1	RFX1	3	affinity chromatography technology, affinity chromatography technology	Huttlin EL (2015), Huttlin EL (2017)	2
NFIB	2	NFIC	5	pull down, affinity chromatography technology	Liu Y (1997), Huttlin EL (2017)	2
SOX2	4	RFX1	3	affinity chromatography technology	Cox JL (2013)	1
SMAD4	9	STUB1	4	pull down, affinity chromatography technology	Li L (2004), Li L (2004)	2
MAGED1	0	RFX1	3	two hybrid	Stelzl U (2005)	1
ABL1	9	NCOA3	3	affinity chromatography technology, pull down	Oh AS (2008), Oh AS (2008)	2
SPATA1	0	RFX1	3	affinity chromatography technology	Huttlin EL (2017)	1
FOXN3	2	RFX3	7	affinity chromatography technology	Huttlin EL (2017)	1
SMAD1	0	SMAD4	9	affinity chromatography technology, affinity chromatography technology, biochemical, affinity chromatography technology, biochemical, two hybrid, affinity chromatography technology, affinity chromatography technology, two hybrid, two hybrid, two hybrid, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology	Harada J (2003), Hanai J (1999), Lopez-Rovira T (2002), Kato Y (2002), Wang L (2011), Li L (2004), Hata A (1998), Barrios-Rodiles M (2005), Wu RY (1997), Wu RY (1997), Colland F (2004), Qiu T (2007), Yan X (2016), Zhou F (2017)	14
SMAD4	9	RFX1	3	two hybrid	Colland F (2004)	1
XYLT2	3	HDAC1	4	affinity chromatography technology	Boldt K (2016)	1
SOX2	4	RFX3	7	affinity chromatography technology	Engelen E (2011)	1
STUB1	4	HSPA8	4	pull down, affinity chromatography technology, two hybrid, affinity chromatography technology, affinity chromatography technology, enzymatic study, x-ray crystallography, pull down, pull down, pull down, pull down, affinity chromatography technology, enzymatic study, two hybrid, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, pull down, enzymatic study, affinity chromatography technology, enzymatic study, affinity chromatography technology, affinity chromatography technology, enzymatic study, pull down, unspecified method, affinity chromatography technology, x-ray crystallography, enzymatic study, pull down, affinity chromatography technology, affinity chromatography technology, x-ray crystallography, enzymatic study	Ballinger CA (1999), Ballinger CA (1999), Ballinger CA (1999), Tateishi Y (2004), Tateishi Y (2004), Jiang J (2001), Wang L (2011), Wang L (2011), Wang L (2011), Stankiewicz M (2010), Yang M (2011), Yang M (2011), Urushitani M (2004), Grelle G (2006), Kim SA (2005), Arndt V (2005), Alberti S (2004), Meacham GC (2001), Smith MC (2013), Smith MC (2013), Matsumura Y (2013), Spooner RA (2008), Taipale M (2014), Taipale M (2014), Heimdal K (2014), Grelle G (2006), Grelle G (2006), Kamynina E (2007), Zhang H (2015), Zhang H (2015), Zhang H (2015), Li P (2015), Guo Y (2016), Zhang H (2017), Pakdaman Y (2017)	35
RFX3	7	XYLT2	3	affinity chromatography technology	Boldt K (2016)	1
RFX1	3	RFX3	7	affinity chromatography technology	Boldt K (2016)	1
SOX2	4	HDAC1	4	affinity chromatography technology	Engelen E (2011)	1
SMAD1	0	HDAC1	4	affinity chromatography technology	Takeda M (2004)	1
FOXN2	2	RFX1	3	affinity chromatography technology, affinity chromatography technology	Li X (2015), Huttlin EL (2017)	2
HDAC1	4	FOXJ1	0	affinity chromatography technology	Boldt K (2016)	1
SMAD4	9	HDAC1	4	affinity chromatography technology	Takeda M (2004)	1
FOXN3	2	RFX1	3	affinity chromatography technology	Huttlin EL (2017)	1
FOXJ2	3	RFX1	3	affinity chromatography technology	Li X (2015)	1
NFIB	2	NFIX	8	pull down, affinity chromatography technology	Liu Y (1997), Huttlin EL (2017)	2
NOTCH1	25	SMAD9	0	affinity chromatography technology	Yatim A (2012)	1
NCOA3	3	RFX1	3	affinity chromatography technology	Lanz RB (2010)	1
TADA3	0	RFX1	3	two hybrid	Stelzl U (2005)	1
SMAD9	0	RFX1	3	two hybrid	Colland F (2004)	1
RFX1	3	HDAC1	4	affinity chromatography technology, affinity chromatography technology, affinity chromatography technology	Xu Y (2006), Wang KR (2007), Boldt K (2016)	3
HSPA8	4	ABL1	9	pull down, affinity chromatography technology	Tsukahara F (2010), Tsukahara F (2010)	2
NOTCH1	25	MAGED1	0	two hybrid	Daakour S (2016)	1
NOTCH1	25	HDAC1	4	affinity chromatography technology, affinity chromatography technology	Yatim A (2012), Yatim A (2012)	2
ARRB2	5	RFX1	3	affinity chromatography technology	Huttlin EL (2017)	1
FOXJ2	3	RFX3	7	affinity chromatography technology	Li X (2015)	1
ABL1	9	RFX1	3	affinity chromatography technology, pull down	Agami R (1998), Agami R (1998)	2
RFX3	7	HDAC1	4	affinity chromatography technology	Boldt K (2016)	1
HSPB8	0	RFX1	3	affinity chromatography technology	Huttlin EL (2017)	1
ARRB2	5	HSPA8	4	affinity chromatography technology, affinity chromatography technology	Xiao K (2007), Xiao K (2007)	2