Coexpression cluster:C1022

Full id: C1022_Ciliary_Lens_Astrocyte_Neural_Iris_retina_Hair

Phase1 CAGE Peaks

Hg19::chr12:97856211..97856221,+	p@chr12:97856211..97856221 +
Hg19::chr2:210798666..210798677,+	p@chr2:210798666..210798677 +
Hg19::chr2:45166478..45166502,-	p3@ENST00000437916
Hg19::chr2:45166504..45166533,-	p2@ENST00000437916
Hg19::chr3:173116225..173116242,+	p10@NLGN1
Hg19::chr3:8536114..8536125,-	p@chr3:8536114..8536125 -
Hg19::chr7:115723897..115723915,-	p@chr7:115723897..115723915 -
Hg19::chr7:115723925..115723935,-	p@chr7:115723925..115723935 -

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0016080	synaptic vesicle targeting	0.00459201695513952
GO:0042043	neurexin binding	0.00459201695513952
GO:0016079	synaptic vesicle exocytosis	0.00459201695513952
GO:0006903	vesicle targeting	0.00459201695513952
GO:0051650	establishment of vesicle localization	0.00459201695513952
GO:0051648	vesicle localization	0.00459201695513952
GO:0048489	synaptic vesicle transport	0.00542692912880125
GO:0051656	establishment of organelle localization	0.00542692912880125
GO:0016339	calcium-dependent cell-cell adhesion	0.00542692912880125
GO:0007416	synaptogenesis	0.00542692912880125
GO:0045664	regulation of neuron differentiation	0.00542692912880125
GO:0051640	organelle localization	0.00631402331331684
GO:0050808	synapse organization and biogenesis	0.00656002422162789
GO:0007269	neurotransmitter secretion	0.00656002422162789
GO:0045055	regulated secretory pathway	0.00811256328741317
GO:0003001	generation of a signal involved in cell-cell signaling	0.0100450370893677
GO:0001505	regulation of neurotransmitter levels	0.0105346271323789
GO:0043062	extracellular structure organization and biogenesis	0.0107147062286589
GO:0006887	exocytosis	0.0134135232110655
GO:0045595	regulation of cell differentiation	0.0162907268170426
GO:0045211	postsynaptic membrane	0.0162907268170426
GO:0044456	synapse part	0.0168026074949424
GO:0030182	neuron differentiation	0.0205790389471068
GO:0006605	protein targeting	0.0205790389471068
GO:0050793	regulation of developmental process	0.0205790389471068
GO:0045045	secretory pathway	0.0205790389471068
GO:0048699	generation of neurons	0.0205790389471068
GO:0022008	neurogenesis	0.0214840793258313
GO:0007268	synaptic transmission	0.0227304839279407
GO:0032940	secretion by cell	0.0227304839279407
GO:0007017	microtubule-based process	0.0233304087236927
GO:0019226	transmission of nerve impulse	0.0236775874249382
GO:0016337	cell-cell adhesion	0.0241428770217184
GO:0046903	secretion	0.0259313898643173
GO:0030054	cell junction	0.0281425039107837
GO:0006886	intracellular protein transport	0.0337385690176223
GO:0016192	vesicle-mediated transport	0.037604895605602
GO:0007267	cell-cell signaling	0.0386696164643328
GO:0007010	cytoskeleton organization and biogenesis	0.0403862004003297
GO:0007399	nervous system development	0.0410985517484988
GO:0015031	protein transport	0.0479666118900987
GO:0046907	intracellular transport	0.0479666118900987
GO:0045184	establishment of protein localization	0.0479666118900987
GO:0022610	biological adhesion	0.0479666118900987
GO:0007155	cell adhesion	0.0479666118900987
GO:0008104	protein localization	0.0479666118900987
GO:0033036	macromolecule localization	0.0494374591340553

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
oligodendrocyte	1.51e-09	7
macroglial cell	1.51e-09	7
astrocyte	1.51e-09	7
oligodendrocyte precursor cell	1.51e-09	7
neural cell	1.60e-09	25
neurectodermal cell	4.14e-09	59
neuronal stem cell	1.39e-07	8
ectodermal cell	2.57e-07	71
embryonic stem cell	3.88e-07	5

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	1.87e-29	94
nervous system	1.87e-29	94
central nervous system	4.51e-29	82
neurectoderm	4.50e-26	90
neural plate	8.68e-26	86
presumptive neural plate	8.68e-26	86
brain	2.33e-21	69
future brain	2.33e-21	69
regional part of brain	2.23e-20	59
neural tube	5.18e-20	57
neural rod	5.18e-20	57
future spinal cord	5.18e-20	57
neural keel	5.18e-20	57
ectoderm	4.04e-18	173
presumptive ectoderm	4.04e-18	173
ectoderm-derived structure	1.25e-17	169
anterior region of body	1.91e-17	129
craniocervical region	1.91e-17	129
head	8.21e-17	123
pre-chordal neural plate	6.91e-16	61
posterior neural tube	4.01e-15	15
chordal neural plate	4.01e-15	15
segmental subdivision of nervous system	8.00e-14	13
segmental subdivision of hindbrain	8.86e-13	12
hindbrain	8.86e-13	12
presumptive hindbrain	8.86e-13	12
pigment epithelium of eye	2.24e-12	11
regional part of metencephalon	1.55e-10	9
metencephalon	1.55e-10	9
future metencephalon	1.55e-10	9
visual system	3.19e-10	21
regional part of forebrain	1.40e-09	41
forebrain	1.40e-09	41
future forebrain	1.40e-09	41
eye	2.55e-09	20
anterior neural tube	3.43e-09	42
nucleus of brain	6.85e-09	9
neural nucleus	6.85e-09	9
cerebellum	1.59e-08	6
rhombic lip	1.59e-08	6
camera-type eye	2.24e-08	19
simple eye	2.24e-08	19
ocular region	2.24e-08	19
optic cup	2.24e-08	19
eye primordium	2.24e-08	19
optic vesicle	2.24e-08	19
sensory system	2.32e-08	24
entire sense organ system	2.32e-08	24
gray matter	4.78e-08	34
brain grey matter	4.78e-08	34
organism subdivision	7.37e-08	365
cell layer	1.35e-07	312
sense organ	1.48e-07	23
telencephalic nucleus	1.68e-07	7
regional part of telencephalon	1.78e-07	33
epithelium	3.12e-07	309
face	3.22e-07	21
basal ganglion	3.28e-07	9
nuclear complex of neuraxis	3.28e-07	9
aggregate regional part of brain	3.28e-07	9
collection of basal ganglia	3.28e-07	9
cerebral subcortex	3.28e-07	9
telencephalon	4.11e-07	34
retina	6.89e-07	5
photoreceptor array	6.89e-07	5
posterior segment of eyeball	6.89e-07	5
vasculature of head	8.79e-07	11
vasculature of organ	8.79e-07	11
atypical epithelium	9.80e-07	4

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.