Cluster composition

Functions

Category	Name	IntersectionWithQuery	PValue	GenesInTerm	GenesInQuery	GenesInTermInQuery	ID
GeneOntologyBiologicalProcess	endosomal vesicle fusion	VPS41 SAMD9 VPS39	2.69e-06	16	36	3	GO:0034058
GeneOntologyCellularComponent	lysosomal HOPS complex	VPS41 VPS39	2.72e-06	2	35	2	GO:1902501
GeneOntologyCellularComponent	vacuolar HOPS complex	VPS41 VPS39	2.72e-06	2	35	2	GO:1902500
GeneOntologyCellularComponent	AP-3 adaptor complex	VPS41 VPS39	2.10e-04	13	35	2	GO:0030123
GeneOntologyCellularComponent	HOPS complex	VPS41 VPS39	2.45e-04	14	35	2	GO:0030897
Domain	CHCR	VPS41 VPS39	8.41e-05	7	38	2	PS50236
Domain	TPR-like_helical_dom	VPS41 C8orf76 SAMD9 TRANK1 LRP2BP	1.04e-04	233	38	5	IPR011990
Domain	Clathrin_H-chain/VPS_repeat	VPS41 VPS39	1.12e-04	8	38	2	IPR000547
Domain	-	VPS41 C8orf76 TRANK1 LRP2BP	8.05e-04	207	38	4	1.25.40.10
Domain	Zinc_finger_PHD-type_CS	SHPRH BRPF3	7.73e-03	65	38	2	IPR019786
Domain	F-box	FBXO25 FBXO3	8.20e-03	67	38	2	PF00646
Domain	LIM	LMO3 LMO1	8.68e-03	69	38	2	PF00412
Domain	-	LMO3 LMO1	8.92e-03	70	38	2	2.10.110.10
Domain	LIM_DOMAIN_2	LMO3 LMO1	9.17e-03	71	38	2	PS50023
Domain	Znf_LIM	LMO3 LMO1	9.17e-03	71	38	2	IPR001781
Domain	LIM_DOMAIN_1	LMO3 LMO1	9.17e-03	71	38	2	PS00478
Domain	LIM	LMO3 LMO1	9.17e-03	71	38	2	SM00132
Domain	FBOX	FBXO25 FBXO3	9.42e-03	72	38	2	PS50181
Domain	F-box_dom	FBXO25 FBXO3	1.02e-02	75	38	2	IPR001810
Pathway	WP_EBOLA_VIRUS_INFECTION_IN_HOST	VPS41 VPS39 PIK3CD HLA-E	4.31e-05	129	22	4	M39693
Pathway	KEGG_MEDICUS_PATHOGEN_SALMONELLA_SIFA_TO_TETHERING_OF_LATE_ENDOSOMES_AND_LYSOSOMES	VPS41 VPS39	8.31e-05	9	22	2	M47777
Pathway	KEGG_MEDICUS_REFERENCE_TETHERING_OF_LATE_ENDOSOMES_AND_LYSOSOMES	VPS41 VPS39	1.04e-04	10	22	2	M47776
Pathway	REACTOME_SARS_COV_2_MODULATES_AUTOPHAGY	VPS41 VPS39	1.27e-04	11	22	2	M45018
Pathway	WP_RESOLVIN_E1_AND_RESOLVIN_D1_SIGNALING_DECREASE_INFLAMMATION	PIK3CD GRK1	1.52e-04	12	22	2	M45559
Pathway	KEGG_MEDICUS_REFERENCE_AUTOPHAGOSOME_AND_LYSOSOME_FUSION_TETHERING_FACTOR	VPS41 VPS39	2.75e-04	16	22	2	M47978
Pubmed	The HOPS proteins hVps41 and hVps39 are required for homotypic and heterotypic late endosome fusion.	VPS41 VPS39	1.16e-06	2	38	2	23167963
Pubmed	Null mutation of the Lmo4 gene or a combined null mutation of the Lmo1/Lmo3 genes causes perinatal lethality, and Lmo4 controls neural tube development in mice.	LMO3 LMO1	3.48e-06	3	38	2	14966285
Pubmed	Expression of LIM protein genes Lmo1, Lmo2, and Lmo3 in adult mouse hippocampus and other forebrain regions: differential regulation by seizure activity.	LMO3 LMO1	3.48e-06	3	38	2	9204936
Pubmed	LIM-domain-only proteins: multifunctional nuclear transcription coregulators that interacts with diverse proteins.	LMO3 LMO1	6.96e-06	4	38	2	24379077
Pubmed	The small GTPase Arl8b regulates assembly of the mammalian HOPS complex on lysosomes.	VPS41 VPS39	1.74e-05	6	38	2	25908847
Pubmed	An Amyotrophic Lateral Sclerosis-Associated Mutant of C21ORF2 Is Stabilized by NEK1-Mediated Hyperphosphorylation and the Inability to Bind FBXO3.	NEK1 FBXO3	1.74e-05	6	38	2	32891887
Pubmed	Polygenic dissection of diagnosis and clinical dimensions of bipolar disorder and schizophrenia.	TRANK1 HLA-E	2.43e-05	7	38	2	24280982
Pubmed	RILP interacts with HOPS complex via VPS41 subunit to regulate endocytic trafficking.	VPS41 VPS39	2.43e-05	7	38	2	25445562
Pubmed	Structural basis of Vps33A recruitment to the human HOPS complex by Vps16.	VPS41 VPS39	3.24e-05	8	38	2	23901104
Pubmed	The HOPS complex mediates autophagosome-lysosome fusion through interaction with syntaxin 17.	VPS41 VPS39	3.24e-05	8	38	2	24554770
Pubmed	Recruitment of VPS33A to HOPS by VPS16 Is Required for Lysosome Fusion with Endosomes and Autophagosomes.	VPS41 VPS39	3.24e-05	8	38	2	25783203
Pubmed	SPE-39 family proteins interact with the HOPS complex and function in lysosomal delivery.	VPS41 VPS39	3.24e-05	8	38	2	19109425
Pubmed	An FTS/Hook/p107(FHIP) complex interacts with and promotes endosomal clustering by the homotypic vacuolar protein sorting complex.	VPS41 VPS39	5.20e-05	10	38	2	18799622
Pubmed	Characterization of the Mammalian CORVET and HOPS Complexes and Their Modular Restructuring for Endosome Specificity.	VPS41 VPS39	5.20e-05	10	38	2	26463206
Pubmed	Clathrin-dependent mechanisms modulate the subcellular distribution of class C Vps/HOPS tether subunits in polarized and nonpolarized cells.	VPS41 VPS39	7.62e-05	12	38	2	21411634
Pubmed	Dynamic spatiotemporal expression of LIM genes and cofactors in the embryonic and postnatal cerebral cortex.	LMO3 LMO1	7.62e-05	12	38	2	12619132
Pubmed	The Rab7 effector PLEKHM1 binds Arl8b to promote cargo traffic to lysosomes.	VPS41 VPS39	9.00e-05	13	38	2	28325809
Pubmed	LIM genes parcellate the embryonic amygdala and regulate its development.	LMO3 LMO1	9.00e-05	13	38	2	15295034
Pubmed	The rhombotin gene family encode related LIM-domain proteins whose differing expression suggests multiple roles in mouse development.	LMO3 LMO1	9.00e-05	13	38	2	1507224
Pubmed	Differential expression of LIM domain-only (LMO) genes in the developing mouse inner ear.	LMO3 LMO1	9.00e-05	13	38	2	16597514
Pubmed	Small molecule inhibition of HIV-1-induced MHC-I down-regulation identifies a temporally regulated switch in Nef action.	PIK3CD HLA-E	1.21e-04	15	38	2	20702582
Pubmed	A signature motif in LIM proteins mediates binding to checkpoint proteins and increases tumour radiosensitivity.	LMO3 LMO1	1.21e-04	15	38	2	28094252
Pubmed	HIV-1 Nef blocks transport of MHC class I molecules to the cell surface via a PI 3-kinase-dependent pathway.	PIK3CD HLA-E	1.38e-04	16	38	2	11289809
Pubmed	Arx acts as a regional key selector gene in the ventral telencephalon mainly through its transcriptional repression activity.	LMO3 LMO1	1.38e-04	16	38	2	19627984
Pubmed	Mammalian late vacuole protein sorting orthologues participate in early endosomal fusion and interact with the cytoskeleton.	VPS41 VPS39	1.56e-04	17	38	2	14668490
Pubmed	HIV-1 Nef downregulates MHC-I by a PACS-1- and PI3K-regulated ARF6 endocytic pathway.	PIK3CD HLA-E	1.76e-04	18	38	2	12526811
Pubmed	ORF3a of the COVID-19 virus SARS-CoV-2 blocks HOPS complex-mediated assembly of the SNARE complex required for autolysosome formation.	VPS41 VPS39	1.96e-04	19	38	2	33422265
Pubmed	LncRNA SLC26A4-AS1 suppresses the MRN complex-mediated DNA repair signaling and thyroid cancer metastasis by destabilizing DDX5.	EEF1D GOLGA6L2	2.41e-04	21	38	2	32939012
Pubmed	Characterization of the proteins of isolated human platelet alpha-granules. Evidence for a separate alpha-granule-pool of the glycoproteins IIb and IIIa.	BRPF3 CAP1	2.41e-04	21	38	2	6457647
Pubmed	Jak2 is essential for signaling through a variety of cytokine receptors.	LMO3 LMO1	2.41e-04	21	38	2	9590173
Pubmed	The transcription regulator Lmo3 is required for the development of medial ganglionic eminence derived neurons in the external globus pallidus.	LMO3 LMO1	2.65e-04	22	38	2	37532091
Pubmed	Prediction of the coding sequences of mouse homologues of KIAA gene: III. the complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.	BRPF3 KLHL9 TRANK1 VPS39 SULF1	2.65e-04	529	38	5	14621295
Pubmed	Phosphoproteomic analysis of the human pituitary.	EEF1D CAP1	4.01e-04	27	38	2	16807684
Pubmed	Interactomes of SARS-CoV-2 and human coronaviruses reveal host factors potentially affecting pathogenesis.	VPS41 VPS39	4.32e-04	28	38	2	34232536
Pubmed	Characterization of the proteins released from activated platelets leads to localization of novel platelet proteins in human atherosclerotic lesions.	BRPF3 CAP1	5.30e-04	31	38	2	14630798
Pubmed	The endolysosomal adaptor PLEKHM1 is a direct target for both mTOR and MAPK pathways.	VPS41 VPS39	6.01e-04	33	38	2	33452816
Pubmed	TRIM65 regulates microRNA activity by ubiquitination of TNRC6.	KLHL9 CCDC124 FBXO3 CNOT2	6.58e-04	364	38	4	24778252
Pubmed	RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway.	EEF1D CCDC124 CNOT2	6.65e-04	156	38	3	26170170
Pubmed	Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder.	ZDBF2 HLA-E	6.76e-04	35	38	2	22688191
Pubmed	Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC.	EEF1D DPP3	7.15e-04	36	38	2	16097034
Pubmed	The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation.	NEK1 EEF1D CCDC124 VPS39 CNOT2 CAP1	7.26e-04	1007	38	6	34597346
Pubmed	Identification of a family of human F-box proteins.	FBXO25 FBXO3	7.56e-04	37	38	2	10531035
Pubmed	Transcriptional network orchestrating regional patterning of cortical progenitors.	LMO3 LMO1	8.40e-04	39	38	2	34921112
Pubmed	A family of mammalian F-box proteins.	FBXO25 FBXO3	9.74e-04	42	38	2	10531037
Pubmed	MET Inhibitors Promote Liver Tumor Evasion of the Immune Response by Stabilizing PDL1.	EEF1D DPP3 CAP1	1.04e-03	182	38	3	30711629
GeneFamily	Cyclins\|F-boxes other	FBXO25 FBXO3	1.32e-03	39	25	2	560
GeneFamily	LIM domain containing	LMO3 LMO1	2.99e-03	59	25	2	1218
ToppCell	MS-CD8-proli_CD4\|MS / Condition, Cell_class and T cell subcluster	SHPRH ZNF567 TRIM68 TASOR2 LRP2BP	3.49e-07	172	38	5	0b6dd257110b3f17fa71ab18a165b091a9d5ae9a
ToppCell	Substantia_nigra-Neuronal-Inhibitory\|Substantia_nigra / BrainAtlas - Mouse McCarroll V32	LMO3 ZDBF2 TRANK1 TBC1D9	1.87e-05	186	38	4	9d3efe2a4feea2bc205a7e45b9b9f9ed9b3609ce
ToppCell	Substantia_nigra-Neuronal-Inhibitory-iN1(Gad1Gad2_Th)\|Substantia_nigra / BrainAtlas - Mouse McCarroll V32	LMO3 ZDBF2 TRANK1 TBC1D9	1.95e-05	188	38	4	b73e8a40393c3f656e2fcfe395a761b1f985c254
ToppCell	COVID_non-vent-Lymphocytic-ILC\|COVID_non-vent / Disease condition, Lineage, Cell class and subclass	SAMD9 TRANK1 FCRL3 HLA-E	2.44e-05	199	38	4	df4f7d5be099e3e6054f3b812ccf70251664e4c0
ToppCell	COVID_non-vent-Lymphocytic-ILC-NK_cell\|COVID_non-vent / Disease condition, Lineage, Cell class and subclass	SAMD9 TRANK1 FCRL3 HLA-E	2.44e-05	199	38	4	ed35d747f11f6ea6a5cb7061057f0a98d9e0db99
ToppCell	COVID-19-COVID-19_Mild-Lymphocyte-T/NK-NK_activated\|COVID-19_Mild / Disease, condition lineage and cell class	SAMD9 TRANK1 FCRL3 HLA-E	2.48e-05	200	38	4	2281debd86e5d92e8fe0397aec9ef670800f7471
ToppCell	COVID-19-COVID-19_Mild-Lymphocyte-T/NK-CD4+_T_activated\|COVID-19_Mild / Disease, condition lineage and cell class	SAMD9 TRANK1 MDN1 HLA-E	2.48e-05	200	38	4	d9e8a0d047d4403fb7265fde7448e23a7780785c
Disease	Testicular Germ Cell Tumor	SLC25A44 CDKL2 PIK3CD	8.98e-05	73	35	3	EFO_1000566
Disease	idiopathic osteonecrosis of the femoral head	FBXO25 SAMD9	1.75e-03	52	35	2	EFO_1001930
Disease	histidine measurement	LMO1 CNOT2	2.80e-03	66	35	2	EFO_0009769
Disease	Disproportionate short stature	NEK1 SULF1	3.78e-03	77	35	2	C0878659

Protein segments in the cluster

Peptide	Gene	Start	Entry
FAKDEDLHDILDYWK	ELFN1	806	P0C7U0
EYKDVDKKHVDWVKA	CAP1	171	Q01518
KEELKYWQKLRHDLE	BRPF3	546	Q9ULD4
KKIYDEATWLHDFGK	ERVV-2	421	B6SEH9
LAHEKIWFDKFKYDD	EEF1D	6	P29692
LLKALDKYWHEDCLK	LMO1	36	P25800
EEFEDKWFRKIKDHF	C8orf76	351	Q96K31
VEWLHKYLEKGKETL	HLA-E	186	P13747
KYWTKIHLDNLDKRE	MDN1	466	Q9NU22
YEREKKVWEEHLVAK	NEK1	631	Q96PY6
DHYAAIKKAWDDLKK	FBXO3	91	Q9UK99
KYDPEKDEWHKVFDL	KLHL9	566	Q9P2J3
KDRYLLKALDKYWHE	LMO3	21	Q8TAP4
FLEEDDKDLYILWKG	DPP3	426	Q9NY33
KEPKELEKAFYWHSE	LRP2BP	186	Q9P2M1
WHKKADRYIEELTKE	GOLGA6L2	191	Q8N9W4
LFWKDYHLALLFKDS	FBXO25	326	Q8TCJ0
KKKKRWYLVFEFVDH	CDKL2	71	Q92772
KEHLKEKLDEYIKLW	GALNT7	251	Q86SF2
TYWYHDEKLLKIKHD	FCRL3	56	Q96P31
KHLPALELWKDIEDY	GRK1	81	Q15835
QKELEDAYWKDDDKH	CCDC124	31	Q96CT7
KHLDFLKEIKWFAVL	SAMD9	426	Q5K651
DLFEAWKKEYKLLHE	SHPRH	1326	Q149N8
ELLHKVSKELAEWYF	WDR17	941	Q8IZU2
EWEHLDKKKFYVFGV	SLC25A44	11	Q96H78
NWRKVAKEFHLEYDK	CNOT2	506	Q9NZN8
EYFLIGHDREKIKDW	PLEKHS1	106	Q5SXH7
ENWKAEDFLVKFKEH	ZNF567	76	Q8N184
YKWELHEALEHLKKE	TRIM68	141	Q6AZZ1
KEFLKEQAWKIHFAE	TBC1D9	481	Q6ZT07
WKEDHIYLEDKSYKL	ZDBF2	1391	Q9HCK1
GELYEHEKDLVWKLR	PIK3CD	521	O00329
DQDDHIDWLLEKKKY	VPS41	361	P49754
WLLHYRENKKLKEDE	TASOR2	2316	Q5VWN6
LLHYWEFLFSKKDKE	TRANK1	2441	O15050
ARAWKDHKAYIDKEI	SULF1	636	Q8IWU6
KKKLQLYFWKDREFH	VPS39	141	Q96JC1