Cluster composition

Functions

Category	Name	IntersectionWithQuery	PValue	GenesInTerm	GenesInQuery	GenesInTermInQuery	ID
GeneOntologyBiologicalProcess	glossopharyngeal nerve morphogenesis	HOXA3 HOXB3 HOXD3	3.62e-08	4	44	3	GO:0021615
GeneOntologyBiologicalProcess	glossopharyngeal nerve development	HOXA3 HOXB3 HOXD3	9.03e-08	5	44	3	GO:0021563
GeneOntologyBiologicalProcess	cranial nerve morphogenesis	HOXA3 HOXB3 HOXD3	4.30e-05	32	44	3	GO:0021602
GeneOntologyBiologicalProcess	thyroid gland development	HOXA3 HOXB3 HOXD3	5.17e-05	34	44	3	GO:0030878
MousePheno	decreased susceptibility to diet-induced hepatic steatosis	ADAM29 IGF2BP2 CNOT6L MFRP	5.10e-05	80	36	4	MP:0031268
MousePheno	decreased susceptibility to hepatic steatosis	ADAM29 IGF2BP2 CNOT6L MFRP	8.81e-05	92	36	4	MP:0002310
Domain	DUF4074	HOXA3 HOXB3 HOXD3	1.31e-08	3	45	3	IPR025281
Domain	DUF4074	HOXA3 HOXB3 HOXD3	1.31e-08	3	45	3	PF13293
Domain	Homeobox_Antennapedia_CS	HOXA3 HOXB3 HOXD3	1.69e-05	21	45	3	IPR001827
Domain	ANTENNAPEDIA	HOXA3 HOXB3 HOXD3	2.55e-05	24	45	3	PS00032
Domain	HTH_motif	HOXA3 HOXB3 HOXD3	6.13e-04	69	45	3	IPR000047
Domain	Homeobox_metazoa	HOXA3 HOXB3 HOXD3	1.33e-03	90	45	3	IPR020479
Domain	p53-like_TF_DNA-bd	TBX19 NFATC3	7.23e-03	53	45	2	IPR008967
Pubmed	Mice with targeted disruptions in the paralogous genes hoxa-3 and hoxd-3 reveal synergistic interactions.	HOXA3 HOXB3 HOXD3	2.31e-09	3	47	3	7913519
Pubmed	Hox group 3 paralogous genes act synergistically in the formation of somitic and neural crest-derived structures.	HOXA3 HOXB3 HOXD3	9.24e-09	4	47	3	9441667
Pubmed	The absence of mutations in homeobox candidate genes HOXA3, HOXB3, HOXD3 and PITX2 in familial and sporadic thyroid hemiagenesis.	HOXA3 HOXB3 HOXD3	9.24e-09	4	47	3	24127533
Pubmed	Hox group 3 paralogs regulate the development and migration of the thymus, thyroid, and parathyroid glands.	HOXA3 HOXB3 HOXD3	2.31e-08	5	47	3	9520319
Pubmed	Retinoic acid regulates a subset of Cdx1 function in vivo.	HOXA3 HOXB3 HOXD3	1.29e-07	8	47	3	14660544
Pubmed	Hox cofactors in vertebrate development.	HOXA3 HOXB3 HOXD3	2.76e-07	10	47	3	16515781
Pubmed	Rostral and caudal pharyngeal arches share a common neural crest ground pattern.	HOXA3 HOXB3 HOXD3	8.33e-07	14	47	3	19168678
Pubmed	A distinct Hox code for the branchial region of the vertebrate head.	HOXA3 HOXB3 HOXD3	1.04e-06	15	47	3	1682814
Pubmed	Hox3 genes coordinate mechanisms of genetic suppression and activation in the generation of branchial and somatic motoneurons.	HOXA3 HOXB3 HOXD3	1.55e-06	17	47	3	12954718
Pubmed	174delG mutation in mouse MFRP causes photoreceptor degeneration and RPE atrophy.	PER3 MFRP	1.79e-06	2	47	2	21810984
Pubmed	Independent regulation of initiation and maintenance phases of Hoxa3 expression in the vertebrate hindbrain involve auto- and cross-regulatory mechanisms.	HOXA3 HOXB3	1.79e-06	2	47	2	11566863
Pubmed	Sequence and expression of the murine Hoxd-3 homeobox gene.	HOXA3 HOXD3	1.79e-06	2	47	2	8710855
Pubmed	Mice homozygous for a targeted disruption of Hoxd-3 (Hox-4.1) exhibit anterior transformations of the first and second cervical vertebrae, the atlas and the axis.	HOXA3 HOXD3	1.79e-06	2	47	2	7910549
Pubmed	Maintenance of functional equivalence during paralogous Hox gene evolution.	HOXA3 HOXD3	1.79e-06	2	47	2	10688203
Pubmed	Crypto-rhombomeres of the mouse medulla oblongata, defined by molecular and morphological features.	HOXA3 HOXB3 HOXD3	3.02e-06	21	47	3	25381007
Pubmed	Targeted disruption of the mouse homologue of the Drosophila polyhomeotic gene leads to altered anteroposterior patterning and neural crest defects.	HOXA3 HOXB3 HOXD3	4.59e-06	24	47	3	9367423
Pubmed	Conserved and distinct roles of kreisler in regulation of the paralogous Hoxa3 and Hoxb3 genes.	HOXA3 HOXB3	5.36e-06	3	47	2	9895323
Pubmed	Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis transcription factors and retinoic acid.	HOXA3 HOXB3 HOXD3	8.25e-06	29	47	3	33298461
Pubmed	HOX gene analysis of endothelial cell differentiation in human bone marrow-derived mesenchymal stem cells.	HOXA3 HOXB3	1.07e-05	4	47	2	17972163
Pubmed	Atlas of Hox gene expression in the developing kidney.	HOXA3 HOXB3 HOXD3	1.89e-05	38	47	3	15042701
Pubmed	Complete mutation analysis panel of the 39 human HOX genes.	HOXA3 HOXB3 HOXD3	1.89e-05	38	47	3	11857506
Pubmed	Lysine demethylase 7a regulates murine anterior-posterior development by modulating the transcription of Hox gene cluster.	HOXA3 HOXB3 HOXD3	2.04e-05	39	47	3	33257809
Pubmed	Quantification of Hox and surfactant protein-B transcription during murine lung development.	HOXA3 HOXB3 HOXD3	2.21e-05	40	47	3	19204410
Pubmed	Lin28a/let-7 pathway modulates the Hox code via Polycomb regulation during axial patterning in vertebrates.	HOXA3 HOXB3 HOXD3	2.38e-05	41	47	3	32479258
Pubmed	Mouse and zebrafish Hoxa3 orthologues have nonequivalent in vivo protein function.	HOXA3 HOXD3	2.67e-05	6	47	2	20498049
Pubmed	Reduction of Hox gene expression by histone H1 depletion.	HOXA3 HOXB3 HOXD3	2.75e-05	43	47	3	22701719
Pubmed	Nomenclature for human homeobox genes.	HOXA3 HOXB3 HOXD3	2.95e-05	44	47	3	1973146
Pubmed	Vertebrate homeobox gene nomenclature.	HOXA3 HOXB3 HOXD3	3.60e-05	47	47	3	1358459
Pubmed	New insights into the role of Jmjd3 and Utx in axial skeletal formation in mice.	HOXA3 HOXB3 HOXD3	4.34e-05	50	47	3	28188179
Pubmed	N6 -methyladenosine-modified lncRNA ARHGAP5-AS1 stabilises CSDE1 and coordinates oncogenic RNA regulons in hepatocellular carcinoma.	ARHGAP5 IGF2BP2	4.98e-05	8	47	2	36354136
Pubmed	The heart LIM protein gene (Hlp), expressed in the developing and adult heart, defines a new tissue-specific LIM-only protein family.	CRIP3 CRIP2	4.98e-05	8	47	2	12128222
Pubmed	c-jun regulation and function in the developing hindbrain.	HOXA3 HOXB3	4.98e-05	8	47	2	12798298
Pubmed	The branchial Hox code and its implications for gene regulation, patterning of the nervous system and head evolution.	HOXA3 HOXB3	4.98e-05	8	47	2	1688181
Pubmed	New murine homeoboxes: structure, chromosomal assignment, and differential expression in adult erythropoiesis.	HOXB3 HOXD3	4.98e-05	8	47	2	2890503
Pubmed	The role of Hoxa-3 in mouse thymus and thyroid development.	HOXA3 HOXB3	4.98e-05	8	47	2	7635047
Pubmed	Local alterations of Krox-20 and Hox gene expression in the hindbrain suggest lack of rhombomeres 4 and 5 in homozygote null Hoxa-1 (Hox-1.6) mutant embryos.	HOXA3 HOXB3	6.40e-05	9	47	2	8102800
Pubmed	The thyroid transcription factor-1 gene is a candidate target for regulation by Hox proteins.	HOXB3 HOXD3	6.40e-05	9	47	2	7913891
Pubmed	Hoxa-2 mutant mice exhibit homeotic transformation of skeletal elements derived from cranial neural crest.	HOXA3 HOXB3	6.40e-05	9	47	2	7903600
Pubmed	In vivo functional analysis of the Hoxa-1 3' retinoic acid response element (3'RARE).	HOXA3 HOXB3	6.40e-05	9	47	2	9053316
Pubmed	Nav2 is necessary for cranial nerve development and blood pressure regulation.	HOXA3 HOXB3	6.40e-05	9	47	2	20184720
Pubmed	Wnt signaling is a key mediator of Cdx1 expression in vivo.	HOXA3 HOXD3	6.40e-05	9	47	2	17537796
Pubmed	HMG1 interacts with HOX proteins and enhances their DNA binding and transcriptional activation.	HOXB3 HOXD3	6.40e-05	9	47	2	8890171
Pubmed	Mouse Af9 is a controller of embryo patterning, like Mll, whose human homologue fuses with Af9 after chromosomal translocation in leukemia.	HOXA3 HOXB3	6.40e-05	9	47	2	12242306
Pubmed	Requirement for downregulation of kreisler during late patterning of the hindbrain.	HOXA3 HOXB3	7.99e-05	10	47	2	11880356
Pubmed	Homeobox genes from clusters A and B demonstrate characteristics of temporal colinearity and differential restrictions in spatial expression domains in the branching mouse lung.	HOXA3 HOXB3	1.17e-04	12	47	2	9415485
Pubmed	Moz and retinoic acid coordinately regulate H3K9 acetylation, Hox gene expression, and segment identity.	HOXA3 HOXB3	1.61e-04	14	47	2	19922872
Pubmed	Hox-1.11 and Hox-4.9 homeobox genes.	HOXA3 HOXB3	1.61e-04	14	47	2	1348361
Pubmed	Embryonic Lethality Due to Arrested Cardiac Development in Psip1/Hdgfrp2 Double-Deficient Mice.	HOXA3 HOXB3	1.86e-04	15	47	2	26367869
Pubmed	Genome-wide association study of recurrent early-onset major depressive disorder.	AMPD2 ATXN7L2	2.12e-04	16	47	2	20125088
Pubmed	Ablation of Zfhx4 results in early postnatal lethality by disrupting the respiratory center in mice.	HOXA3 HOXD3	2.12e-04	16	47	2	33475140
Pubmed	Contribution of Hox genes to the diversity of the hindbrain sensory system.	HOXA3 HOXB3	2.40e-04	17	47	2	14960494
Pubmed	Multiple roles for HOXA3 in regulating thymus and parathyroid differentiation and morphogenesis in mouse.	HOXA3 HOXD3	3.01e-04	19	47	2	25249461
Pubmed	Single-cell transcriptomics uncovers a non-autonomous Tbx1-dependent genetic program controlling cardiac neural crest cell development.	HOXB3 CNN1	3.69e-04	21	47	2	36941249
Pubmed	Hox paralog group 2 genes control the migration of mouse pontine neurons through slit-robo signaling.	HOXA3 HOXB3	3.69e-04	21	47	2	18547144
Pubmed	Organization of human class I homeobox genes.	HOXB3 HOXD3	4.06e-04	22	47	2	2576652
Pubmed	Ethanol exposure induces differential microRNA and target gene expression and teratogenic effects which can be suppressed by folic acid supplementation.	HOXA3 HOXD3	4.44e-04	23	47	2	19091803
Pubmed	A dynamic expression survey identifies transcription factors relevant in mouse digestive tract development.	HOXA3 HOXB3 HOXD3	5.54e-04	118	47	3	16971476
Pubmed	Fine mapping of human HOX gene clusters.	HOXA3 HOXB3	5.69e-04	26	47	2	8646877
Pubmed	Requirement for Pbx1 in skeletal patterning and programming chondrocyte proliferation and differentiation.	HOXA3 HOXD3	6.14e-04	27	47	2	11566859
Pubmed	The human HOX gene family.	HOXB3 HOXD3	7.09e-04	29	47	2	2574852
Pubmed	Control of stomach smooth muscle development and intestinal rotation by transcription factor BARX1.	CNN1 CRIP2	7.59e-04	30	47	2	26057579
Pubmed	An atlas of combinatorial transcriptional regulation in mouse and man.	HOXA3 TBX19 CNOT6L HOXD3 SPEN NFATC3	1.12e-03	877	47	6	20211142
Pubmed	Identification of 10 murine homeobox genes.	HOXB3 HOXD3	1.22e-03	38	47	2	1683707
Interaction	KRTAP6-1 interactions	CCDC120 AMPD2 VGLL3 CATSPER1 NAF1	2.93e-06	103	44	5	int:KRTAP6-1
Cytoband	16q22.2	PKD1L3 NFATC3	2.34e-04	22	47	2	16q22.2
Cytoband	1p13.3	AMPD2 ATXN7L2	2.30e-03	69	47	2	1p13.3
Cytoband	2q35	ZNF142 MARCHF4	3.01e-03	79	47	2	2q35
GeneFamily	HOXL subclass homeoboxes	HOXA3 HOXB3 HOXD3	9.53e-05	52	31	3	518
GeneFamily	LIM domain containing	CRIP3 CRIP2	4.58e-03	59	31	2	1218
ToppCell	droplet-Pancreas-Exocrine-21m-Epithelial-pancreatic_ductal_cell\|Pancreas / Large_Intestine_Pancreas_Liver - method, tissue, subtissue, age, lineage, cell ontology and free annotation	KCP BBOX1 CNN1 CRIP2	3.39e-05	174	47	4	a0ccda8fd6f55251cdeff24cf66e72e4a31d2104
ToppCell	droplet-Lung-LUNG-30m-Epithelial-ciliated_columnar_cell_of_tracheobronchial_tree\|Lung / Lung_Trachea - method, tissue, subtissue, age, lineage, cell ontology and free annotation	CD164L2 KLHDC7A MARCHF4 BBOX1	4.12e-05	183	47	4	3991830726d05cf19606d540de04093985b7bdeb
ToppCell	droplet-Lung-LUNG-30m-Epithelial-Ciliated_cell\|Lung / Lung_Trachea - method, tissue, subtissue, age, lineage, cell ontology and free annotation	CD164L2 KLHDC7A MARCHF4 BBOX1	4.12e-05	183	47	4	cc844f54c7564bf432b179ca63bc7c4b9b8cfdd9
ToppCell	droplet-Lung-21m-Epithelial-airway_epithelial-club_cell\|21m / method, tissue, age, lineage, sublineage, cell ontologies, cell type and subtype	CD164L2 CCDC120 BBOX1 CNN1	4.21e-05	184	47	4	9365cdc52a2419e3f27e1c1c9310fa707d1e506b
ToppCell	droplet-Lung-21m-Epithelial-airway_epithelial-club_cell-club_cell\|21m / method, tissue, age, lineage, sublineage, cell ontologies, cell type and subtype	CD164L2 CCDC120 BBOX1 CNN1	4.21e-05	184	47	4	204d16c48f822c98dc4118ac97a4f99f7e1163c8
ToppCell	renal_cortex_nuclei-Hypertensive_with+without-CKD-Epithelial-Distal_tubule_epithelial_cell-kidney_loop_of_Henle_thick_ascending_limb_epithelial_cell-Macula_Densa_Cell\|Hypertensive_with+without-CKD / Celltypes from Cells and Nuclei per compartment and clinical group	PAPPA2 HOXB3 HOXD3 BBOX1	4.21e-05	184	47	4	d33de57876817050b294f2ecb0a4eb0634cfa7f0
ToppCell	droplet-Lung-nan-21m-Epithelial-club_cell_of_bronchiole\|Lung / Lung_Trachea - method, tissue, subtissue, age, lineage, cell ontology and free annotation	CD164L2 CCDC120 BBOX1 CNN1	4.21e-05	184	47	4	7cc3b9bba1f600b40b02fe2456b5d007dbf9fa37
ToppCell	droplet-Lung-nan-21m-Epithelial-Club_Cell\|Lung / Lung_Trachea - method, tissue, subtissue, age, lineage, cell ontology and free annotation	CD164L2 CCDC120 BBOX1 CNN1	4.21e-05	184	47	4	53b71c4ac86dc5e42763b8f64fbc917177531017
ToppCell	COVID-19-kidney-TAL\|COVID-19 / Disease (COVID-19 only), tissue and cell type	PAPPA2 HOXB3 HOXD3 BBOX1	4.87e-05	191	47	4	fe55475ce0666ab5122447a813dc2369e24947b8
ToppCell	COVID-19-kidney-Mito-rich_Distal\|COVID-19 / Disease (COVID-19 only), tissue and cell type	PAPPA2 HOXB3 HOXD3 BBOX1	4.87e-05	191	47	4	0965f621ebcd92ccdeb21cc27022180ce3cfe910
ToppCell	renal_medulla_nuclei-CKD+DKD_normotensive-Epithelial-Intermediate_tubule_epithelial_cell-kidney_loop_of_Henle_thick_ascending_limb_epithelial_cell-Adaptive_/_Maladaptive_/_Repairing_Thick_Ascending_Limb_Cell\|CKD+DKD_normotensive / Celltypes from Cells and Nuclei per compartment and clinical group	PAPPA2 KCP HOXB3 BBOX1	5.07e-05	193	47	4	f42a0f02ed00fe1bb833ff0a0640d9131bca89bd
ToppCell	renal_medulla_nuclei-CKD+DKD_normotensive-Epithelial-Intermediate_tubule_epithelial_cell-kidney_loop_of_Henle_thick_ascending_limb_epithelial_cell\|CKD+DKD_normotensive / Celltypes from Cells and Nuclei per compartment and clinical group	PAPPA2 KCP HOXB3 BBOX1	5.07e-05	193	47	4	42df7ed37d11fb542b4d1d714b6f87ae8e1396a6
ToppCell	Tracheal-NucSeq-Epithelial-Epi_airway_neuro-secretory-Neuroendocrine\|NucSeq / Cell types per location group and 10X technology with lineage, and cell group designations	KLHDC7A HOXD3 PKD1L3 MARCHF4	5.38e-05	196	47	4	95544097577f20ed7f4144bd940471cde0617554
ToppCell	Brain_organoid-organoid_Tanaka_cellReport-1m-Mesenchymal-Mesoderm\|1m / Sample Type, Dataset, Time_group, and Cell type.	HOXA3 PAPPA2 HOXD3 CNN1	5.82e-05	200	47	4	c0ad32e9dd7f481c2665587fd8bd9fffc2e725f9
ToppCell	droplet-Liver-Npc-21m-Myeloid-nan\|Liver / Large_Intestine_Pancreas_Liver - method, tissue, subtissue, age, lineage, cell ontology and free annotation	KCP ZNF142 SPEN	6.84e-05	75	47	3	7f3be37cc378ee115fcb4b0eb9653fc77447aa0a
Disease	hypertension	HOXA3 KCP CD164L2 HOXB3 CRIP3	8.22e-05	307	43	5	EFO_0000537
Disease	pulse pressure measurement	HOXA3 PIK3R4 PAPPA2 CD164L2 HOXB3 HOXD3 PKD1L3 CRIP3	7.97e-04	1392	43	8	EFO_0005763
Disease	motion sickness	HOXB3 HOXD3	2.24e-03	48	43	2	EFO_0006928
Disease	breast carcinoma	ARHGAP5 ADAM29 AMPD2 VGLL3 KLHDC7A BBOX1	3.42e-03	1019	43	6	EFO_0000305
Disease	Malignant neoplasm of breast	HOXA3 PIK3R4 KLHDC7A PER3 SPEN PGBD3	4.42e-03	1074	43	6	C0006142
Disease	nicotine dependence symptom count, depressive symptom measurement	IGF2BP2 VGLL3	5.38e-03	75	43	2	EFO_0007006, EFO_0009262
Disease	Mental Depression	TBX19 PER3 GRPR	6.03e-03	254	43	3	C0011570
Disease	sleep duration, low density lipoprotein cholesterol measurement	ATXN7L2 PKD1L3	7.82e-03	91	43	2	EFO_0004611, EFO_0005271
Disease	Depressive disorder	TBX19 PER3 GRPR	8.59e-03	289	43	3	C0011581

Protein segments in the cluster

Peptide	Gene	Start	Entry
CSGHIQDEHPQYHSP	ADAM29	16	Q9UKF5
GEHRHSYPGSHPAEP	ELFN1	701	P0C7U0
HVGCRPYSIPPCEHH	CTSB	176	P07858
PYSIPPCEHHVNGSR	CTSB	181	P07858
PHGPNPYSESFHHSE	CATSPER1	181	Q8NEC5
PVHPPALEQHPYEHC	AMPD2	296	Q01433
PAEGCHRHYLHPEEP	CAMSAP1	391	Q5T5Y3
TSDDLHPPPDCHYAT	ATXN7L2	391	Q5T6C5
FCGAEPPPHLVSSHH	MFRP	376	Q9BY79
PFCGHQIIPHTYGEH	OR52E1	166	Q8NGJ3
EPHPTYTDLTGHHPS	HOXA3	416	O43365
SACYHHQQGPGLTPP	KIF12	466	Q96FN5
GPFHVASPELHPLYH	B4GALT7	181	Q9UBV7
AYPPPHPNQAHHSLC	CCDC120	91	Q96HB5
HVHHPAQPELESEPC	PER3	236	P56645
HGGHELSHPFCYHPE	OR51T1	171	Q8NGJ9
AHPYCPLIEPHNTST	LMNTD1	341	Q8N9Z9
GHPHSHGTPHCYSAE	IL17C	26	Q9P0M4
GPFPHHHSYPEQEIV	IGF2BP2	416	Q9Y6M1
PGNHHHGPCDPHPTY	HOXD3	396	P31249
HGPCDPHPTYTDLSA	HOXD3	401	P31249
YNHPHQFCPPGSLLH	IQSEC3	1156	Q9UPP2
EASPPLNHIHGAPYC	PAPPA2	1101	Q9BXP8
CAPYPHSNELHPKIH	GRPR	196	P30550
QHHGPCEPHPTYTDL	HOXB3	396	P14651
FHTDYPALHHPPGVQ	BBOX1	201	O75936
GSHAEHDGVPYCHVP	CRIP3	161	Q6Q6R5
GHPSGPLSHHHCAYT	MARCHF4	366	Q9P2E8
HPGLGQLEPPHCHYV	KLHDC7A	196	Q5VTJ3
EACPAAHHHPTYEPK	CD164L2	106	Q6UWJ8
TPGGHAEHDGQPYCH	CRIP2	161	P52943
TYPCPPHFNHLGSDV	POLRMT	806	O00411
HVLSPEPDHDSLYHP	PRAP1	101	Q96NZ9
CHYLETHGHPPEPGQ	PGBD3	521	Q8N328
HARHQEYFSPPGDPC	KCP	676	Q6ZWJ8
GHLPTTCHYPLPAHL	PKD1L3	181	Q7Z443
GNEYPIHSTPNCHDH	ARHGAP5	1016	Q13017
PEYPELGEPAHNHHA	CNN1	276	P51911
NITGCPHPHIPSDHF	CNOT6L	516	Q96LI5
QPSPHSVHGIYCSPA	PIK3R4	1236	Q99570
ASQHPPEEEVHYHLP	SPEN	3151	Q96T58
VCYAGSLSPHHSPVP	NFATC3	281	Q12968
HQHIHPGEKPYSCGE	ZNF229	451	Q9UJW7
PCSPQYLTHPAHPAH	ZSWIM8	1516	A7E2V4
HLHLHFPDPSLQCPN	ZNF142	181	P52746
HHHPPAGSALDPSYG	VGLL3	246	A8MV65
PAPHTHHGCEHYSGL	TBX19	271	O60806
LHYPSCHRSHPNQPL	TTC31	471	Q49AM3
CHGRPPPQHFYNSEH	NAF1	386	Q96HR8