Cluster composition

Functions

Category	Name	IntersectionWithQuery	PValue	GenesInTerm	GenesInQuery	GenesInTermInQuery	ID
GeneOntologyMolecularFunction	mitochondrial promoter sequence-specific DNA binding	LONP1 POLRMT	4.98e-05	3	82	2	GO:0001018
GeneOntologyMolecularFunction	semaphorin receptor binding	SEMA3A SEMA6D SEMA6A	1.11e-04	23	82	3	GO:0030215
GeneOntologyMolecularFunction	chemorepellent activity	SEMA3A SEMA6D SEMA6A	2.26e-04	29	82	3	GO:0045499
Domain	SPIN/Ssty	SPIN2A SPIN2B SPIN3	7.81e-07	5	81	3	IPR003671
Domain	Spin-Ssty	SPIN2A SPIN2B SPIN3	7.81e-07	5	81	3	PF02513
Domain	SPIN-2	SPIN2A SPIN2B	1.86e-05	2	81	2	IPR029564
Domain	Semaphorin	SEMA3A SEMA6D SEMA6A	8.49e-05	20	81	3	IPR027231
Domain	PPR	DENND4A DENND4C	1.11e-04	4	81	2	PF01535
Domain	Pentatricopeptide_repeat	DENND4A POLRMT DENND4C	1.31e-04	23	81	3	IPR002885
Domain	DMAP_binding	DIP2A DIP2C	1.84e-04	5	81	2	PF06464
Domain	DMAP1-bd	DIP2A DIP2C	2.76e-04	6	81	2	IPR010506
Domain	DMAP_binding	DIP2A DIP2C	2.76e-04	6	81	2	SM01137
Domain	Semap_dom	SEMA3A SEMA6D SEMA6A	3.24e-04	31	81	3	IPR001627
Domain	SEMA	SEMA3A SEMA6D SEMA6A	3.24e-04	31	81	3	PS51004
Domain	Sema	SEMA3A SEMA6D SEMA6A	3.24e-04	31	81	3	SM00630
Domain	Sema	SEMA3A SEMA6D SEMA6A	3.24e-04	31	81	3	PF01403
Domain	Sc_DH/Rdtase_CS	RDH16 HSD11B1 DHRS7B	4.65e-04	35	81	3	IPR020904
Domain	PPR	DENND4A DENND4C	5.11e-04	8	81	2	PS51375
Domain	-	RDH16 ACLY AHCYL2 HSD11B1 DHRS7B	8.41e-04	169	81	5	3.40.50.720
Domain	PSI	SEMA3A SEMA6D SEMA6A	9.16e-04	44	81	3	IPR016201
Domain	NAD(P)-bd_dom	RDH16 ACLY AHCYL2 HSD11B1 DHRS7B	9.34e-04	173	81	5	IPR016040
Domain	PSI	SEMA3A SEMA6D SEMA6A	1.04e-03	46	81	3	SM00423
Domain	ADH_SHORT	RDH16 HSD11B1 DHRS7B	1.57e-03	53	81	3	PS00061
Domain	adh_short	RDH16 HSD11B1 DHRS7B	1.75e-03	55	81	3	PF00106
Domain	SDR_fam	RDH16 HSD11B1 DHRS7B	1.85e-03	56	81	3	IPR002347
Domain	PI3/4_kinase_CS	MTOR PI4KA	1.88e-03	15	81	2	IPR018936
Domain	DENN	DENND4A DENND4C	2.14e-03	16	81	2	SM00799
Domain	-	MTOR PI4KA	2.14e-03	16	81	2	1.10.1070.11
Domain	DENN	DENND4A DENND4C	2.14e-03	16	81	2	PF02141
Domain	dDENN	DENND4A DENND4C	2.14e-03	16	81	2	PF03455
Domain	PI3Kc	MTOR PI4KA	2.14e-03	16	81	2	SM00146
Domain	UDENN	DENND4A DENND4C	2.14e-03	16	81	2	PS50946
Domain	DDENN	DENND4A DENND4C	2.14e-03	16	81	2	PS50947
Domain	dDENN	DENND4A DENND4C	2.14e-03	16	81	2	SM00801
Domain	dDENN_dom	DENND4A DENND4C	2.14e-03	16	81	2	IPR005112
Domain	uDENN_dom	DENND4A DENND4C	2.14e-03	16	81	2	IPR005113
Domain	DENN	DENND4A DENND4C	2.14e-03	16	81	2	PS50211
Domain	DENN_dom	DENND4A DENND4C	2.14e-03	16	81	2	IPR001194
Domain	PI3_PI4_kinase	MTOR PI4KA	2.72e-03	18	81	2	PF00454
Domain	PI3_4_KINASE_1	MTOR PI4KA	2.72e-03	18	81	2	PS00915
Domain	PI3_4_KINASE_2	MTOR PI4KA	2.72e-03	18	81	2	PS00916
Domain	-	ACLY MCCC1	2.72e-03	18	81	2	3.30.470.20
Domain	PI3/4_kinase_cat_dom	MTOR PI4KA	2.72e-03	18	81	2	IPR000403
Domain	PI3_4_KINASE_3	MTOR PI4KA	2.72e-03	18	81	2	PS50290
Pubmed	Repression of rRNA transcription by PARIS contributes to Parkinson's disease.	PRPF31 ACLY USP9X RPS4Y1 POLD1 POLRMT MYO1B MCCC1 ATP5F1B	1.71e-08	272	82	9	25315684
Pubmed	Gain of Additional BIRC3 Protein Functions through 3'-UTR-Mediated Protein Complex Formation.	PRPF31 LONP1 XRN2 DENND4A MTOR ACLY USP9X CFL1 POLD1 PI4KA POLRMT CPSF1 MYO1B LAP3 PCNA ATP5F1B MYBPC1	3.05e-08	1425	82	17	30948266
Pubmed	The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation.	PRPF31 XRN2 AGO1 ACLY USP9X RPS4Y1 CFL1 POLRMT DYNLRB1 CHD9 AHCYL2 YES1 ENO3 PCNA ATP5F1B	7.31e-08	1153	82	15	29845934
Pubmed	Identifying biological pathways that underlie primordial short stature using network analysis.	PRPF31 LONP1 XRN2 TIAL1 ACLY USP9X CFL1 PI4KA TJP2 CPSF1 MYO1B YES1 PCNA ATP5F1B	1.15e-07	1024	82	14	24711643
Pubmed	KCTD13-mediated ubiquitination and degradation of GluN1 regulates excitatory synaptic transmission and seizure susceptibility.	PITPNM2 DIP2A LONP1 AGO1 CADPS ACLY USP9X RPS4Y1 CFL1 PI4KA TJP2 MTMR1 PIP4K2C RAPGEF2 CNTN1 ATP5F1B	1.99e-07	1431	82	16	37142655
Pubmed	A transcriptional coregulator, SPIN·DOC, attenuates the coactivator activity of Spindlin1.	SPIN2A SPIN2B SPIN3	2.51e-07	6	82	3	29061846
Pubmed	A Human Tyrosine Phosphatase Interactome Mapped by Proteomic Profiling.	TMTC3 PTPRK MTOR ACLY POLD1 POLRMT TJP2 MTMR1 OSGEP TMX3 PREPL USP47 ATP5F1B	4.50e-07	974	82	13	28675297
Pubmed	USP11 mediates repair of DNA-protein cross-links by deubiquitinating SPRTN metalloprotease.	TMTC3 PTPRK RPS4Y1 CFL1 MYO1B OSGEP ENO3 PCNA ATP5F1B DHRS7B	8.87e-07	565	82	10	33567341
Pubmed	C9orf72 protein quality control by UBR5-mediated heterotypic ubiquitin chains.	XRN2 TIAL1 ACLY USP9X CFL1 POLD1 CPSF1 DYNLRB1 MYO1B OSGEP TMX3 PCNA ATP5F1B DHRS7B	1.34e-06	1257	82	14	37317656
Pubmed	Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions.	LONP1 XRN2 ACLY CFL1 TJP2 CPSF1 AHCYL2 MCCC1 PREPL PCNA DHRS7B SPIN3	1.58e-06	916	82	12	32203420
Pubmed	RUFY1 binds Arl8b and mediates endosome-to-TGN CI-M6PR retrieval for cargo sorting to lysosomes.	ACLY USP9X RPS4Y1 CFL1 DYNLRB1 MYO1B MCCC1 ATP5F1B	1.59e-06	344	82	8	36282215
Pubmed	Hdac4 Interactions in Huntington's Disease Viewed Through the Prism of Multiomics.	PITPNM2 AGO1 CADPS USP9X PI4KA ITGB1BP1 MTMR1 RAPGEF2 ENO3	1.86e-06	475	82	9	31040226
Pubmed	Network organization of the huntingtin proteomic interactome in mammalian brain.	MTOR ACLY RPS4Y1 HCN1 MTMR1 MCCC1 ENO3 CARD14 CNTN1 ATP5F1B	2.07e-06	621	82	10	22794259
Pubmed	BAP1 regulation of the key adaptor protein NCoR1 is critical for γ-globin gene repression.	PRPF31 LONP1 XRN2 ACLY RPS4Y1 CFL1 POLD1 TJP2 ZCCHC17 MCCC1 PIP4K2C LAP3 PCNA ATP5F1B	2.33e-06	1318	82	14	30463901
Pubmed	FBXO22 promotes leukemogenesis by targeting BACH1 in MLL-rearranged acute myeloid leukemia.	PRPF31 DIP2A TIAL1 USP9X POLD1 POLRMT TJP2 CPSF1 CHD9	2.69e-06	497	82	9	36774506
Pubmed	Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function.	PRPF31 LONP1 XRN2 ACLY CFL1 POLD1 PI4KA POLRMT CPSF1 MYO1B MCCC1 PIP4K2C PCNA ATP5F1B	3.15e-06	1353	82	14	29467282
Pubmed	Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription.	LONP1 XRN2 MTOR ACLY USP9X POLRMT TJP2 CPSF1 MYO1B USP47	3.23e-06	653	82	10	22586326
Pubmed	Defining the membrane proteome of NK cells.	LONP1 XRN2 MTOR ACLY USP9X RPS4Y1 CFL1 POLD1 PI4KA DYNLRB1 HSD11B1 ATP5F1B DHRS7B	3.36e-06	1168	82	13	19946888
Pubmed	WWP2-WWP1 ubiquitin ligase complex coordinated by PPM1G maintains the balance between cellular p73 and ΔNp73 levels.	XRN2 USP9X CFL1 PCNA DHRS7B	3.50e-06	97	82	5	25071155
Pubmed	TrkB-dependent EphrinA reverse signaling regulates callosal axon fasciculate growth downstream of Neurod2/6.	SEMA3A SEMA6D SEMA6A CNTN1	4.74e-06	47	82	4	35462405
Pubmed	Host E3 ligase HUWE1 attenuates the proapoptotic activity of the MERS-CoV accessory protein ORF3 by promoting its ubiquitin-dependent degradation.	LONP1 TIAL1 USP9X POLD1 CPSF1 OSGEP ALDH6A1 LAP3 DHRS7B	4.81e-06	534	82	9	35032548
Pubmed	A Single Adaptable Cochaperone-Scaffold Complex Delivers Nascent Iron-Sulfur Clusters to Mammalian Respiratory Chain Complexes I-III.	DENND4A TMTC3 TIAL1 POLD1 CPSF1 SEMA6A TMX3 DENND4C PCNA DHRS7B	4.98e-06	686	82	10	28380382
Pubmed	The human cytoplasmic dynein interactome reveals novel activators of motility.	LONP1 AGO1 HGS TJP2 DYNLRB1 ZCCHC17 MCCC1 OSGEP YES1 PCNA USP47	5.20e-06	853	82	11	28718761
Pubmed	Identification of new ciliary signaling pathways in the brain and insights into neurological disorders.	PI4KA HCN1 HGS MTMR1 AHCYL2 TMX3 YES1 ATP5F1B	5.30e-06	405	82	8	38187761
Pubmed	Cloning, genomic organization and expression pattern of a novel Drosophila gene, the disco-interacting protein 2 (dip2), and its murine homolog.	DIP2A DIP2C	5.49e-06	2	82	2	12137943
Pubmed	Deubiquitinase USP9X loss sensitizes renal cancer cells to mTOR inhibition.	MTOR USP9X	5.49e-06	2	82	2	37260183
Pubmed	mTORC1 is a critical mediator of oncogenic Semaphorin3A signaling.	SEMA3A MTOR	5.49e-06	2	82	2	27246732
Pubmed	Cloning and expression of a novel murine semaphorin with structural similarity to insect semaphorin I.	SEMA3A SEMA6A	5.49e-06	2	82	2	9204478
Pubmed	Functional cloning of SPIN-2, a nuclear anti-apoptotic protein with roles in cell cycle progression.	SPIN2A SPIN2B	5.49e-06	2	82	2	12145692
Pubmed	mTOR regulates the nucleoplasmic diffusion of Xrn2 under conditions of heat stress.	XRN2 MTOR	5.49e-06	2	82	2	25128458
Pubmed	A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning.	PITPNM2 PRPF31 TIAL1 MTOR USP9X POLD1 ITGB1BP1 TJP2 AHCYL2 RAPGEF2 DENND4C USP47	5.69e-06	1038	82	12	26673895
Pubmed	KAP1 facilitates reinstatement of heterochromatin after DNA replication.	PRPF31 XRN2 TIAL1 MTOR POLD1 POLRMT OSGEP YES1 LAP3 PCNA	6.25e-06	704	82	10	29955894
Pubmed	BioID-based intact cell interactome of the Kv1.3 potassium channel identifies a Kv1.3-STAT3-p53 cellular signaling pathway.	SH3RF1 ACLY USP9X CFL1 HGS MTMR1 MYO1B XPNPEP1 DENND4C ATP5F1B	6.56e-06	708	82	10	39231216
Pubmed	Optic chiasm presentation of Semaphorin6D in the context of Plexin-A1 and Nr-CAM promotes retinal axon midline crossing.	SEMA3A SEMA6D SEMA6A	6.92e-06	16	82	3	22632726
Pubmed	Irisin Mediates Effects on Bone and Fat via αV Integrin Receptors.	SEMA3A LONP1 TMTC3 PTPRK ACLY USP9X RPS4Y1 CFL1 CPSF1 MCCC1 PIP4K2C PCNA ATP5F1B DHRS7B	7.01e-06	1451	82	14	30550785
Pubmed	Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15.	PRPF31 XRN2 ACLY CFL1 SPIN2A TJP2 ALDH6A1 PCNA ATP5F1B SPIN3	7.07e-06	714	82	10	28302793
Pubmed	A high-throughput approach for measuring temporal changes in the interactome.	MTOR ACLY USP9X CFL1 POLD1 HGS TJP2 DYNLRB1 XPNPEP1 OSGEP LAP3 PCNA USP47 ATP5F1B	7.23e-06	1455	82	14	22863883
Pubmed	Interactome of the Autoimmune Risk Protein ANKRD55.	ACLY USP9X CFL1 PI4KA PCNA ATP5F1B	7.49e-06	197	82	6	31620119
Pubmed	Variability in Streptavidin-Sepharose Matrix Quality Can Significantly Affect Proximity-Dependent Biotinylation (BioID) Data.	PRPF31 LONP1 POLRMT TMX3 ALDH6A1 PREPL ATP5F1B DHRS7B	9.37e-06	438	82	8	32628020
Pubmed	Chr21 protein-protein interactions: enrichment in proteins involved in intellectual disability, autism, and late-onset Alzheimer's disease.	HDAC9 DIP2A XRN2 PTPRK CADPS USP9X HCN1 ZBTB4 CHD9 RAPGEF2 PREPL USP47 ATP5F1B	9.40e-06	1285	82	13	35914814
Pubmed	Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions.	LONP1 DENND4A SH3RF1 USP9X HGS TJP2 RAPGEF2 DENND4C	1.07e-05	446	82	8	24255178
Pubmed	Progesterone induced Warburg effect in HEK293 cells is associated with post-translational modifications and proteasomal degradation of progesterone receptor membrane component 1.	PTPRK MTOR USP9X PI4KA	1.11e-05	58	82	4	31067491
Pubmed	Immunoaffinity profiling of tyrosine phosphorylation in cancer cells.	TIAL1 ACLY USP9X CFL1 HGS TJP2 YES1	1.27e-05	327	82	7	15592455
Pubmed	Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease-relevant pathologies.	PITPNM2 LONP1 CADPS USP9X RPS4Y1 PI4KA HCN1 TJP2 AHCYL2 MCCC1 ALDH6A1 ATP5F1B	1.44e-05	1139	82	12	36417873
Pubmed	Ubiquitin-Activated Interaction Traps (UBAITs) identify E3 ligase binding partners.	USP9X POLD1 HGS PCNA	1.44e-05	62	82	4	26508657
Pubmed	Interaction of LATS1 with SMAC links the MST2/Hippo pathway with apoptosis in an IAP-dependent manner.	PRPF31 CPSF1 MYO1B TMX3 ENO3 SPIN3	1.48e-05	222	82	6	35941108
Pubmed	Tumor suppressor BAP1 nuclear import is governed by transportin-1.	PRPF31 ACLY USP9X CFL1 POLD1 MTMR1 DYNLRB1 MYO1B PREPL LAP3 PCNA ATP5F1B	1.57e-05	1149	82	12	35446349
Pubmed	Molecular cloning, structural analysis, and expression of a human IRLB, MYC promoter-binding protein: new DENN domain-containing protein family emerges.	DENND4A DENND4C	1.64e-05	3	82	2	12906859
Pubmed	Control of the ATP synthase beta subunit expression by RNA-binding proteins TIA-1, TIAR, and HuR.	TIAL1 ATP5F1B	1.64e-05	3	82	2	16890199
Pubmed	Shear stress-regulated miR-27b controls pericyte recruitment by repressing SEMA6A and SEMA6D.	SEMA6D SEMA6A	1.64e-05	3	82	2	28453731
Pubmed	ATM protein physically and functionally interacts with proliferating cell nuclear antigen to regulate DNA synthesis.	MTOR PCNA	1.64e-05	3	82	2	22362778
Pubmed	Semaphorin 3A suppresses VEGF-mediated angiogenesis yet acts as a vascular permeability factor.	SEMA3A YES1	1.64e-05	3	82	2	18180379
Pubmed	CGG-repeat expansion in the DIP2B gene is associated with the fragile site FRA12A on chromosome 12q13.1.	DIP2A DIP2C	1.64e-05	3	82	2	17236128
Pubmed	mTORC1/C2 and pan-HDAC inhibitors synergistically impair breast cancer growth by convergent AKT and polysome inhibiting mechanisms.	HDAC9 MTOR	1.64e-05	3	82	2	24562770
Pubmed	Proliferating cell nuclear antigen (PCNA) may function as a double homotrimer complex in the mammalian cell.	POLD1 PCNA	1.64e-05	3	82	2	15805117
Pubmed	A protein interaction landscape of breast cancer.	LONP1 XRN2 USP9X PI4KA HGS POLRMT MYO1B PIP4K2C DHRS7B	1.89e-05	634	82	9	34591612
Pubmed	UBE2O promotes lipid metabolic reprogramming and liver cancer progression by mediating HADHA ubiquitination.	PRPF31 AGO1 ACLY RPS4Y1 CFL1 MYO1B ZCCHC17 PIP4K2C	2.13e-05	491	82	8	36273042
Pubmed	SARS-CoV-2 Nsp6 damages Drosophila heart and mouse cardiomyocytes through MGA/MAX complex-mediated increased glycolysis.	PRPF31 TMTC3 MTOR ACLY USP9X CFL1 TMX3 PCNA ATP5F1B	2.49e-05	657	82	9	36180527
Pubmed	A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape.	LONP1 XRN2 MTOR POLD1 POLRMT TJP2 DYNLRB1 MYO1B MCCC1 TMX3 YES1 PCNA ATP5F1B	3.10e-05	1440	82	13	30833792
Pubmed	Plexin-A4 negatively regulates T lymphocyte responses.	SEMA3A SEMA6A	3.28e-05	4	82	2	18209113
Pubmed	The human homologue of fission Yeast cdc27, p66, is a component of active human DNA polymerase delta.	POLD1 PCNA	3.28e-05	4	82	2	11328591
Pubmed	Dynamic DNA-bound PCNA complexes co-ordinate Okazaki fragment synthesis, processing and ligation.	POLD1 PCNA	3.28e-05	4	82	2	33157085
Pubmed	Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis.	LONP1 ACLY CFL1 HGS MCCC1 TMX3 RAB26 LAP3 NEK11 ATP5F1B	3.45e-05	859	82	10	31536960
Pubmed	A protein interaction network for the large conductance Ca(2+)-activated K(+) channel in the mouse cochlea.	CFL1 ALDH6A1 ENO3 PCNA ATP5F1B	3.63e-05	157	82	5	19423573
Pubmed	Histone methyltransferase DOT1L coordinates AR and MYC stability in prostate cancer.	XRN2 RPS4Y1 POLD1 MYO1B YES1 ATP5F1B	3.91e-05	264	82	6	32814769
Pubmed	Expression of Robo/Slit and Semaphorin/Plexin/Neuropilin family members in the developing hypothalamic paraventricular and supraoptic nuclei.	SEMA3A SEMA6D SEMA6A	3.97e-05	28	82	3	18617019
Pubmed	The Deubiquitinating Enzyme USP48 Interacts with the Retinal Degeneration-Associated Proteins UNC119a and ARL3.	TIAL1 CADPS ACLY RPS4Y1 CFL1 MYO1B ENO3 ATP5F1B	4.87e-05	552	82	8	36293380
Pubmed	Upregulation of TIPE1 in tubular epithelial cell aggravates diabetic nephropathy by disrupting PHB2 mediated mitophagy.	CFL1 PIP4K2C ATP5F1B	4.90e-05	30	82	3	35152003
Pubmed	SPATA2 Links CYLD to LUBAC, Activates CYLD, and Controls LUBAC Signaling.	PRPF31 RPS4Y1 CFL1 MYO1B ENO3 PCNA ATP5F1B SPIN3	5.26e-05	558	82	8	27591049
Pubmed	USP36 promotes tumorigenesis and drug sensitivity of glioblastoma by deubiquitinating and stabilizing ALKBH5.	USP9X USP47	5.47e-05	5	82	2	36239338
Pubmed	mTORC2 Assembly Is Regulated by USP9X-Mediated Deubiquitination of RICTOR.	MTOR USP9X	5.47e-05	5	82	2	33378666
Pubmed	Semaphorins guide the entry of dendritic cells into the lymphatics by activating myosin II.	SEMA3A SEMA6D	5.47e-05	5	82	2	20512151
Pubmed	Control of complex formation of DNA polymerase alpha-primase and cell-free DNA replication by the C-terminal amino acids of the largest subunit p180.	POLD1 PCNA	5.47e-05	5	82	2	12220650
Pubmed	The post-translational modifications of proliferating cell nuclear antigen: acetylation, not phosphorylation, plays an important role in the regulation of its function.	POLD1 PCNA	5.47e-05	5	82	2	14988403
Pubmed	Use of a reverse transcriptase-polymerase chain reaction assay to analyze allele-specific expression in individual hippocampal neurons.	RPS4Y1 CNTN1	5.47e-05	5	82	2	9562962
Pubmed	Mediation of proliferating cell nuclear antigen (PCNA)-dependent DNA replication through a conserved p21(Cip1)-like PCNA-binding motif present in the third subunit of human DNA polymerase delta.	POLD1 PCNA	5.47e-05	5	82	2	11595739
Pubmed	Metalloprotease SPRTN/DVC1 Orchestrates Replication-Coupled DNA-Protein Crosslink Repair.	POLD1 PCNA	5.47e-05	5	82	2	27871366
Pubmed	Aphidicolin-resistant and -sensitive base excision repair in wild-type and DNA polymerase beta-defective mouse cells.	POLD1 PCNA	5.47e-05	5	82	2	15177179
Pubmed	Reconstitution and characterization of the human DNA polymerase delta four-subunit holoenzyme.	POLD1 PCNA	5.47e-05	5	82	2	12403614
Pubmed	CBP and p300 acetylate PCNA to link its degradation with nucleotide excision repair synthesis.	POLD1 PCNA	5.47e-05	5	82	2	24939902
Pubmed	The HECT type ubiquitin ligase NEDL2 is degraded by anaphase-promoting complex/cyclosome (APC/C)-Cdh1, and its tight regulation maintains the metaphase to anaphase transition.	USP9X CFL1 POLRMT ZCCHC17 CARD14 DHRS7B	5.52e-05	281	82	6	24163370
Pubmed	Synaptic GAP and GEF Complexes Cluster Proteins Essential for GTP Signaling.	PITPNM2 MTOR USP9X PI4KA RAPGEF2 PCNA	5.52e-05	281	82	6	28706196
Pubmed	A dual-activity topoisomerase complex regulates mRNA translation and turnover.	PITPNM2 DIP2A SH3RF1 MTOR CFL1 PI4KA ZBTB4 POLRMT DIP2C CPSF1 LRRK1	5.65e-05	1105	82	11	35748872
Pubmed	The layered structure of human mitochondrial DNA nucleoids.	LONP1 POLRMT ATP5F1B	5.96e-05	32	82	3	18063578
Pubmed	Identification of Zika Virus and Dengue Virus Dependency Factors using Functional Genomics.	PRPF31 LONP1 TMTC3 ACLY ENO3 PCNA ATP5F1B	6.40e-05	422	82	7	27342126
Pubmed	A directed protein interaction network for investigating intracellular signal transduction.	PTPRK TMEM98 MTOR CFL1 PI4KA ITGB1BP1 XPNPEP1 OSGEP LAP3 CNTN1 ATP5F1B	6.57e-05	1124	82	11	21900206
Pubmed	Sema6D acts downstream of bone morphogenetic protein signalling to promote atrioventricular cushion development in mice.	SEMA6D SEMA6A TBX20	7.83e-05	35	82	3	28172500
Pubmed	Functional roles of p12, the fourth subunit of human DNA polymerase delta.	POLD1 PCNA	8.19e-05	6	82	2	16510448
Pubmed	Possible roles of Plexin-A4 in positioning of oligodendrocyte precursor cells in developing cerebral cortex.	SEMA3A SEMA6A	8.19e-05	6	82	2	22516460
Pubmed	UBR5 interacts with the replication fork and protects DNA replication from DNA polymerase η toxicity.	POLD1 PCNA	8.19e-05	6	82	2	31586398
Pubmed	The guidance molecule Semaphorin3A is differentially involved in the arealization of the mouse and primate neocortex.	SEMA3A SEMA6A	8.19e-05	6	82	2	23709645
Pubmed	Proteome-wide identification of HSP70/HSC70 chaperone clients in human cells.	XRN2 MTOR USP9X CFL1 TJP2 XPNPEP1 MCCC1 YES1 ALDH6A1 LAP3 PCNA ATP5F1B	8.44e-05	1367	82	12	32687490
Pubmed	Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disorders.	AGO1 MTOR USP9X CFL1 PI4KA HCN1 PIP4K2C RAPGEF2 PREPL CNTN1	8.92e-05	963	82	10	28671696
Pubmed	Comprehensive proteomic analysis of interphase and mitotic 14-3-3-binding proteins.	DENND4A MTOR CFL1 RAPGEF2 ATP5F1B	8.96e-05	190	82	5	15161933
Pubmed	Comparative interactome analysis of α-arrestin families in human and Drosophila.	USP9X POLD1 PI4KA CPSF1 MYO1B CNTN1	9.99e-05	313	82	6	38270169
Pubmed	Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.	PITPNM2 SH3RF1 SEMA6D ZBTB4	1.06e-04	103	82	4	10819331
Pubmed	TNRC6 proteins modulate hepatitis C virus replication by spatially regulating the binding of miR-122/Ago2 complexes to viral RNA.	XRN2 AGO1 TIAL1 MYO1B MCCC1 ATP5F1B	1.07e-04	317	82	6	30997501
Pubmed	MYC multimers shield stalled replication forks from RNA polymerase.	PRPF31 XRN2 ACLY CFL1 POLD1 MYO1B MCCC1 LAP3 PCNA ATP5F1B	1.11e-04	989	82	10	36424410
Pubmed	Modification of PCNA by ISG15 plays a crucial role in termination of error-prone translesion DNA synthesis.	POLD1 PCNA	1.14e-04	7	82	2	24768535
Pubmed	Aberrant trajectory of ascending dopaminergic pathway in mice lacking Nkx2.1.	SEMA3A PCNA	1.14e-04	7	82	2	12821380
Interaction	RHOD interactions	LONP1 SEMA6D TMTC3 MTOR USP9X PI4KA ITGB1BP1 MTMR1 MYO1B YES1 DENND4C DHRS7B	2.53e-06	572	80	12	int:RHOD
Interaction	C11orf52 interactions	DIP2A LONP1 PI4KA HGS MYO1B SEMA6A AHCYL2 LRRK1 YES1	3.92e-06	311	80	9	int:C11orf52
Interaction	NRP1 interactions	SEMA3A LONP1 SEMA6D USP9X HGS DYNLRB1 SEMA6A YES1 DHRS7B	5.47e-06	324	80	9	int:NRP1
Interaction	ZNF746 interactions	PRPF31 ACLY USP9X RPS4Y1 POLD1 POLRMT MYO1B MCCC1 ATP5F1B	5.75e-06	326	80	9	int:ZNF746
Interaction	HDAC4 interactions	PITPNM2 HDAC9 LONP1 DENND4A AGO1 CADPS USP9X PI4KA ITGB1BP1 MTMR1 RAPGEF2 DENND4C ATP5F1B	6.85e-06	744	80	13	int:HDAC4
Interaction	RHOJ interactions	DIP2A LONP1 TMTC3 PTPRK MTOR USP9X PI4KA HGS POLRMT MTMR1 YES1 DHRS7B	7.11e-06	633	80	12	int:RHOJ
Interaction	PAK6 interactions	LONP1 ACLY USP9X AHCYL2 LRRK1	1.06e-05	73	80	5	int:PAK6
Interaction	RHOF interactions	LONP1 SEMA6D TMTC3 MTOR USP9X PI4KA MTMR1 AHCYL2 YES1 DENND4C PCNA DHRS7B	1.32e-05	673	80	12	int:RHOF
Interaction	HSCB interactions	DENND4A TMTC3 TIAL1 POLD1 POLRMT CPSF1 SEMA6A TMX3 PREPL DENND4C PCNA ATP5F1B DHRS7B	1.85e-05	817	80	13	int:HSCB
Interaction	RHOB interactions	DIP2A LONP1 SEMA6D TMTC3 PTPRK USP9X PI4KA HGS TJP2 MTMR1 AHCYL2 PIP4K2C YES1	2.48e-05	840	80	13	int:RHOB
Interaction	KCTD13 interactions	PITPNM2 DIP2A LONP1 AGO1 CADPS ACLY USP9X CFL1 PI4KA TJP2 MTMR1 AHCYL2 PIP4K2C RAPGEF2 PCNA CNTN1 ATP5F1B	2.69e-05	1394	80	17	int:KCTD13
Interaction	ANKRD55 interactions	ACLY USP9X CFL1 PI4KA HGS PCNA ATP5F1B	3.41e-05	228	80	7	int:ANKRD55
Interaction	TMCC2 interactions	PRPF31 DIP2A RPS4Y1 HGS	4.61e-05	50	80	4	int:TMCC2
Interaction	RHOV interactions	LONP1 SH3RF1 MTOR USP9X PI4KA MYO1B YES1	5.11e-05	243	80	7	int:RHOV
Interaction	HEXA interactions	LONP1 XRN2 XPNPEP1 TMX3 PCNA	9.09e-05	114	80	5	int:HEXA
Interaction	CAMKV interactions	USP9X CHD9 AHCYL2 PIP4K2C YES1	1.07e-04	118	80	5	int:CAMKV
Interaction	CUL7 interactions	LONP1 XRN2 TIAL1 CADPS ACLY CFL1 SPIN2A CPSF1 MYO1B YES1 PCNA ATP5F1B	1.19e-04	845	80	12	int:CUL7
Interaction	SPRTN interactions	TMTC3 PTPRK RPS4Y1 CFL1 POLD1 OSGEP ENO3 PCNA ATP5F1B DHRS7B	1.22e-04	596	80	10	int:SPRTN
Interaction	MKRN2 interactions	SEMA3A LONP1 XRN2 AGO1 SEMA6D MTOR SEMA6A CNTN1	1.44e-04	385	80	8	int:MKRN2
Interaction	CYLD interactions	PRPF31 MGAM AGO1 ACLY RPS4Y1 CFL1 PPIP5K1 MYO1B ENO3 PCNA ATP5F1B SPIN3	1.53e-04	868	80	12	int:CYLD
Interaction	SSTR3 interactions	PI4KA HCN1 HGS TJP2 MTMR1 AHCYL2 YES1 ATP5F1B	1.66e-04	393	80	8	int:SSTR3
Interaction	PLXNA4 interactions	SEMA3A SEMA6D SEMA6A	1.84e-04	28	80	3	int:PLXNA4
Interaction	RHOH interactions	LONP1 MTOR USP9X PI4KA ITGB1BP1 MTMR1 SEMA6A XPNPEP1 YES1	1.92e-04	512	80	9	int:RHOH
Interaction	FAM13A interactions	AHCYL2 YES1 PCNA	2.04e-04	29	80	3	int:FAM13A
Interaction	BIRC3 interactions	LONP1 XRN2 DENND4A MTOR ACLY USP9X CFL1 POLD1 POLRMT CPSF1 MYO1B LAP3 PCNA ATP5F1B MYBPC1	2.13e-04	1334	80	15	int:BIRC3
Interaction	KIF20A interactions	LONP1 XRN2 AGO1 RPS4Y1 CFL1 POLRMT TJP2 CPSF1 PPIP5K1 MYO1B LRRK1 YES1 ATP5F1B	2.41e-04	1052	80	13	int:KIF20A
Interaction	HEXIM1 interactions	XRN2 AGO1 ACLY USP9X RPS4Y1 CFL1 POLRMT AHCYL2 YES1 ENO3 PCNA ATP5F1B	2.45e-04	913	80	12	int:HEXIM1
Interaction	RAC1 interactions	LONP1 SH3RF1 SEMA6D TMTC3 MTOR USP9X PI4KA ITGB1BP1 MTMR1 AHCYL2 YES1 DENND4C DHRS7B	2.66e-04	1063	80	13	int:RAC1
Interaction	FBXO22 interactions	PRPF31 DIP2A TIAL1 USP9X POLD1 POLRMT TJP2 CPSF1 CHD9	2.85e-04	540	80	9	int:FBXO22
Interaction	GLDC interactions	XRN2 AGO1 CAPN6 POLRMT TJP2 MYO1B ATP5F1B	2.86e-04	321	80	7	int:GLDC
Interaction	CAPG interactions	HDAC9 PRPF31 CFL1 HCN1	2.90e-04	80	80	4	int:CAPG
Interaction	HECW2 interactions	USP9X CFL1 POLRMT ZCCHC17 CARD14 PCNA DHRS7B	2.92e-04	322	80	7	int:HECW2
Interaction	MAST1 interactions	LONP1 XRN2 CYP2C8 USP9X POLRMT AHCYL2	2.94e-04	228	80	6	int:MAST1
Cytoband	Xp11.1	SPIN2A SPIN2B	1.89e-05	4	82	2	Xp11.1
GeneFamily	Tudor domain containing\|Spindlin family	SPIN2A SPIN2B SPIN3	2.51e-07	5	54	3	1089
GeneFamily	Immunoglobulin like domain containing\|Semaphorins	SEMA3A SEMA6D SEMA6A	2.77e-05	20	54	3	736
GeneFamily	Tudor domain containing	SPIN2A SPIN2B SPIN3	1.82e-04	37	54	3	780
GeneFamily	Aminopeptidases\|CD molecules	XPNPEP1 LAP3	1.16e-03	17	54	2	104
GeneFamily	Short chain dehydrogenase/reductase superfamily	RDH16 HSD11B1 DHRS7B	1.52e-03	76	54	3	743
GeneFamily	Guanylate cyclase receptors\|DENN/MADD domain containing	DENND4A DENND4C	2.51e-03	25	54	2	504
GeneFamily	Calcium voltage-gated channel subunits\|Membrane associated guanylate kinases	TJP2 CARD14	2.72e-03	26	54	2	904
Coexpression	GSE18281_CORTICAL_THYMOCYTE_VS_WHOLE_CORTEX_THYMUS_UP	SLC26A3 RDH16 CAPN6 SPIN2A PACRG NEK11 CNTN1	2.78e-06	196	82	7	M7238
ToppCell	facs-Pancreas-Endocrine-3m-Epithelial-pancreatic_B_cell\|Pancreas / Large_Intestine_Pancreas_Liver - method, tissue, subtissue, age, lineage, cell ontology and free annotation	TMTC3 CADPS ACLY USP9X PREPL DENND4C	1.45e-06	191	82	6	f76f3f5c7902a3659d8cbe470f96ce57c8a6744d
ToppCell	facs-Pancreas-Endocrine-3m-Epithelial-pancreatic_B_cell\|Pancreas / Large_Intestine_Pancreas_Liver - method, tissue, subtissue, age, lineage, cell ontology and free annotation	TMTC3 CADPS ACLY USP9X PREPL DENND4C	1.49e-06	192	82	6	5b7093d5af5ae7b0e6d3a464cc56272440ecedad
ToppCell	droplet-Fat-Scat-18m-Mesenchymal-nan\|Fat / Fat_BAT_GAT_MAT_SCAT - method, tissue, subtissue, age, lineage, cell ontology and free annotation	HSD11B1 ALDH6A1 CARD14 CNTN1 MYBPC1	1.28e-05	163	82	5	1eec7f5e5fed05fa21d3f81db588f10605f08ea7
ToppCell	Control-Myeloid-Mast\|World / Disease state, Lineage and Cell class	DENND4A CADPS DIP2C RAPGEF2 YES1	1.61e-05	171	82	5	ed8e61d524f4cddc6084b261175df54d2a64a60f
ToppCell	facs-Pancreas-Exocrine-3m-Epithelial-pancreatic_B_cell\|Pancreas / Large_Intestine_Pancreas_Liver - method, tissue, subtissue, age, lineage, cell ontology and free annotation	TMTC3 CADPS USP9X PREPL DENND4C	1.95e-05	178	82	5	fcbbcc44271515de1969b4732b6441c012693d5f
ToppCell	COPD-Myeloid-Mast\|World / Disease state, Lineage and Cell class	DENND4A CADPS DIP2C RAPGEF2 YES1	2.17e-05	182	82	5	68a1e7b804f309bfd6c23d65fad20a9a962712ae
ToppCell	ASK454-Endothelial-Lymphatic\|Endothelial / Donor, Lineage and Cell class of Lung cells from Dropseq	SEMA3A TMEM98 HGS PIP4K2C ALDH6A1	2.60e-05	189	82	5	316c857dec9383823e09f966bca62d52d933b141
ToppCell	renal_cortex_nuclei\|World / Celltypes from Cells and Nuclei per compartment and clinical group	SH3RF1 PTPRK DIP2C AHCYL2 RAPGEF2	2.81e-05	192	82	5	e8cc4d08fcfceeab75a02558817e4ccd7dbafe3a
ToppCell	Children_(3_yrs)-Epithelial-alveolar_epithelial_cell_type_2-D032\|Children_(3_yrs) / Lineage, Cell type, age group and donor	PITPNM2 SH3RF1 PTPRK MYO1B MCCC1	2.95e-05	194	82	5	97534c8bba895a7913665e03ae4e5c4a6ad71daf
ToppCell	Parenchymal-NucSeq\|Parenchymal / Cell types per location group and 10X technology with lineage, and cell group designations	SLC26A3 SH3RF1 PTPRK DIP2C RAPGEF2	3.25e-05	198	82	5	1996373bdccc55aac347d349bd22f6aad6d0c668
Disease	status epilepticus (biomarker_via_orthology)	XRN2 CFL1 HCN1 HSD11B1	1.46e-04	100	78	4	DOID:1824 (biomarker_via_orthology)
Disease	type 2 diabetes mellitus (biomarker_via_orthology)	CYP2C8 MTOR HSD11B1 ATP5F1B	6.34e-04	147	78	4	DOID:9352 (biomarker_via_orthology)
Disease	transient cerebral ischemia (biomarker_via_orthology)	TIAL1 MTOR PCNA ATP5F1B	8.10e-04	157	78	4	DOID:224 (biomarker_via_orthology)
Disease	congenital heart disease (implicated_via_orthology)	CHD9 TBX20 MYBPC1	8.21e-04	69	78	3	DOID:1682 (implicated_via_orthology)
Disease	mitochondrial heteroplasmy measurement	MGAM LONP1 POLRMT	8.21e-04	69	78	3	EFO_0600008
Disease	fasting blood glucose measurement	HDAC9 AGO1 CADPS CARD14 DHRS7B	9.95e-04	287	78	5	EFO_0004465
Disease	QRS duration	HCN1 ZBTB4 TBX20 CNTN1 ATP5F1B	1.18e-03	298	78	5	EFO_0005055
Disease	aggressive behavior	PHEX TBX20	1.99e-03	25	78	2	EFO_0003015

Protein segments in the cluster

Peptide	Gene	Start	Entry
YRVKFLVMNDEGPVA	UPK3BL1	161	B0FP48
GQTVDDPYATFVKML	CFL1	61	P23528
PGYRAEEAVEMLKTF	ADAT2	156	Q7Z6V5
AFYKAQPVIEFMCEV	AGO1	221	Q9UL18
MNPIVVFHGYEAVKE	CYP2C8	71	P10632
VVVSSLAGKVAYPMV	HSD11B1	166	P28845
NEIMVAPDKDYFLIV	DYNLRB1	76	Q9NP97
AFYMVGPIEEAVAKA	ATP5F1B	506	P06576
FPGESIKAIVKDVMY	MTMR1	101	Q13613
MIEDKGPRVADYFVV	DENND4A	1	Q7Z401
GVDFYDVAFKVMLVG	RAB26	56	Q9ULW5
VVSAEMVGKALVPYY	PACRG	176	Q96M98
DIAGVMTNKDEVPYL	LAP3	481	P28838
DVPKPGMDVADAYVT	CADPS	1221	Q9ULU8
MTCYKEEIFGPVLVV	ALDH6A1	411	Q02252
AMDGVVAIFYTVLTP	OR10G4	266	Q8NGN3
MAKYDLPGVIDFIVN	LIPN	146	Q5VXI9
KVPEGDSIADVSIMY	LRRK1	1806	Q38SD2
ITPVLDEGAEKVMAY	MGAM	766	O43451
KPLEVYSVDFMVDNA	CPSF1	1251	Q10570
ADVPLVVEYKIADMG	PCNA	231	P12004
VFEADPYKAVLTENM	FAT2	2796	Q9NYQ8
GMVTCYTQEEVPFKL	PCDHGB1	376	Q9Y5G3
YFEEQLLITMGKEPT	NEK11	626	Q8NG66
EAIVLDIDYKSGTPM	PI4KA	1781	P42356
VGKPVFTVERMYDVT	LONP1	746	P36776
YPIKMVVRGDHTFAD	PITPNM2	1081	Q9BZ72
VELPYTVKGMDVSFS	OSGEP	191	Q9NPF4
YEISVEAVDKGNIPM	PCDHA13	316	Q9Y5I0
DVVKQSGFLPESMYE	CHD9	2601	Q3L8U1
PVDYIFLIVEKGMDS	HCN1	231	O60741
VMVDYEASEPLFKAV	CARD14	616	Q9BXL6
PADIVVQFKDVYALM	CNTN1	241	Q12860
ATALAVEPMKFVYRG	DIP2C	811	Q9Y2E4
MIEDKGPRVTDYFVV	DENND4C	1	Q5VZ89
KAVNYVGAGTVEFIM	MCCC1	311	Q96RQ3
YPDKVVIGMDVAASE	ENO3	236	P13929
VDVDKRVMETNYFGP	DHRS7B	156	Q6IAN0
RVMETNYFGPVALTK	DHRS7B	161	Q6IAN0
ATALAVEPMKFVYRG	DIP2A	826	Q14689
PMGDVEYLEAFRTIV	HDAC9	881	Q9UKV0
QYIFTVPEDGHKVIM	CAPN6	386	Q9Y6Q1
VYVLFMVKDAGLTPD	POLRMT	281	O00411
KGVAAYMKSEDPLFV	POLD1	931	P28340
PEEEFIMGVSKYGIK	ITGB1BP1	106	O14713
YGDFKVTCVEMEPLA	PTPRK	1006	Q15262
IRSAEGAPQKEVYFM	PIP4K2C	356	Q8TBX8
KDSVMAVLEAFVYDP	MTOR	2411	P42345
ELDMEPYTVAGVAKL	USP9X	1821	Q93008
YRVKFLVMNDEGPVA	UPK3BL2	161	E5RIL1
LKAMGSIVYVTEIDP	AHCYL2	411	Q96HN2
VAMIEPGYFKTAVTS	RDH16	201	O75452
VRVDVTYPAGFMDVI	RPS4Y1	76	P22090
TYPAGFMDVISIEKT	RPS4Y1	81	P22090
GMVIHQVETKPSVYF	SPIN2A	226	Q99865
PIEFIMTVIAAGVSY	SLC26A3	291	P40879
YDVMFIGTDVGTVLK	SEMA3A	446	Q14563
MLADKIGIFPISYVE	SH3RF1	241	Q7Z6J0
ELIYAGMPITEVFKE	ACLY	851	P53396
EMPAVLVFKDETYFV	TMX3	196	Q96JJ7
VEVTYPDGKAEILCM	RAPGEF2	181	Q9Y4G8
FVIYGMEGSPKEEVF	SUN5	296	Q8TC36
EDEAIYGPNTKMVRF	TJP2	501	Q9UDY2
YKTFSDEPLEAGMIV	XPNPEP1	506	Q9NQW7
GEVAMVTDYGAFIKI	ZCCHC17	21	Q9NP64
GMVIHQVEAKPSVYF	SPIN3	226	Q5JUX0
VEYNTMGKVVFPRVA	SEMA6A	241	Q9H2E6
GMVIHQVEAKPSVYF	SPIN2B	226	Q9BPZ2
AEDYIFKAVMLPGAR	XRN2	761	Q9H0D6
TYQIMKVEGHVFPEF	HGS	131	O14964
KASEVMGPVEAAPEY	PRPF31	76	Q8WWY3
FQSYKPGEVMVKVHV	USP47	706	Q96K76
RMEGIGAAKVTFYPE	ZBTB4	906	Q9P1Z0
ESALPYVVGKMFVDV	PHEX	411	P78562
AVLAKVGYPEFIMND	PHEX	471	P78562
YILTNVGEPTEFKLM	PREPL	311	Q4J6C6
SFSGVDPEAKYIVLM	TBX20	136	Q9UMR3
FVVAERVLYVPSMGF	TMTC3	371	Q6ZXV5
YTVIFVGSEAGMVLK	SEMA6D	436	Q8NFY4
IMEIRVFPEKGYSFV	TIAL1	231	Q01085
IYEEFMPTDGTDVKV	PPIP5K1	246	Q6PFW1
YDSKPIVDLIGAMET	TMEM98	41	Q9Y2Y6
EEPIYIVTEFMSKGS	YES1	341	P07947
KVMGVLDIYGFEIFE	MYO1B	381	O43795
ETTFEPKKMIEGVAY	MYBPC1	676	Q00872