Cluster composition

Functions

Category	Name	IntersectionWithQuery	PValue	GenesInTerm	GenesInQuery	GenesInTermInQuery	ID
GeneOntologyMolecularFunction	snoRNA binding	WDR3 PRKDC	2.11e-03	34	40	2	GO:0030515
GeneOntologyCellularComponent	DNA-dependent protein kinase-DNA ligase 4 complex	PRKDC XRCC4	7.45e-05	7	40	2	GO:0005958
GeneOntologyCellularComponent	nonhomologous end joining complex	PRKDC XRCC4	1.27e-04	9	40	2	GO:0070419
GeneOntologyCellularComponent	DNA repair complex	PRKDC XRCC4	8.81e-04	23	40	2	GO:1990391
Domain	TPR-like_helical_dom	ADCY10 SRP68 PRKDC SAMD9	1.52e-03	233	40	4	IPR011990
Domain	ARM-type_fold	PRKDC IPO8 CEBPZ PPP4R4	5.82e-03	339	40	4	IPR016024
Domain	RNaseH-like_dom	ZMYM1 ESRP1	9.58e-03	69	40	2	IPR012337
Domain	HEAT_REPEAT	PRKDC PPP4R4	9.85e-03	70	40	2	PS50077
Domain	-	PRKDC IPO8 PPP4R4	1.18e-02	222	40	3	1.25.10.10
Pathway	WP_NONHOMOLOGOUS_END_JOINING	PRKDC XRCC4	1.11e-04	7	33	2	MM15989
Pathway	WP_NONHOMOLOGOUS_END_JOINING	PRKDC XRCC4	2.36e-04	10	33	2	M39469
Pathway	KEGG_MEDICUS_REFERENCE_V_D_J_RECOMBINATION	PRKDC XRCC4	3.46e-04	12	33	2	M47856
Pathway	KEGG_MEDICUS_REFERENCE_NON_HOMOLOGOUS_END_JOINING	PRKDC XRCC4	4.08e-04	13	33	2	M47837
Pathway	KEGG_NON_HOMOLOGOUS_END_JOINING	PRKDC XRCC4	4.08e-04	13	33	2	M7857
Pathway	PID_DNA_PK_PATHWAY	PRKDC XRCC4	6.25e-04	16	33	2	M42
Pubmed	In cellulo phosphorylation of DNA double-strand break repair protein XRCC4 on Ser260 by DNA-PK.	PRKDC XRCC4	1.29e-06	2	40	2	30247612
Pubmed	The XRCC4 gene product is a target for and interacts with the DNA-dependent protein kinase.	PRKDC XRCC4	1.29e-06	2	40	2	9430729
Pubmed	Two-Stage Synapsis of DNA Ends during Non-homologous End Joining.	PRKDC XRCC4	1.29e-06	2	40	2	26990988
Pubmed	In cellulo phosphorylation of XRCC4 Ser320 by DNA-PK induced by DNA damage.	PRKDC XRCC4	1.29e-06	2	40	2	26666690
Pubmed	Association of genetic polymorphisms in PRKDC and XRCC4 with risk of ESCC in a high-incidence region of North China.	PRKDC XRCC4	1.29e-06	2	40	2	26166223
Pubmed	Phosphorylation and regulation of DNA ligase IV stability by DNA-dependent protein kinase.	PRKDC XRCC4	3.87e-06	3	40	2	15194694
Pubmed	Mammalian DNA double-strand break repair protein XRCC4 interacts with DNA ligase IV.	PRKDC XRCC4	3.87e-06	3	40	2	9259561
Pubmed	Kinase-dependent structural role of DNA-PKcs during immunoglobulin class switch recombination.	PRKDC XRCC4	3.87e-06	3	40	2	30072430
Pubmed	Ionizing radiation-induced XRCC4 phosphorylation is mediated through ATM in addition to DNA-PK.	PRKDC XRCC4	3.87e-06	3	40	2	25391321
Pubmed	Defining interactions between DNA-PK and ligase IV/XRCC4.	PRKDC XRCC4	3.87e-06	3	40	2	12509254
Pubmed	Extensive ssDNA end formation at DNA double-strand breaks in non-homologous end-joining deficient cells during the S phase.	PRKDC XRCC4	3.87e-06	3	40	2	17963495
Pubmed	Interaction of the Ku heterodimer with the DNA ligase IV/Xrcc4 complex and its regulation by DNA-PK.	PRKDC XRCC4	3.87e-06	3	40	2	17241822
Pubmed	The STUbL RNF4 regulates protein group SUMOylation by targeting the SUMO conjugation machinery.	SLC25A3 WDR3 CD81 ZMYM1 PRKDC IPO8 NDC80 CEBPZ GNPAT	7.15e-06	1203	40	9	29180619
Pubmed	Ku DNA end-binding protein modulates homologous repair of double-strand breaks in mammalian cells.	PRKDC XRCC4	7.73e-06	4	40	2	11751629
Pubmed	Artemis C-terminal region facilitates V(D)J recombination through its interactions with DNA Ligase IV and DNA-PKcs.	PRKDC XRCC4	7.73e-06	4	40	2	22529269
Pubmed	X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology.	PRKDC XRCC4	7.73e-06	4	40	2	34056803
Pubmed	Functional redundancy between the XLF and DNA-PKcs DNA repair factors in V(D)J recombination and nonhomologous DNA end joining.	PRKDC XRCC4	1.29e-05	5	40	2	23345432
Pubmed	DNA damage-induced phosphorylation of CtIP at a conserved ATM/ATR site T855 promotes lymphomagenesis in mice.	PRKDC XRCC4	1.29e-05	5	40	2	34521752
Pubmed	Defective embryonic neurogenesis in Ku-deficient but not DNA-dependent protein kinase catalytic subunit-deficient mice.	PRKDC XRCC4	1.29e-05	5	40	2	10716994
Pubmed	DNA-dependent protein kinase and XRCC4-DNA ligase IV mobilization in the cell in response to DNA double strand breaks.	PRKDC XRCC4	1.29e-05	5	40	2	15520013
Pubmed	Synthetic lethality between murine DNA repair factors XLF and DNA-PKcs is rescued by inactivation of Ku70.	PRKDC XRCC4	1.29e-05	5	40	2	28759779
Pubmed	Breast cancer risk associated with genotypic polymorphism of the nonhomologous end-joining genes: a multigenic study on cancer susceptibility.	PRKDC XRCC4	1.29e-05	5	40	2	12750264
Pubmed	Coordinated assembly of Ku and p460 subunits of the DNA-dependent protein kinase on DNA ends is necessary for XRCC4-ligase IV recruitment.	PRKDC XRCC4	1.29e-05	5	40	2	12547193
Pubmed	Repression of rRNA transcription by PARIS contributes to Parkinson's disease.	SLC25A3 WDR3 SRP68 PRKDC CEBPZ	1.48e-05	272	40	5	25315684
Pubmed	Cryo-EM of NHEJ supercomplexes provides insights into DNA repair.	PRKDC XRCC4	1.93e-05	6	40	2	34352203
Pubmed	RAD52 polymorphisms contribute to the development of papillary thyroid cancer susceptibility in Middle Eastern population.	PRKDC XRCC4	2.70e-05	7	40	2	19092295
Pubmed	Ku is a 5'-dRP/AP lyase that excises nucleotide damage near broken ends.	PRKDC XRCC4	2.70e-05	7	40	2	20383123
Pubmed	Differential phosphorylation of DNA-PKcs regulates the interplay between end-processing and end-ligation during nonhomologous end-joining.	PRKDC XRCC4	2.70e-05	7	40	2	25818648
Pubmed	XLS (c9orf142) is a new component of mammalian DNA double-stranded break repair.	PRKDC XRCC4	3.60e-05	8	40	2	25941166
Pubmed	Meta-analysis identifies loci affecting levels of the potential osteoarthritis biomarkers sCOMP and uCTX-II with genome wide significance.	CSMD1 XRCC4	4.62e-05	9	40	2	25057126
Pubmed	MRI Is a DNA Damage Response Adaptor during Classical Non-homologous End Joining.	PRKDC XRCC4	8.45e-05	12	40	2	30017584
Pubmed	Identification and functional characterization of transcriptional activators in human cells.	WDR3 ZMYM1 PRKDC FSCN1 GNPAT	9.06e-05	398	40	5	35016035
Pubmed	Phosphoproteome analysis of the human mitotic spindle.	WDR3 PRKDC NDC80 CEBPZ	9.96e-05	210	40	4	16565220
Pubmed	Functional analysis of candidate genes from genome-wide association studies of hearing.	CSMD1 SLC16A6	1.73e-04	17	40	2	31927188
Pubmed	SARS-CoV-2 nucleocapsid protein binds host mRNAs and attenuates stress granules to impair host stress response.	SLC25A3 WDR3 ZMYM1 PRKDC IPO8	1.83e-04	463	40	5	34901782
Pubmed	Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV.	TBC1D8 CD81 PRKDC ELOVL6 SLC16A6 FSCN1 GNPAT	1.86e-04	1061	40	7	33845483
Pubmed	Discovery of a Human Testis-specific Protein Complex TEX101-DPEP3 and Selection of Its Disrupting Antibodies.	SLC25A3 CD81 PDE6A PKD1L1	1.91e-04	249	40	4	30097533
Pubmed	The E3 ubiquitin ligase HECTD1 contributes to cell proliferation through an effect on mitosis.	WDR3 SRP68 PRKDC XRCC4 IPO8 CEBPZ	2.16e-04	759	40	6	35915203
Pubmed	CHFR regulates chemoresistance in triple-negative breast cancer through destabilizing ZEB1.	SLC25A3 PRKDC IPO8	2.17e-04	101	40	3	34462429
Pubmed	Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity.	CD81 PRKDC PSD XRCC4	2.36e-04	263	40	4	19773279
Pubmed	Stasimon/Tmem41b localizes to mitochondria-associated ER membranes and is essential for mouse embryonic development.	SLC25A3 PRKDC IPO8	3.02e-04	113	40	3	30352685
Pubmed	ATP-citrate lyase deficiency in the mouse.	ELOVL6 G6PC1	3.21e-04	23	40	2	14662765
Pubmed	Xrcc4 physically links DNA end processing by polynucleotide kinase to DNA ligation by DNA ligase IV.	PRKDC XRCC4	3.80e-04	25	40	2	15385968
Pubmed	Hepatitis B Virus HBx Protein Mediates the Degradation of Host Restriction Factors through the Cullin 4 DDB1 E3 Ubiquitin Ligase Complex.	SLC25A3 KNDC1 PDE6A PPP4R4	4.08e-04	304	40	4	32235678
Pubmed	Gamma-radiation sensitivity and polymorphisms in RAD51L1 modulate glioma risk.	PRKDC XRCC4	4.45e-04	27	40	2	20610542
Pubmed	Role of the E3 ubiquitin-ligase Hakai in intestinal inflammation and cancer bowel disease.	PRKDC FSCN1	4.45e-04	27	40	2	36266428
Pubmed	Targeting USP10 induces degradation of oncogenic ANLN in esophageal squamous cell carcinoma.	SLC25A3 WDR3 SRP68 PRKDC SAMD9 FSCN1 CEBPZ	5.19e-04	1257	40	7	36526897
Pubmed	UBR-box containing protein, UBR5, is over-expressed in human lung adenocarcinoma and is a potential therapeutic target.	SLC25A3 PRKDC	5.50e-04	30	40	2	32867711
Pubmed	Mechanistic rationale for inhibition of poly(ADP-ribose) polymerase in ETS gene fusion-positive prostate cancer.	PRKDC XRCC4	5.50e-04	30	40	2	21575865
Pubmed	Polymorphisms in DNA repair genes and risk of non-Hodgkin lymphoma in a pooled analysis of three studies.	PRKDC XRCC4	5.87e-04	31	40	2	20813000
Pubmed	CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality.	SLC25A3 WDR3 SRP68 PRKDC CEBPZ	6.23e-04	605	40	5	28977666
Pubmed	Common genetic variants in candidate genes and risk of familial lymphoid malignancies.	CD81 PRKDC XRCC4	6.26e-04	145	40	3	19573080
Pubmed	TTF-1/NKX2-1 binds to DDB1 and confers replication stress resistance to lung adenocarcinomas.	SLC25A3 PRKDC XRCC4	7.18e-04	152	40	3	28192407
Pubmed	The Hsp70-Hsp90 co-chaperone Hop/Stip1 shifts the proteostatic balance from folding towards degradation.	SLC25A3 WDR3 SRP68 PRKDC IPO8	7.91e-04	638	40	5	33239621
Pubmed	Suppression of ACE2 SUMOylation protects against SARS-CoV-2 infection through TOLLIP-mediated selective autophagy.	SLC25A3 WDR3 PRKDC IPO8 FSCN1	8.08e-04	641	40	5	36057605
Pubmed	Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription.	WDR3 SRP68 PRKDC FSCN1 CEBPZ	8.78e-04	653	40	5	22586326
Pubmed	HIV-1 Nef and Vpu are functionally redundant broad-spectrum modulators of cell surface receptors, including tetraspanins.	CD81 CD164	9.79e-04	40	40	2	25275127
Pubmed	The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking.	SLC25A3 PRKDC GNPAT	1.11e-03	177	40	3	26485645
Coexpression	GSE17721_CTRL_VS_POLYIC_1H_BMDC_DN	TBC1D8 SLC16A6 FSCN1 CEBPZ GNPAT	1.27e-05	199	40	5	M3709
Coexpression	FARMER_BREAST_CANCER_CLUSTER_2	PRKDC NDC80 ESRP1	1.74e-05	33	40	3	M17333
Coexpression	RIEGE_DELTANP63_DIRECT_TARGETS_UP	XDH FSCN1 PPP4R4 ESRP1	5.80e-05	138	40	4	M41739
Coexpression	WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP	ELOVL6 GPR160 CD164 ESRP1	6.14e-05	140	40	4	M2435
Coexpression	WILCOX_RESPONSE_TO_PROGESTERONE_UP	SAMD9 ELOVL6 XRCC4 NDC80	8.66e-05	153	40	4	M18058
Coexpression	RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP	ZNF131 SAMD9 ELOVL6 XRCC4 NDC80 CEBPZ NXPH4	9.79e-05	721	40	7	M10237
ToppCell	Thalamus-Endothelial-ENDOTHELIAL_STALK-Flt1_1\|Thalamus / BrainAtlas - Mouse McCarroll V32	XDH SLCO1C1 NDC80 G6PC1	2.78e-06	109	40	4	4e4a884b8979f4ff8b232c1581ea78884dda29ed
Disease	glucose metabolism decline measurement, cingulate cortex measurement	TBC1D8 VPS53	6.09e-05	9	39	2	EFO_0007738, EFO_0009392
Disease	Situs ambiguous	MMP21 PKD1L1	6.09e-05	9	39	2	C1167664
Disease	Situs Inversus	MMP21 PKD1L1	9.29e-05	11	39	2	C0037221
Disease	visceral heterotaxy (is_implicated_in)	MMP21 PKD1L1	1.11e-04	12	39	2	DOID:0050545 (is_implicated_in)
Disease	Situs ambiguus	MMP21 PKD1L1	1.77e-04	15	39	2	C0266642
Disease	amygdala volume change measurement	CSMD1 PKD1L1	2.02e-04	16	39	2	EFO_0021490
Disease	Alpha ketoglutarate measurement	SRP68 SAMD9	2.02e-04	16	39	2	EFO_0010457
Disease	triacylglycerol 48:2 measurement	CSMD1 VPS53	3.87e-04	22	39	2	EFO_0010405
Disease	airway responsiveness measurement	CSMD1 IPO8	4.61e-04	24	39	2	EFO_0006897
Disease	triacylglycerol 50:2 measurement	CSMD1 VPS53	7.73e-04	31	39	2	EFO_0010409
Disease	triacylglycerol 50:3 measurement	CSMD1 VPS53	1.22e-03	39	39	2	EFO_0010410
Disease	obsessive-compulsive disorder, attention deficit hyperactivity disorder, Tourette syndrome, unipolar depression, bipolar disorder, autism spectrum disorder, schizophrenia, anorexia nervosa	TMCO5A CSMD1 NXPH4	2.34e-03	200	39	3	EFO_0003756, EFO_0003761, EFO_0003888, EFO_0004242, EFO_0004895, MONDO_0004985, MONDO_0005090, MONDO_0005351

Protein segments in the cluster

Peptide	Gene	Start	Entry
SKKIFCCLFFITLFF	TMCO5A	221	Q8N6Q1
FTYKSEVFFQCKSPF	CSMD1	3171	Q96PZ7
IAVQLFKGKFFYCTD	CACNA1E	1306	Q15878
HIFSKAFFYFVCLDI	ADCY10	1371	Q96PN6
CTKCIKYLLFVFNFV	CD81	6	P60033
ECFYSFFDLRKEFKK	ESRP1	131	Q6NXG1
VICIFVSFLSFDYKL	NXPH4	276	O95158
CKFGFYEVFKVLYSN	SLC25A3	136	Q00325
VQAVIFFLYKFCKSK	CD164	176	Q04900
KLIYFFKESLVFAFD	MMP21	461	Q8N119
IEKVCFVVFSFFYII	OR4S2	21	Q8NH73
FIDFVCTFVYKEFSR	PDE6A	776	P16499
VGCFKTFESIYLKTF	CYB5RL	216	Q6IPT4
ILAFICFIFAFKGKY	GPRC6A	761	Q5T6X5
SFKCQKLFYFFTVIL	GPR160	131	Q9UJ42
KKSFLFSALYAAFIF	ELOVL6	31	Q9H5J4
FFFEFCDYNKVAIKV	FSCN1	451	Q16658
FCAFTLSKVFKQIFS	GNPAT	121	O15228
LKKYFLITFFLFSFA	G6PC1	206	P35575
EYIFALKDLTFATFC	KNDC1	921	Q76NI1
LKKFTEYFTSVLCFT	SDK2	861	Q58EX2
FRKLFYCKFTEYLED	PKD1L1	1921	Q8TDX9
LITVYFCFFRTCVKK	CEBPZ	461	Q03701
NVTKEYFEFSEFFLK	IPO8	281	O15397
FSILKEKSFICYALF	SLC16A6	286	O15403
EFIIEIFSKSFFCKY	PPP4R4	591	Q6NUP7
IFSKSFFCKYFFLPA	PPP4R4	596	Q6NUP7
FSKLVAGEYLKFFVF	PSD	586	A5PKW4
KFSLKKSFDFFDEYF	SAMD9	1261	Q5K651
LKTLVFKAYRCFFIA	SRP68	456	Q9UHB9
ATFLSVFYCKKITTF	TAS2R5	96	Q9NYW4
LFQDFKDCDFFSKTY	UHRF1BP1L	626	A0JNW5
CFYSFFLGKELKLVV	TBC1D8	186	O95759
ELKVFLCALSFVYFA	SLCO1C1	41	Q9NYB5
ESCYFFFEKNLKDVS	XRCC4	91	Q13426
DFRCTLTLSFFFKFY	XDH	506	P47989
KYFTQFCVKFANSFI	VPS53	661	Q5VIR6
YSCFALFVKFGKEVA	PRKDC	701	P78527
VLAACSKFFYKFFQE	ZNF131	51	P52739
TLVSKFEFVFCLKFL	ZMYM1	851	Q5SVZ6
FEFVFCLKFLYRVLS	ZMYM1	856	Q5SVZ6
CTVKIFYVDTLKFFL	WDR3	571	Q9UNX4
SVKDFLKIFTFLYGF	NDC80	121	O14777