Cluster composition

Functions

Category	Name	IntersectionWithQuery	PValue	GenesInTerm	GenesInQuery	GenesInTermInQuery	ID
GeneOntologyMolecularFunction	DNA-binding transcription factor activity, RNA polymerase II-specific	FOXD4L1 UNCX KLF13 GLI1 DUX4L9 KLF14 CC2D1A DUX4L2 DUX4 RUNX2 LYL1 DUX4L4 ZNF574	9.21e-05	1412	55	13	GO:0000981
GeneOntologyBiologicalProcess	positive regulation of mitochondrial transcription	CHCHD10 SIRT3	1.94e-05	3	53	2	GO:1903109
Pubmed	Nucleotide sequence of the partially deleted D4Z4 locus in a patient with FSHD identifies a putative gene within each 3.3 kb element.	DUX4L9 DUX4L2 DUX4 DUX4L5 DUX4L6 DUX4L3 DUX4L4 DUX4L7	2.06e-20	12	59	8	10433963
Pubmed	Evolutionary conservation of a coding function for D4Z4, the tandem DNA repeat mutated in facioscapulohumeral muscular dystrophy.	DUX4L9 DUX4L2 DUX4 DUX4L5 DUX4L6 DUX4L3 DUX4L4 DUX4L7	5.34e-20	13	59	8	17668377
Pubmed	The DUX4 gene at the FSHD1A locus encodes a pro-apoptotic protein.	DUX4L2 DUX4 DUX4L5 DUX4L6 DUX4L3 DUX4L4 DUX4L7	2.23e-19	8	59	7	17588759
Pubmed	DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1.	DUX4L2 DUX4 DUX4L5 DUX4L6 DUX4L3 DUX4L4 DUX4L7	3.34e-18	10	59	7	17984056
Pubmed	Characterization of a tandemly repeated 3.3-kb KpnI unit in the facioscapulohumeral muscular dystrophy (FSHD) gene region on chromosome 4q35.	DUX4L2 DUX4 DUX4L5 DUX4L6 DUX4L3 DUX4L4 DUX4L7	4.76e-17	13	59	7	7739628
Pubmed	Active genes in junk DNA? Characterization of DUX genes embedded within 3.3 kb repeated elements.	DUX4L2 DUX4 DUX4L5 DUX4L6 DUX4L3 DUX4L4 DUX4L7	5.37e-16	17	59	7	11245978
Pubmed	The homeobox transcription factor DUXBL controls exit from totipotency.	DUX4L9 DUX4L2 DUX4L4	1.85e-08	4	59	3	38509386
Pubmed	Expression profiling of immature thymocytes revealed a novel homeobox gene that regulates double-negative thymocyte development.	DUX4L9 DUX4L2 DUX4L4	1.85e-08	4	59	3	17911620
Pubmed	Characterization of genomic structures and expression profiles of three tandem repeats of a mouse double homeobox gene: Duxbl.	DUX4L9 DUX4L2 DUX4L4	4.63e-08	5	59	3	20063414
Pubmed	The transcription factor Duxbl mediates elimination of pre-T cells that fail β-selection.	DUX4L9 DUX4L2 DUX4L4	1.62e-07	7	59	3	30765463
Pubmed	Proteins recruited by SH3 domains of Ruk/CIN85 adaptor identified by LC-MS/MS.	SAMD1 KLF13 PABPC4 LEMD2 MAP7	1.15e-06	108	59	5	19531213
Pubmed	Mutations in MINAR2 encoding membrane integral NOTCH2-associated receptor 2 cause deafness in humans and mice.	DUX4L9 DUX4L2 DUX4L4	2.08e-06	15	59	3	35727972
Pubmed	Proteomic analysis identifies transcriptional cofactors and homeobox transcription factors as TBX18 binding proteins.	DUX4L9 DUX4L2 DUX4L4	2.08e-06	15	59	3	30071041
Pubmed	Defective regulation of microRNA target genes in myoblasts from facioscapulohumeral dystrophy patients.	DUX4L9 DUX4	2.83e-06	2	59	2	24145033
Pubmed	Serum Deprivation-Induced Human GM3 Synthase (hST3Gal V) Gene Expression Is Mediated by Runx2 in Human Osteoblastic MG-63 Cells.	ST3GAL5 RUNX2	2.83e-06	2	59	2	26729095
Pubmed	DUX4c is up-regulated in FSHD. It induces the MYF5 protein and human myoblast proliferation.	DUX4L9 DUX4	1.69e-05	4	59	2	19829708
Pubmed	Wdpcp regulates cellular proliferation and differentiation in the developing limb via hedgehog signaling.	GLI1 RUNX2	1.69e-05	4	59	2	34225660
Pubmed	Runx2+ Niche Cells Maintain Incisor Mesenchymal Tissue Homeostasis through IGF Signaling.	GLI1 RUNX2	1.69e-05	4	59	2	32783935
Pubmed	The functional interactome of PYHIN immune regulators reveals IFIX is a sensor of viral DNA.	SAMD1 UTP18 DDX31 PABPC4 LEMD2 NOL9	2.82e-05	349	59	6	25665578
Pubmed	RNA transcripts, miRNA-sized fragments and proteins produced from D4Z4 units: new candidates for the pathophysiology of facioscapulohumeral dystrophy.	DUX4L2 DUX4	2.82e-05	5	59	2	19359275
Pubmed	Ihh signaling is directly required for the osteoblast lineage in the endochondral skeleton.	GLI1 RUNX2	5.91e-05	7	59	2	14973297
Pubmed	Ihh and Runx2/Runx3 signaling interact to coordinate early chondrogenesis: a mouse model.	GLI1 RUNX2	7.87e-05	8	59	2	23383321
Pubmed	DUX is a non-essential synchronizer of zygotic genome activation.	DUX4L9 DUX4L2 DUX4L4	8.59e-05	50	59	3	31806660
Pubmed	Does adult fracture repair recapitulate embryonic skeletal formation?	GLI1 RUNX2	1.01e-04	9	59	2	10495271
Pubmed	G9a is involved in the regulation of cranial bone formation through activation of Runx2 function during development.	GLI1 RUNX2	1.01e-04	9	59	2	32344102
Pubmed	Finding the Unicorn, a New Mouse Model of Midfacial Clefting.	GLI1 RUNX2	1.01e-04	9	59	2	31940751
Pubmed	Regulation of Calvarial Osteogenesis by Concomitant De-repression of GLI3 and Activation of IHH Targets.	GLI1 RUNX2	1.01e-04	9	59	2	29311969
Pubmed	Impaired skin and hair follicle development in Runx2 deficient mice.	GLI1 RUNX2	1.01e-04	9	59	2	18262513
Pubmed	Ligand-dependent hedgehog signaling maintains an undifferentiated, malignant osteosarcoma phenotype.	GLI1 RUNX2	1.26e-04	10	59	2	37845394
Pubmed	Sonic hedgehog is not a limb morphogen but acts as a trigger to specify all digits in mice.	UNCX GLI1	1.26e-04	10	59	2	35977544
Pubmed	Role of Indian hedgehog signaling in palatal osteogenesis.	GLI1 RUNX2	1.54e-04	11	59	2	21364421
Pubmed	Indian hedgehog signaling regulates proliferation and differentiation of chondrocytes and is essential for bone formation.	GLI1 RUNX2	1.54e-04	11	59	2	10465785
Pubmed	Gli1 protein participates in Hedgehog-mediated specification of osteoblast lineage during endochondral ossification.	GLI1 RUNX2	1.54e-04	11	59	2	22493482
Pubmed	Runx2 (Cbfa1) inhibits Shh signaling in the lower but not upper molars of mouse embryos and prevents the budding of putative successional teeth.	GLI1 RUNX2	1.54e-04	11	59	2	15668330
Pubmed	Prickle1 regulates differentiation of frontal bone osteoblasts.	GLI1 RUNX2	1.54e-04	11	59	2	30575813
Pubmed	Role of GSK-3β in the osteogenic differentiation of palatal mesenchyme.	GLI1 RUNX2	1.85e-04	12	59	2	22022457
Pubmed	Sonic hedgehog regulates proliferation and inhibits differentiation of CNS precursor cells.	GDF7 GLI1	2.18e-04	13	59	2	10516314
Pubmed	Spatial Multi-omics Reveals the Role of the Wnt Modulator, Dkk2, in Palatogenesis'.	GLI1 RUNX2	2.18e-04	13	59	2	38910391
Pubmed	Interactions of the Antiviral Factor Interferon Gamma-Inducible Protein 16 (IFI16) Mediate Immune Signaling and Herpes Simplex Virus-1 Immunosuppression.	UTP18 CENPB LEMD2 NOL9 ZNF574	2.52e-04	332	59	5	25693804
Pubmed	Class III myosins shape the auditory hair bundles by limiting microvilli and stereocilia growth.	TRIOBP MYO15A	2.54e-04	14	59	2	26754646
Pubmed	The transcription factor Foxc1 is necessary for Ihh-Gli2-regulated endochondral ossification.	GLI1 RUNX2	2.54e-04	14	59	2	25808752
Pubmed	Regulation of cranial morphogenesis and cell fate at the neural crest-mesoderm boundary by engrailed 1.	GLI1 RUNX2	2.54e-04	14	59	2	22395741
Pubmed	The E3 ubiquitin ligase HECTD1 contributes to cell proliferation through an effect on mitosis.	SAMD1 UTP18 DDX31 CENPB PABPC4 RBM15B NOL9	2.92e-04	759	59	7	35915203
Pubmed	RGS12 polarizes the GPSM2-GNAI complex to organize and elongate stereocilia in sensory hair cells.	TRIOBP MYO15A	2.93e-04	15	59	2	36260679
Pubmed	Bobby sox homolog regulates tooth root formation through modulation of dentin sialophosphoprotein.	GLI1 RUNX2	2.93e-04	15	59	2	32537777
Pubmed	The collagen receptor, discoidin domain receptor 2, functions in Gli1-positive skeletal progenitors and chondrocytes to control bone development.	GLI1 RUNX2	3.34e-04	16	59	2	35140200
Pubmed	Long bone development requires a threshold of Hox function.	GLI1 RUNX2	3.79e-04	17	59	2	24930703
Pubmed	Different roles of Runx2 during early neural crest-derived bone and tooth development.	GLI1 RUNX2	3.79e-04	17	59	2	16813524
Pubmed	Distinct roles of Hand2 in initiating polarity and posterior Shh expression during the onset of mouse limb bud development.	GLI1 RUNX2	4.25e-04	18	59	2	20386744
Pubmed	Sonic hedgehog signaling regulates a novel epithelial progenitor domain of the hindbrain choroid plexus.	GDF7 GLI1	4.25e-04	18	59	2	19570847
Pubmed	Analysis of expansion of myeloid progenitors in mice to identify leukemic susceptibility genes.	KLF13 RUNX2	4.25e-04	18	59	2	16897342
Pubmed	Expression of a Constitutively Active Form of Hck in Chondrocytes Activates Wnt and Hedgehog Signaling Pathways, and Induces Chondrocyte Proliferation in Mice.	GLI1 RUNX2	4.75e-04	19	59	2	32290615
Pubmed	Disrupted dorsal neural tube BMP signaling in the cilia mutant Arl13b hnn stems from abnormal Shh signaling.	GDF7 GLI1	4.75e-04	19	59	2	21539826
Pubmed	Segmental variations in trabecular bone density and microstructure of the spine in senescence-accelerated mouse (SAMP6): a murine model for senile osteoporosis.	GLI1 RUNX2	4.75e-04	19	59	2	22342532
Pubmed	Cooperative activity of noggin and gremlin 1 in axial skeleton development.	UNCX GLI1	4.75e-04	19	59	2	21303853
Pubmed	Ventral specification and perturbed boundary formation in the mouse midbrain in the absence of Hedgehog signaling.	GDF7 GLI1	4.75e-04	19	59	2	18429041
Pubmed	Fuz regulates craniofacial development through tissue specific responses to signaling factors.	GLI1 RUNX2	5.27e-04	20	59	2	21935430
Pubmed	FKBP8 is a negative regulator of mouse sonic hedgehog signaling in neural tissues.	GDF7 GLI1	5.27e-04	20	59	2	15105374
Pubmed	Receptor tyrosine kinase-like orphan receptor 2 (ROR2) and Indian hedgehog regulate digit outgrowth mediated by the phalanx-forming region.	GLI1 RUNX2	5.27e-04	20	59	2	20660756
Pubmed	Deletion of Fibroblast growth factor 9 globally and in skeletal muscle results in enlarged tuberosities at sites of deltoid tendon attachments.	GLI1 CHRNE	5.27e-04	20	59	2	34091985
Pubmed	RAB23 coordinates early osteogenesis by repressing FGF10-pERK1/2 and GLI1.	GLI1 RUNX2	5.27e-04	20	59	2	32662771
Pubmed	Ror2 knockout mouse as a model for the developmental pathology of autosomal recessive Robinow syndrome.	UNCX GLI1	5.82e-04	21	59	2	14745966
Pubmed	Temporomandibular joint formation requires two distinct hedgehog-dependent steps.	GDF7 GLI1	5.82e-04	21	59	2	19815519
Pubmed	Suppressor of Fused restraint of Hedgehog activity level is critical for osteogenic proliferation and differentiation during calvarial bone development.	GLI1 RUNX2	5.82e-04	21	59	2	28794157
Pubmed	Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes.	TPR SAMD1 FOXD4L1 CENPB ING1 GLI1 NOL9	6.03e-04	857	59	7	25609649
Pubmed	Specification of the mammalian cochlea is dependent on Sonic hedgehog.	GLI1 MYO15A	6.39e-04	22	59	2	12231626
Pubmed	Conditional Deletion of Indian Hedgehog in Limb Mesenchyme Results in Complete Loss of Growth Plate Formation but Allows Mature Osteoblast Differentiation.	GLI1 RUNX2	6.39e-04	22	59	2	26094741
Pubmed	Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets.	C15orf39 DUX4 TP53INP2 WNK2	6.69e-04	233	59	4	37704626
Pubmed	The G protein-coupled receptor Gpr161 regulates forelimb formation, limb patterning and skeletal morphogenesis in a primary cilium-dependent manner.	GLI1 RUNX2	7.00e-04	23	59	2	29222391
Pubmed	Genetic variation in healthy oldest-old.	ING1 SIRT3	7.62e-04	24	59	2	19680556
Pubmed	FOXC1 and FOXC2 regulate growth plate chondrocyte maturation towards hypertrophy in the embryonic mouse limb skeleton.	GLI1 RUNX2	7.62e-04	24	59	2	39012257
Pubmed	Disruption of GMNC-MCIDAS multiciliogenesis program is critical in choroid plexus carcinoma development.	GDF7 GLI1	7.62e-04	24	59	2	35322202
Pubmed	Anti-osteogenic function of a LIM-homeodomain transcription factor LMX1B is essential to early patterning of the calvaria.	GLI1 RUNX2	7.62e-04	24	59	2	29852132
Pubmed	Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation.	UNCX GLI1	7.62e-04	24	59	2	24946904
Pubmed	Functional proteomic analysis of human nucleolus.	UTP18 DDX31 NOL9	7.90e-04	106	59	3	12429849
Pubmed	Forward genetics defines Xylt1 as a key, conserved regulator of early chondrocyte maturation and skeletal length.	GLI1 RUNX2	8.28e-04	25	59	2	24161523
Pubmed	Mammalian SP/KLF transcription factors: bring in the family.	KLF13 KLF14	8.28e-04	25	59	2	15820306
Pubmed	The RNA-mediated estrogen receptor α interactome of hormone-dependent human breast cancer cell nuclei.	SAMD1 DDX31 GTPBP6 PABPC4 RBM15B TRIOBP NOL9 MAP7 ZNF574	8.92e-04	1497	59	9	31527615
Pubmed	Notch pathway regulation of chondrocyte differentiation and proliferation during appendicular and axial skeleton development.	UNCX RUNX2	8.96e-04	26	59	2	19590010
Pubmed	Ssdp1 regulates head morphogenesis of mouse embryos by activating the Lim1-Ldb1 complex.	FOXD4L1 UNCX	8.96e-04	26	59	2	15857913
Pubmed	Gli3 coordinates three-dimensional patterning and growth of the tectum and cerebellum by integrating Shh and Fgf8 signaling.	GDF7 GLI1	9.66e-04	27	59	2	18480159
Pubmed	Single-cell analysis identifies a key role for Hhip in murine coronal suture development.	GLI1 RUNX2	1.04e-03	28	59	2	34880220
Pubmed	Temporospatial regulation of intraflagellar transport is required for the endochondral ossification in mice.	GLI1 RUNX2	1.12e-03	29	59	2	34929174
Pubmed	Intraflagellar transport protein 122 antagonizes Sonic Hedgehog signaling and controls ciliary localization of pathway components.	GDF7 GLI1	1.12e-03	29	59	2	21209331
Pubmed	Evc works in chondrocytes and osteoblasts to regulate multiple aspects of growth plate development in the appendicular skeleton and cranial base.	GLI1 RUNX2	1.19e-03	30	59	2	21911092
Pubmed	Molecular profiling of the vestibular lamina highlights a key role for Hedgehog signalling.	GLI1 RUNX2	1.27e-03	31	59	2	36971701
Pubmed	The transcription factor Otx2 regulates choroid plexus development and function.	GDF7 GLI1	1.44e-03	33	59	2	23364326
Pubmed	H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids.	SAMD1 UTP18 KLF13 ING1 LEMD2 RBM15B NOL9 MAP7	1.48e-03	1294	59	8	30804502
Pubmed	Twist function is required for the morphogenesis of the cephalic neural tube and the differentiation of the cranial neural crest cells in the mouse embryo.	UNCX GLI1	1.53e-03	34	59	2	12086465
Pubmed	ISLET1-Dependent β-Catenin/Hedgehog Signaling Is Required for Outgrowth of the Lower Jaw.	GLI1 RUNX2	1.62e-03	35	59	2	28069742
Pubmed	A probability-based approach for high-throughput protein phosphorylation analysis and site localization.	TPR UTP18 CC2D1A MAP7 ZNF574	1.63e-03	503	59	5	16964243
Cytoband	4q35.2	DUX4L2 DUX4L5 DUX4L6 DUX4L3 DUX4L4 DUX4L7	1.00e-12	27	59	6	4q35.2
Cytoband	Ensembl 112 genes in cytogenetic band chr4q35	DUX4L9 DUX4L2 DUX4 DUX4L5 DUX4L6 DUX4L3 DUX4L4 DUX4L7	2.78e-12	117	59	8	chr4q35
Cytoband	19p13.12	SAMD1 CC2D1A	1.91e-03	50	59	2	19p13.12
GeneFamily	PRD class homeoboxes and pseudogenes	UNCX DUX4L9 DUX4L2 DUX4L5 DUX4L6 DUX4L3 DUX4L4 DUX4L7	5.03e-11	92	44	8	521
GeneFamily	Zinc fingers C2H2-type\|Kruppel like factors	KLF13 KLF14	8.64e-04	18	44	2	624
CoexpressionAtlas	facebase_RNAseq_e9.5_MaxArch_2500_K4	SAMD1 DDX31 FBXL18 GLI1 PABPC4 DACT3 RBM15B C15orf39 NOL9 LYL1 ZNF574	5.92e-05	1125	51	11	facebase_RNAseq_e9.5_MaxArch_2500_K4
CoexpressionAtlas	facebase_RNAseq_e9.5_MaxArch_2500	SAMD1 CHCHD10 DDX31 FBXL18 GLI1 PABPC4 DACT3 RBM15B C15orf39 NOL9 LYL1 ZNF574	7.53e-05	1371	51	12	facebase_RNAseq_e9.5_MaxArch_2500
Disease	total hip arthroplasty, osteoarthritis	TRIOBP RUNX2	2.14e-03	42	48	2	EFO_0009806, MONDO_0005178
Disease	BMI-adjusted waist-hip ratio, sex interaction measurement	KLF14 TP53INP2	2.24e-03	43	48	2	EFO_0007788, EFO_0008343
Disease	Nonsyndromic Hearing Loss and Deafness, Autosomal Recessive	TRIOBP MYO15A	3.14e-03	51	48	2	cv:CN043650

Protein segments in the cluster

Peptide	Gene	Start	Entry
AARAAPALQPSQAAP	DUX4L4	211	P0CJ87
PLAAPPAQDSRARRS	ATP8B3	876	O60423
AARAAPALQPSQAAP	DUX4L6	211	P0CJ89
EAPRAASPPRRASSV	CHRNE	361	Q04844
APPLREPRARHAAAA	RBM15B	271	Q8NDT2
RAAAARRPNTATPSP	NOL9	71	Q5SY16
LAPRAAVAAAAPRAV	PABPC4	506	Q13310
RRAVSPSNPKARQPA	MAP7	311	Q14244
AARAAPALQPSQAAP	DUX4	211	Q9UBX2
RSAPRAAAPSCPARA	GTPBP6	21	O43824
DAPLRARPAAASPRA	LEMD2	71	Q8NC56
AQPRARSSNDARRPP	MYO15A	631	Q9UKN7
APQRPRAAEVAPAAR	C17orf58	56	Q2M2W7
ARPSSAAPASRGAPR	CCDC120	421	Q96HB5
SQAPREAPARRAPSS	CORO7	866	P57737
AARAAPALQPSQAAP	DUX4L3	211	P0CJ86
PQPRSPAARRAAARS	NRG2	71	O14511
DPAQAADRPAPARVQ	GLI1	641	P08151
NPRTFSRRPPAQASR	DDX31	116	Q9H8H2
ARARNAAPRTPAAPA	CENPB	141	P07199
RPRRGPAPTLAAQAA	DACT3	456	Q96B18
RSAASRPASRPAAPS	CHCHD10	6	Q8WYQ3
AARAAPALQPSQAAP	DUX4L9	211	Q6RFH8
PAPARESGNRSARPL	CC2D1A	831	Q6P1N0
AARAAPALQPSQAAP	DUX4L7	211	P0CJ90
RRAEAAARSQPAPPA	LYL1	241	P12980
GPAAARRNPFARLDN	DONSON	71	Q9NYP3
APPRSAAASEDARQP	FOXD4L1	91	Q9NU39
PAPAPAERREGAAAR	KLF13	76	Q9Y2Y9
APAADQAPRRRSVTP	KLF14	176	Q8TD94
AARAAPALQPSQAAP	DUX4L5	211	P0CJ88
ARAPRAAAAAATAPP	SAMD1	146	Q6SPF0
TPAARAAAPSPDRRD	HCN2	851	Q9UL51
PEAAAPRERPARLSA	FAM8A1	96	Q9UBU6
AAAAAAAAAVPRLRP	RUNX2	81	Q13950
AAPARVSAQRATPRD	SFI1	1096	A8K8P3
SQRKPPARPSAAAAA	UTP18	46	Q9Y5J1
APDAAARPPRAAELS	LRRC56	521	Q8IYG6
PRPAGPARRQFQAAS	ING1	161	Q9UK53
GAARPASPAARVSPR	PKDREJ	151	Q9NTG1
ADSAPRADRAPAQPA	FBXL18	426	Q96ME1
RAAPPAPRLDDAAAS	SLC2A8	56	Q9NY64
AVPAAAVPRARAARR	GDF7	61	Q7Z4P5
QTGRPPARARDTAAP	SHISA8	116	B8ZZ34
RRPLQPRTEAAAAPA	ST3GAL5	11	Q9UNP4
PRAFRRQPRAAAPSF	SIRT3	76	Q9NTG7
RRPRAASDSNPAGPL	METTL22	126	Q9BUU2
PRASSPNRAARDNPT	TRIOBP	536	Q9H2D6
PPRPRGAAASRDLAA	CHST13	291	Q8NET6
AAPRPRSPAEAEARG	CLEC2L	26	P0C7M8
SPAPARAQAPASARD	C15orf39	726	Q6ZRI6
EPRAARHAAPLPARA	TP53INP2	146	Q8IXH6
SASERQAPRAPQSPR	TPR	2061	P12270
TALAAPSPPRARARG	SCARF2	736	Q96GP6
EAQAARLAAAAPPPR	PRX	201	Q9BXM0
RAPRATRAPVASPAA	ZNF574	706	Q6ZN55
AERARGRPAAPAPAA	WNK2	86	Q9Y3S1
SPPRRKAASNAAAAA	UNCX	341	A6NJT0
AARAAPALQPSQAAP	DUX4L2	211	P0CJ85