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
EP300	36	SMAD3	1	affinity chromatography technology, affinity chromatography technology, pull down, pull down, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, pull down, two hybrid, affinity chromatography technology, pull down, affinity chromatography technology, pull down, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology	Qiu P (2006), Furumatsu T (2005), Itoh S (2000), Akiyoshi S (1999), Abecassis L (2004), Kaimori A (2010), Janknecht R (1998), Janknecht R (1998), Nishihara A (1999), Nishihara A (1999), Furumatsu T (2005), Ghosh AK (2004), Shen X (1998), Shen X (1998), Ghosh AK (2001), Postigo AA (2003), Postigo AA (2003), Yang WS (2005), Lim JY (2012), Lim JY (2012), Jinnin M (2007), Wang G (2005)	22
DNMT3L	2	PAX6	3	pull down, imaging technique, affinity chromatography technology	Pacaud R (2014), Pacaud R (2014), Pacaud R (2014)	3
EP300	36	SMAD4	9	affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, pull down, unspecified method, affinity chromatography technology	Kim RH (2000), Luciakova K (2008), Janknecht R (1998), Chung CL (2011), Shen X (1998), Dornan D (2003), Yang Y (2015)	7
SUMO1	0	HIPK2	0	two hybrid, imaging technique, pull down	Lee BH (2003), de la Vega L (2011), de la Vega L (2011)	3
RB1	2	TRAP1	0	two hybrid, pull down, affinity chromatography technology, affinity chromatography technology	Chen CF (1996), Chen CF (1996), Chen CF (1996), Chen CF (1996)	4
SUMO1	0	TP73	2	two hybrid	Minty A (2000)	1
AR	3	SMAD3	1	affinity chromatography technology, two hybrid, pull down, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, pull down, affinity chromatography technology, affinity chromatography technology, pull down, pull down, pull down	Chipuk JE (2002), Hayes SA (2001), Hayes SA (2001), Hayes SA (2001), Chipuk JE (2002), Hayes SA (2001), Hayes SA (2001), Kang HY (2002), Kang HY (2002), Kang HY (2002), Kang HY (2002), Chipuk JE (2002)	12
CDX2	4	SMARCA4	19	pull down	Yamamichi N (2009)	1
MID1	1	AR	3	affinity chromatography technology, affinity chromatography technology	Koehler A (2014), Koehler A (2014)	2
PAX6	3	TRAP1	0	affinity chromatography technology	Hein MY (2015)	1
PAX6	3	EP300	36	pull down, affinity chromatography technology, affinity chromatography technology	Hussain MA (1999), Hussain MA (1999), Hussain MA (1999)	3
RB1	2	AR	3	pull down, pull down, two hybrid, affinity chromatography technology	Lu J (1998), Yeh S (1998), Yeh S (1998), Gamble SC (2007)	4
SMAD1	0	PAX6	3	affinity chromatography technology	Grocott T (2007)	1
SMAD4	9	SMAD5	2	affinity chromatography technology, two hybrid, two hybrid	Hanai J (1999), Haag J (2006), Colland F (2004)	3
PAX6	3	PCNT	10	affinity chromatography technology	Hein MY (2015)	1
IPO13	6	RAN	1	pull down, affinity chromatography technology	Gruenwald M (2011), Liang J (2008)	2
PAX6	3	APOB	8	affinity chromatography technology	Hein MY (2015)	1
PAX6	3	PROX1	0	pull down	Mikkola I (2001)	1
HIPK2	0	EP300	36	enzymatic study, affinity chromatography technology, affinity chromatography technology, pull down	Aikawa Y (2006), Aikawa Y (2006), Aikawa Y (2006), Aikawa Y (2006)	4
SOX2	4	RBM4	1	affinity chromatography technology	Cox JL (2013)	1
PAX6	3	AR	3	two hybrid, affinity chromatography technology, affinity chromatography technology, fluorescent resonance energy transfe, pull down, affinity chromatography technology, affinity chromatography technology	Shyr CR (2010), Shyr CR (2010), Shyr CR (2010), Elvenes J (2011), Elvenes J (2011), Elvenes J (2011), Elvenes J (2011)	7
IPO13	6	PAX6	3	two hybrid, two hybrid, pull down, affinity chromatography technology	Ploski JE (2004), Rual JF (2005), Ploski JE (2004), Ploski JE (2004)	4
DNMT3L	2	SMAD1	0	pull down	Pacaud R (2014)	1
PAX6	3	PKNOX1	1	pull down	Mikkola I (2001)	1
TBP	0	EP300	36	affinity chromatography technology	Dallas PB (1997)	1
SOX2	4	TP73	2	affinity chromatography technology	Cox JL (2013)	1
PAX6	3	MITF	3	pull down	Planque N (2001)	1
SMAD5	2	RBM4	1	two hybrid	Colland F (2004)	1
PAX6	3	TMEM189	0	affinity chromatography technology	Hein MY (2015)	1
AR	3	SMARCA4	19	affinity chromatography technology, two hybrid, affinity chromatography technology, bioid	Wang Q (2004), van de Wijngaart DJ (2009), Dai Y (2008), Lempiaeinen JK (2017)	4
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
PROX1	0	SMAD3	1	two hybrid	Wang J (2011)	1
SMAD3	1	SMAD1	0	affinity chromatography technology, two hybrid, two hybrid	Brown KA (2008), Wu RY (1997), Wu RY (1997)	3
PAX6	3	LHX2	0	pull down	Mikkola I (2001)	1
AR	3	RAN	1	two hybrid	Hsiao PW (1999)	1
RBM4	1	TMEM189	0	biochemical	Havugimana PC (2012)	1
SOX2	4	SUMO1	0	two hybrid	Rolland T (2014)	1
PAX6	3	RAN	1	affinity chromatography technology	Hein MY (2015)	1
PAX6	3	VSX2	1	pull down	Mikkola I (2001)	1
MAFB	1	PAX6	3	affinity chromatography technology	Scoville DW (2015)	1
SMAD3	1	HIPK2	0	pull down	Harada J (2003)	1
RB1	2	EP300	36	affinity chromatography technology, affinity chromatography technology, enzymatic study	Iyer NG (2007), Iyer NG (2007), Chan HM (2001)	3
DNMT3L	2	CDX2	4	pull down	Pacaud R (2014)	1
AR	3	EP300	36	affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, enzymatic study, affinity chromatography technology, affinity chromatography technology	Dai Y (2008), Minges JT (2013), Zhong J (2014), Fu M (2000), McClurg UL (2016), Tan G (2017)	6
SMAD3	1	PAX6	3	affinity chromatography technology	Grocott T (2007)	1
EP300	36	SMAD5	2	affinity chromatography technology, two hybrid	Jeon EJ (2006), Haag J (2006)	2
PAX6	3	SUMO1	0	pull down	Yan Q (2010)	1
TAF1	9	RB1	2	genetic interference, pull down, pull down, affinity chromatography technology, pull down, affinity chromatography technology, pull down	Siegert JL (2000), Siegert JL (2000), Shao Z (1995), Shao Z (1995), Siegert JL (1999), Shao Z (1997), Shao Z (1997)	7
AR	3	TAF1	9	affinity chromatography technology, two hybrid, pull down	Tavassoli P (2010), Tavassoli P (2010), Tavassoli P (2010)	3
SUMO1	0	MITF	3	affinity chromatography technology	Murakami H (2005)	1
PAX6	3	3211	0	pull down	Mikkola I (2001)	1
PAX6	3	RBM26	3	affinity chromatography technology	Hein MY (2015)	1
NKIRAS2	1	PAX6	3	two hybrid	Wang J (2011)	1
PAX6	3	EN1	1	pull down	Mikkola I (2001)	1
SMAD1	0	AR	3	affinity chromatography technology, affinity chromatography technology, protein complementation assay, imaging technique, affinity chromatography technology	Qiu T (2007), Qiu T (2007), Qiu T (2007), Qiu T (2007), Li Y (2013)	5
PAX6	3	SMARCA4	19	affinity chromatography technology, affinity chromatography technology	Yang Y (2006), Yang Y (2006)	2
CDX2	4	EP300	36	pull down, affinity chromatography technology, affinity chromatography technology	Hussain MA (1999), Hussain MA (1999), Hussain MA (1999)	3
EP300	36	MITF	3	affinity chromatography technology	Price ER (1998)	1
PAX6	3	HIPK2	0	affinity chromatography technology, enzymatic study	Kim EA (2006), Kim EA (2006)	2
APOB	8	SMAD3	1	two hybrid	Wang J (2011)	1
PAX6	3	RBM4	1	affinity chromatography technology	Hein MY (2015)	1
DNMT3L	2	LHX2	0	pull down	Pacaud R (2014)	1
TP73	2	EP300	36	affinity chromatography technology, affinity chromatography technology, biochemical, biochemical, affinity chromatography technology, affinity chromatography technology, pull down, affinity chromatography technology, x-ray crystallography, pull down, enzymatic study, affinity chromatography technology, affinity chromatography technology	Strano S (2005), Uramoto H (2004), Zeng X (2000), Zeng X (2000), Zeng X (2000), Zeng X (2000), Zeng X (2000), Mantovani F (2004), Burge S (2009), Burge S (2009), Costanzo A (2002), Hoffmann A (2008), Kramer D (2015)	13
PAX6	3	CDX2	4	pull down, pull down, affinity chromatography technology, affinity chromatography technology	Hussain MA (1999), Hussain MA (1999), Hussain MA (1999), Hussain MA (1999)	4
PROX1	0	EP300	36	two hybrid, affinity chromatography technology	Chen Q (2002), Chen Q (2002)	2
MAFA	0	PAX6	3	affinity chromatography technology	Scoville DW (2015)	1
PAX6	3	UBE2M	0	affinity chromatography technology	Hein MY (2015)	1
SMAD4	9	SUMO1	0	affinity chromatography technology	Lee PS (2003)	1
TAF1	9	PAX6	3	affinity chromatography technology	Cvekl A (1999)	1
SMAD5	2	PAX6	3	affinity chromatography technology	Grocott T (2007)	1
PAX6	3	RB1	2	pull down	Cvekl A (1999)	1
SMAD3	1	SMAD4	9	affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, pull down, affinity chromatography technology, affinity chromatography technology, pull down, pull down, pull down, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, pull down, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, pull down, pull down, x-ray crystallography, pull down, affinity chromatography technology, pull down, affinity chromatography technology, affinity chromatography technology, two hybrid, two hybrid, pull down, pull down, pull down, two hybrid, two hybrid, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, two hybrid, affinity chromatography technology, pull down, pull down, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, protein complementation assay, affinity chromatography technology, affinity chromatography technology	Seoane J (2004), Moren A (2003), Wu JW (2002), Nakao A (1997), Hanai J (1999), Lebrun JJ (1999), Poncelet AC (2001), Jablonska E (2010), Prunier C (2003), Kato Y (2002), Kaimori A (2010), Tang LY (2011), Tang LY (2011), Dupont S (2009), Dupont S (2009), Pardali K (2000), Kardassis D (2000), Xu L (2003), Fu G (2011), Chen W (2007), Kang JM (2012), Gao S (2009), Li H (2009), Li H (2009), Brown KA (2008), Brown KA (2008), Halder SK (2005), Barrios-Rodiles M (2005), Dai F (2007), Dai F (2007), Chacko BM (2004), Chacko BM (2004), Chacko BM (2004), Stroschein SL (1999), Stroschein SL (1999), Stroschein SL (1999), Wu RY (1997), Wu RY (1997), Wu RY (1997), Wu RY (1997), Tomita M (2004), Colland F (2004), Colland F (2004), Tang Y (2003), Ding L (2009), Fattet L (2013), Wang J (2011), Xue J (2014), Ali A (2013), Gao S (2009), Yamakawa N (2002), Yamakawa N (2002), Wang G (2005), Li X (2015), Zhou F (2014), Yang Y (2015), Yan X (2016), Yan X (2016), Wu Y (2017), Wu Y (2017)	60
PAX6	3	SIX3	3	pull down	Mikkola I (2001)	1
DNMT3L	2	SMAD4	9	pull down	Pacaud R (2014)	1
RB1	2	RBM26	3	affinity chromatography technology	Hein MY (2015)	1
EP300	36	SMAD1	0	affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology	Pearson KL (1999), Nakashima K (1999), Nakashima K (1999), Jeon EJ (2006), Jun JH (2010), Weng Q (2012)	6
PAX6	3	MARCKSL1	0	affinity chromatography technology	Hein MY (2015)	1
SMAD3	1	SMARCA4	19	affinity chromatography technology, affinity chromatography technology	Xi Q (2008), Xi Q (2008)	2
TP73	2	PAX6	3	affinity chromatography technology	Lunardi A (2010)	1
PAX6	3	RAX	0	genetic interference, pull down, affinity chromatography technology	Mikkola I (2001), Mikkola I (2001), Mikkola I (2001)	3
SMAD3	1	SMAD5	2	affinity chromatography technology	Brown KA (2008)	1
PAX6	3	AP5M1	1	affinity chromatography technology	Hein MY (2015)	1
PAX6	3	EPB41L2	2	affinity chromatography technology	Hein MY (2015)	1
PAX6	3	MID1	1	affinity chromatography technology, pull down	Pfirrmann T (2016), Pfirrmann T (2016)	2
RB1	2	TBP	0	pull down	Shao Z (1997)	1
AR	3	TBP	0	pull down	McEwan IJ (1997)	1
PAX6	3	PAX6	3	pull down, affinity chromatography technology	Mikkola I (2001), Mikkola I (2001)	2
TAF1	9	TBP	0	pull down, biochemical, biochemical, affinity chromatography technology, pull down, affinity chromatography technology, affinity chromatography technology, biochemical, affinity chromatography technology, biochemical, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology	Siegert JL (1999), Bellorini M (1997), Ruppert S (1993), OBrien T (1998), Knuesel MT (2009), Hilton TL (2005), Liu X (2008), Demeny MA (2007), Dikstein R (1996), Wieczorek E (1998), Dantonel JC (1997), Klemm RD (1995), Dallas PB (1997), Ogryzko VV (1998), Gupta K (2017)	15
PAX6	3	GMPS	1	affinity chromatography technology	Hein MY (2015)	1
PAX6	3	FYCO1	6	affinity chromatography technology	Hein MY (2015)	1
SOX2	4	PAX6	3	affinity chromatography technology, affinity chromatography technology	Aota S (2003), Aota S (2003)	2
SMAD4	9	PAX6	3	affinity chromatography technology	Grocott T (2007)	1
TBP	0	PAX6	3	affinity chromatography technology, pull down	Cvekl A (1999), Cvekl A (1999)	2
DNMT3L	2	SMAD3	1	pull down	Pacaud R (2014)	1
RB1	2	SMARCA4	19	affinity chromatography technology, biochemical, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, affinity chromatography technology, two hybrid, affinity chromatography technology	Dunaief JL (1994), Reyes JC (1997), Qiu Z (2008), Dasgupta P (2004), Zhang HS (2000), Zhang HS (2000), Napolitano MA (2007), Dunaief JL (2002), Tu Z (2013)	9
SMAD4	9	AR	3	affinity chromatography technology, affinity chromatography technology, pull down, pull down	Kang HY (2002), Kang HY (2002), Kang HY (2002), Kang HY (2002)	4
TP73	2	RB1	2	affinity chromatography technology	Ozaki T (2003)	1
SMAD1	0	HIPK2	0	pull down, affinity chromatography technology, affinity chromatography technology	Harada J (2003), Harada J (2003), Harada J (2003)	3
SMAD1	0	SMAD5	2	two hybrid	Colland F (2004)	1
TP73	2	HIPK2	0	two hybrid	Kim EJ (2002)	1