Cluster composition

Functions

Category	Name	IntersectionWithQuery	PValue	GenesInTerm	GenesInQuery	GenesInTermInQuery	ID
GeneOntologyBiologicalProcess	positive regulation of DNA binding	HIPK2 POU4F2 NEUROD1	1.95e-05	52	21	3	GO:0043388
GeneOntologyBiologicalProcess	neural retina development	HIPK2 POU4F2 NEUROD1	1.46e-04	102	21	3	GO:0003407
GeneOntologyBiologicalProcess	amacrine cell differentiation	POU4F2 NEUROD1	1.50e-04	18	21	2	GO:0035881
GeneOntologyBiologicalProcess	positive regulation of transcription regulatory region DNA binding	POU4F2 NEUROD1	1.86e-04	20	21	2	GO:2000679
GeneOntologyBiologicalProcess	regulation of DNA binding	HIPK2 POU4F2 NEUROD1	2.09e-04	115	21	3	GO:0051101
GeneOntologyCellularComponent	chromatin	RFX7 JMJD1C POU4F2 SOX14 NEUROD1 FOXN3 EVX2	4.22e-04	1480	21	7	GO:0000785
Pubmed	Egr-1 and Hipk2 are required for the TrkA to p75(NTR) switch that occurs downstream of IGF1-R.	HIPK2 POU4F2	8.01e-06	7	22	2	18378044
Pubmed	Math5 defines the ganglion cell competence state in a subpopulation of retinal progenitor cells exiting the cell cycle.	POU4F2 NEUROD1	8.01e-06	7	22	2	22445509
Pubmed	Comparative expression analysis of POU4F1, POU4F2 and ISL1 in developing mouse cochleovestibular ganglion neurons.	POU4F2 NEUROD1	8.01e-06	7	22	2	24709358
Pubmed	Ptf1a determines horizontal and amacrine cell fates during mouse retinal development.	POU4F2 NEUROD1	1.37e-05	9	22	2	17075007
Pubmed	Beta-catenin controls differentiation of the retinal pigment epithelium in the mouse optic cup by regulating Mitf and Otx2 expression.	POU4F2 NEUROD1	1.37e-05	9	22	2	19553286
Pubmed	Reprogramming amacrine and photoreceptor progenitors into retinal ganglion cells by replacing Neurod1 with Atoh7.	POU4F2 NEUROD1	1.37e-05	9	22	2	23293286
Pubmed	A census of human transcription factors: function, expression and evolution.	RFX7 POU4F2 SOX14 NEUROD1 FOXN3 EVX2	1.62e-05	908	22	6	19274049
Pubmed	Regulation of Brn3b by DLX1 and DLX2 is required for retinal ganglion cell differentiation in the vertebrate retina.	POU4F2 NEUROD1	2.09e-05	11	22	2	28356311
Pubmed	RNF43 inhibits WNT5A-driven signaling and suppresses melanoma invasion and resistance to the targeted therapy.	XRN1 POM121C ATXN2 JMJD1C	2.10e-05	263	22	4	34702444
Pubmed	Brn3a-expressing retinal ganglion cells project specifically to thalamocortical and collicular visual pathways.	POU4F2 NEUROD1	2.51e-05	12	22	2	16354917
Pubmed	Math5 is required for both early retinal neuron differentiation and cell cycle progression.	POU4F2 NEUROD1	2.97e-05	13	22	2	16690048
Pubmed	Ikaros confers early temporal competence to mouse retinal progenitor cells.	POU4F2 NEUROD1	2.97e-05	13	22	2	18940586
Pubmed	Expression of the LIM-homeodomain protein Isl1 in the developing and mature mouse retina.	POU4F2 NEUROD1	3.46e-05	14	22	2	17480014
Pubmed	Precocious retinal neurons: Pax6 controls timing of differentiation and determination of cell type.	POU4F2 NEUROD1	3.46e-05	14	22	2	15733660
Pubmed	Integral bHLH factor regulation of cell cycle exit and RGC differentiation.	POU4F2 NEUROD1	3.99e-05	15	22	2	29770538
Pubmed	Induction of sonic hedgehog mediators by transforming growth factor-beta: Smad3-dependent activation of Gli2 and Gli1 expression in vitro and in vivo.	POU4F2 NEUROD1	4.56e-05	16	22	2	17638910
Pubmed	BARHL2 differentially regulates the development of retinal amacrine and ganglion neurons.	POU4F2 NEUROD1	4.56e-05	16	22	2	19339595
Pubmed	Math5 determines the competence state of retinal ganglion cell progenitors.	POU4F2 NEUROD1	5.16e-05	17	22	2	14623245
Pubmed	SOX2 is a dose-dependent regulator of retinal neural progenitor competence.	POU4F2 NEUROD1	6.49e-05	19	22	2	16651659
Pubmed	Altered visual function and interneuron survival in Atrx knockout mice: inference for the human syndrome.	POU4F2 NEUROD1	7.21e-05	20	22	2	19088125
Pubmed	ISL1 and POU4F1 Directly Interact to Regulate the Differentiation and Survival of Inner Ear Sensory Neurons.	POU4F2 NEUROD1	7.21e-05	20	22	2	38267260
Pubmed	Zac1 functions through TGFbetaII to negatively regulate cell number in the developing retina.	POU4F2 NEUROD1	7.96e-05	21	22	2	17559664
Pubmed	Sip1 regulates the generation of the inner nuclear layer retinal cell lineages in mammals.	POU4F2 NEUROD1	7.96e-05	21	22	2	27385012
Pubmed	Neuronal transcriptional repressor REST suppresses an Atoh7-independent program for initiating retinal ganglion cell development.	POU4F2 NEUROD1	7.96e-05	21	22	2	20969844
Pubmed	Sequential Role of SOXB2 Factors in GABAergic Neuron Specification of the Dorsal Midbrain.	SOX14 NEUROD1	7.96e-05	21	22	2	29867344
Pubmed	Multiple requirements for Hes 1 during early eye formation.	POU4F2 NEUROD1	8.76e-05	22	22	2	16038893
Pubmed	MATH5 controls the acquisition of multiple retinal cell fates.	POU4F2 NEUROD1	8.76e-05	22	22	2	21087508
Pubmed	A comprehensive negative regulatory program controlled by Brn3b to ensure ganglion cell specification from multipotential retinal precursors.	POU4F2 NEUROD1	9.59e-05	23	22	2	18367606
Pubmed	Requirement for Bhlhb5 in the specification of amacrine and cone bipolar subtypes in mouse retina.	POU4F2 NEUROD1	1.05e-04	24	22	2	17092954
Pubmed	GDF11 controls the timing of progenitor cell competence in developing retina.	POU4F2 NEUROD1	1.14e-04	25	22	2	15976303
Pubmed	Rewiring the retinal ganglion cell gene regulatory network: Neurod1 promotes retinal ganglion cell fate in the absence of Math5.	POU4F2 NEUROD1	1.23e-04	26	22	2	18787067
Pubmed	miR-124a is required for hippocampal axogenesis and retinal cone survival through Lhx2 suppression.	POU4F2 NEUROD1	1.23e-04	26	22	2	21857657
Pubmed	Forkhead box N4 (Foxn4) activates Dll4-Notch signaling to suppress photoreceptor cell fates of early retinal progenitors.	POU4F2 NEUROD1	1.33e-04	27	22	2	22323600
Pubmed	Rnf220 cooperates with Zc4h2 to specify spinal progenitor domains.	SOX14 EVX2	1.53e-04	29	22	2	30177510
Pubmed	An isoform of retinoid-related orphan receptor β directs differentiation of retinal amacrine and horizontal interneurons.	POU4F2 NEUROD1	1.53e-04	29	22	2	23652001
Pubmed	Transdifferentiation of the retina into pigmented cells in ocular retardation mice defines a new function of the homeodomain gene Chx10.	POU4F2 NEUROD1	1.64e-04	30	22	2	15459106
Pubmed	Polycomb repression complex 2 is required for the maintenance of retinal progenitor cells and balanced retinal differentiation.	POU4F2 NEUROD1	1.64e-04	30	22	2	29137925
Pubmed	Comparative Application of BioID and TurboID for Protein-Proximity Biotinylation.	XRN1 POM121C ATXN2 JMJD1C	1.78e-04	457	22	4	32344865
Pubmed	An inducible CRISPR/Cas9 screen identifies DTX2 as a transcriptional regulator of human telomerase.	RFX7 POM121C JMJD1C	1.95e-04	180	22	3	35198878
Pubmed	Prdm12 Directs Nociceptive Sensory Neuron Development by Regulating the Expression of the NGF Receptor TrkA.	NEUROD1 EVX2	1.99e-04	33	22	2	30917309
Pubmed	Blimp1 suppresses Chx10 expression in differentiating retinal photoreceptor precursors to ensure proper photoreceptor development.	POU4F2 NEUROD1	1.99e-04	33	22	2	20463215
Pubmed	Human transcription factor protein interaction networks.	RFX7 XRN1 POM121C HIPK2 ATXN2 JMJD1C	2.01e-04	1429	22	6	35140242
Pubmed	A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.	ATXN2 JMJD1C	2.12e-04	34	22	2	24026423
Pubmed	Histone Deacetylase 3 Governs Perinatal Cerebral Development via Neural Stem and Progenitor Cells.	JMJD1C NEUROD1	2.12e-04	34	22	2	31569049
Pubmed	Roles for Dicer1 in the patterning and differentiation of the optic cup neuroepithelium.	POU4F2 NEUROD1	2.12e-04	34	22	2	21138975
Pubmed	Spatial proteomics reveal that the protein phosphatase PTP1B interacts with and may modify tyrosine phosphorylation of the rhomboid protease RHBDL4.	XRN1 POM121C JMJD1C	2.32e-04	191	22	3	31177093
Pubmed	Prediction of the coding sequences of mouse homologues of KIAA gene: IV. 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.	POM121C ABLIM3 JMJD1C PDZRN3	2.38e-04	493	22	4	15368895
Pubmed	Phox2a Defines a Developmental Origin of the Anterolateral System in Mice and Humans.	PDZRN3 POU4F2	2.94e-04	40	22	2	33238113
Pubmed	RONIN Is an Essential Transcriptional Regulator of Genes Required for Mitochondrial Function in the Developing Retina.	POU4F2 NEUROD1	3.24e-04	42	22	2	26876175
Pubmed	Six3 and Six6 Are Jointly Required for the Maintenance of Multipotent Retinal Progenitors through Both Positive and Negative Regulation.	POU4F2 NEUROD1	3.24e-04	42	22	2	30485816
Pubmed	Onecut1 and Onecut2 redundantly regulate early retinal cell fates during development.	POU4F2 NEUROD1	3.40e-04	43	22	2	25228773
Pubmed	Impact of cytosine methylation on DNA binding specificities of human transcription factors.	RFX7 SOX14 NEUROD1 EVX2	3.46e-04	544	22	4	28473536
Pubmed	Two Pairs of ON and OFF Retinal Ganglion Cells Are Defined by Intersectional Patterns of Transcription Factor Expression.	POU4F2 SOX14	5.16e-04	53	22	2	27210758
Pubmed	A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB.	TENT4A FAT4	6.18e-04	58	22	2	19734545
Interaction	MIXL1 interactions	POU4F2 NEUROD1	5.66e-05	11	21	2	int:MIXL1
Interaction	F12 interactions	POM121C WDR81 ATXN2	6.79e-05	77	21	3	int:F12
Interaction	DYRK1B interactions	RFX7 POM121C HIPK2	1.12e-04	91	21	3	int:DYRK1B
Cytoband	Ensembl 112 genes in cytogenetic band chr2q31	NEUROD1 EVX2	3.28e-03	178	22	2	chr2q31
ToppCell	IPF-Stromal-Myofibroblast\|Stromal / Disease state, Lineage and Cell class	ABLIM3 PDZRN3 FAT4 FOXN3	2.45e-06	197	22	4	f304d42fc4936fe20996e07c8dccc698a6e5e5ef
ToppCell	ILEUM-non-inflamed-(3)_MNP-(3)_moDC\|(3)_MNP / shred on tissue, inflammation_status, cell class(v3), cell subclass (v2)	HIPK2 ATXN2 JMJD1C	3.90e-05	135	22	3	b7a792a7c0c22d8b703509f134115f0e394d7de0
ToppCell	TCGA-Bladder-Primary_Tumor-Urothelial_Carcinoma-Non-Papillary_Muscle_Invasive_Urothelial_Carcinoma-5\|TCGA-Bladder / Sample_Type by Project: Shred V9	POU4F2 SOX14 NEUROD1	7.61e-05	169	22	3	9c4e83fe8225d16173a103bf5a57b17d623be923
ToppCell	facs-Trachea-24m-Mesenchymal-fibroblast-fibroblast_of_trachea-\|24m / method, tissue, age, lineage, sublineage, cell ontologies, cell type and subtype	WDR81 ATXN2 IGSF11	8.44e-05	175	22	3	bb898796662b97f7459b7dda7cecf6a9bde8b055
ToppCell	Control-Endothelial-Endothelial\|Control / V2 postpublication: Rhesus Genome Updated; Treatment groups by lineage, cell_type_level1, cell_type_level2	HIPK2 FAT4 FOXN3	1.13e-04	193	22	3	aff0649c73c634bc6ff0dc7759b4693a9236bf05
ToppCell	Mesenchymal-matrix_fibroblast_1_cell\|World / Lineage, Cell type, age group and donor	ABLIM3 PDZRN3 FAT4	1.13e-04	193	22	3	acad568621ed677031797b8c2e34dafea798d681
ToppCell	Control-Endothelial\|Control / V2 postpublication: Rhesus Genome Updated; Treatment groups by lineage, cell_type_level1, cell_type_level2	HIPK2 FAT4 FOXN3	1.13e-04	193	22	3	c5f9fe03e64c211d4bcd4959e5b32f14841e336a
ToppCell	Fetal_29-31_weeks-Mesenchymal-matrix_fibroblast_1_cell\|Fetal_29-31_weeks / Lineage, Cell type, age group and donor	ABLIM3 PDZRN3 FAT4	1.14e-04	194	22	3	011e14d9ed1393275f892060e7708ffadcd0767f
ToppCell	COVID-19_Mild\|World / Disease group, lineage and cell class	XRN1 JMJD1C FOXN3	1.20e-04	197	22	3	5c33454b10023decd2f5ccda9229b6512659711e
ToppCell	PBMC-Mild\|PBMC / Location, Disease Group, Cell group, Cell class (2021.03.09)	XRN1 JMJD1C FOXN3	1.22e-04	198	22	3	44417089b62056269cac38d3134ff209c05b7007
ToppCell	PBMC-Mild\|PBMC / Location, Disease Group, Cell group, Cell class and sub_cluster (2021.03.01)	XRN1 JMJD1C FOXN3	1.22e-04	198	22	3	28ef3fc4c17dcb765537b75917f7db78baa522db
ToppCell	distal-mesenchymal-Myofibroblast-2\|distal / Location, Lineage, Cell class (ontology) and Donor from 10X sequencing (macrophage renamed)	P4HA3 PDZRN3 SOX14	1.22e-04	198	22	3	beef5075ba6dcd4d0a447bc4e57efcaf2e93c546
ToppCell	Fetal_29-31_weeks-Mesenchymal\|Fetal_29-31_weeks / Lineage, Cell type, age group and donor	ABLIM3 PDZRN3 FAT4	1.22e-04	198	22	3	21cf4d81386761d09d0f6829c01c198e5524176d
ToppCell	distal-2-mesenchymal-Myofibroblast\|2 / Location, Lineage, Cell class (ontology) and Donor from 10X sequencing (macrophage renamed)	P4HA3 PDZRN3 SOX14	1.23e-04	199	22	3	b8f3cf5bcfde1066bdb49b14fdc842fe9692a6b7
ToppCell	Mesenchymal\|World / Lineage, Cell type, age group and donor	ABLIM3 PDZRN3 FAT4	1.23e-04	199	22	3	4bac110c2b3609f6ee5d0e3275da0824a6240270
ToppCell	Tracheal-NucSeq-Stromal-Fibroblastic-Fibro_alveolar\|NucSeq / Cell types per location group and 10X technology with lineage, and cell group designations	ABLIM3 PDZRN3 FAT4	1.25e-04	200	22	3	3dd022e974fec7013ba18f333da63f58fbf2dd7c
Disease	coffee consumption measurement, tea consumption measurement	XRN1 ATXN2 JMJD1C	4.04e-06	44	21	3	EFO_0006781, EFO_0010091
Disease	C-X-C motif chemokine 11 measurement	ATXN2 JMJD1C	4.37e-05	14	21	2	EFO_0008057
Disease	lymphocyte measurement	RFX7 ATXN2 JMJD1C	7.67e-05	117	21	3	EFO_0803546
Disease	heart failure	POM121C ATXN2 FOXN3	2.97e-04	185	21	3	EFO_0003144
Disease	fibrinogen measurement, tissue plasminogen activator measurement	ATXN2 JMJD1C	4.69e-04	45	21	2	EFO_0004623, EFO_0004791
Disease	fibrinogen measurement, plasminogen activator inhibitor 1 measurement	ATXN2 JMJD1C	4.69e-04	45	21	2	EFO_0004623, EFO_0004792
Disease	electrocardiography	ABLIM3 JMJD1C PDZRN3 FOXN3	4.83e-04	530	21	4	EFO_0004327
Disease	triglycerides to total lipids in medium LDL percentage	TENT4A JMJD1C	5.79e-04	50	21	2	EFO_0022334
Disease	triglycerides to total lipids in large LDL percentage	TENT4A JMJD1C	6.02e-04	51	21	2	EFO_0022331
Disease	free cholesterol in large LDL measurement	ATXN2 JMJD1C	6.02e-04	51	21	2	EFO_0022176
Disease	Ischemic stroke, fibrinogen measurement	ATXN2 JMJD1C	7.00e-04	55	21	2	EFO_0004623, HP_0002140
Disease	free cholesterol to total lipids in medium VLDL percentage	ATXN2 JMJD1C	7.52e-04	57	21	2	EFO_0022284
Disease	cholesterol in IDL measurement	ATXN2 JMJD1C	7.78e-04	58	21	2	EFO_0021899
Disease	cholesterol to total lipids in IDL percentage	TENT4A JMJD1C	8.33e-04	60	21	2	EFO_0022233
Disease	total lipids in IDL	ATXN2 JMJD1C	8.33e-04	60	21	2	EFO_0022161
Disease	free cholesterol in IDL measurement	ATXN2 JMJD1C	8.61e-04	61	21	2	EFO_0022181
Disease	cholesteryl esters to total lipids in medium VLDL percentage	TENT4A JMJD1C	9.47e-04	64	21	2	EFO_0022253
Disease	sphingomyelin measurement	TENT4A ATXN2 JMJD1C	9.70e-04	278	21	3	EFO_0010118
Disease	juvenile idiopathic arthritis	ATXN2 JMJD1C	1.26e-03	74	21	2	EFO_0002609
Disease	free cholesterol to total lipids in large LDL percentage	TENT4A JMJD1C	1.26e-03	74	21	2	EFO_0022280
Disease	phospholipids:total lipids ratio, high density lipoprotein cholesterol measurement	POM121C ATXN2 JMJD1C	1.29e-03	307	21	3	EFO_0004612, EFO_0020946
Disease	waist-hip ratio	RFX7 XRN1 ABLIM3 ATXN2 JMJD1C	1.43e-03	1226	21	5	EFO_0004343
Disease	non-high density lipoprotein cholesterol measurement	XRN1 WDR81 ATXN2 FOXN3	1.46e-03	713	21	4	EFO_0005689
Disease	lipoprotein measurement, phospholipid measurement	TENT4A ATXN2	1.66e-03	85	21	2	EFO_0004639, EFO_0004732
Disease	intermediate density lipoprotein measurement	ATXN2 JMJD1C	1.74e-03	87	21	2	EFO_0008595
Disease	left ventricular structural measurement	ATXN2 PDZRN3	1.78e-03	88	21	2	EFO_0008205
Disease	cholesteryl ester measurement, intermediate density lipoprotein measurement	ATXN2 JMJD1C	2.03e-03	94	21	2	EFO_0008595, EFO_0010351
Disease	small vessel stroke	ATXN2 FAT4	2.11e-03	96	21	2	EFO_1001504
Disease	lipid measurement, intermediate density lipoprotein measurement	ATXN2 JMJD1C	2.11e-03	96	21	2	EFO_0004529, EFO_0008595

Protein segments in the cluster

Peptide	Gene	Start	Entry
TPTSYQAPKHFHIPA	ABLIM3	421	O94929
TGSLPYPFHSHVPLH	EVX2	271	Q03828
FQHHPYVTHIPSPTL	FAT4	2466	Q6V0I7
STPHKYPSVHPETRH	BTBD11	636	A6QL63
PSYHHSPYKHAHIPA	PDZRN3	861	Q9UPQ7
HYEPHFDHATSPSSP	P4HA3	436	Q7Z4N8
YSFPHNSPSHGTVHP	HIPK2	1071	Q9H2X6
ETSIKYVSHQHPSHP	FLCN	101	Q8NFG4
SHVQPAYTNPPHMAH	ATXN2	1231	Q99700
PFLSQHPFPLHSSSH	JMJD1C	731	Q15652
SPNPLSSPHLYHKQH	TENT4A	696	Q5XG87
STPPSQPTHRVHHFY	POM121C	161	A8CG34
QPTHRVHHFYPSLPT	POM121C	166	A8CG34
PRPPHTHSYTISHAT	IGSF11	396	Q5DX21
PPHSVKYTFPSTHHQ	NCOR1P1	21	Q9H4R4
QALKKTPYHPHPHVF	FOXN3	201	O00409
AHHHPTYEPKTVTTG	CD164L2	111	Q6UWJ8
QPLYAAPPHVIHHTT	FAM168B	106	A1KXE4
PHHSPFKPDATYHTM	POU4F2	131	Q12837
SVPVPGKPFHHTLYS	XRN1	1571	Q8IZH2
HFYHPIHSNGTPIHT	RFX7	836	Q2KHR2
HTHTHPSPTNPGYVV	SOX14	186	O95416
PTHHYKSASDPIHTF	WDR81	1861	Q562E7
SSHVFHVKPPPHAYS	NEUROD1	236	Q13562