Coexpression cluster:C789

Full id: C789_retina_Retinal_medulla_stomach_lung_eye_corpus

Phase1 CAGE Peaks

Hg19::chr11:109990513..109990520,-	p@chr11:109990513..109990520 -
Hg19::chr11:61522820..61522823,+	p9@C11orf9
Hg19::chr11:61522844..61522875,+	p2@C11orf9
Hg19::chr13:99135322..99135327,-	p@chr13:99135322..99135327 -
Hg19::chr14:87636652..87636657,-	p@chr14:87636652..87636657 -
Hg19::chr21:36041264..36041274,+	p3@CLIC6
Hg19::chr21:36041275..36041282,+	p5@CLIC6
Hg19::chr21:36041286..36041333,+	p1@CLIC6
Hg19::chr5:70308745..70308754,-	p@chr5:70308745..70308754 -
Hg19::chr9:140088882..140088898,-	p@chr9:140088882..140088898 -

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:0005247	voltage-gated chloride channel activity	0.0445095728958841
GO:0022844	voltage-gated anion channel activity	0.0445095728958841
GO:0043168	anion binding	0.0445095728958841
GO:0031404	chloride ion binding	0.0445095728958841
GO:0005254	chloride channel activity	0.0445095728958841
GO:0006821	chloride transport	0.0445095728958841
GO:0005253	anion channel activity	0.0445095728958841

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
retinal pigment epithelial cell	8.77e-27	3
visual pigment cell	3.00e-20	4
pigment cell	4.09e-10	14

Uber Anatomy

Ontology term	p-value	n
neural plate	5.02e-33	82
presumptive neural plate	5.02e-33	82
neurectoderm	2.30e-31	86
pigmented layer of retina	8.77e-27	3
presumptive retinal pigmented epithelium	8.77e-27	3
neural tube	7.91e-26	56
neural rod	7.91e-26	56
future spinal cord	7.91e-26	56
neural keel	7.91e-26	56
ecto-epithelium	1.90e-25	104
retina	1.73e-23	6
photoreceptor array	1.73e-23	6
posterior segment of eyeball	1.73e-23	6
regional part of nervous system	1.76e-23	53
regional part of brain	1.76e-23	53
brainstem	7.54e-23	6
adult organism	2.05e-20	114
pre-chordal neural plate	2.33e-20	61
layer of retina	3.00e-20	4
central nervous system	1.08e-19	81
structure with developmental contribution from neural crest	2.03e-19	132
brain	1.30e-17	68
future brain	1.30e-17	68
telencephalon	1.61e-17	34
nervous system	1.64e-17	89
ectoderm-derived structure	7.46e-16	171
ectoderm	7.46e-16	171
presumptive ectoderm	7.46e-16	171
regional part of forebrain	2.16e-14	41
forebrain	2.16e-14	41
anterior neural tube	2.16e-14	41
future forebrain	2.16e-14	41
posterior neural tube	5.80e-14	15
chordal neural plate	5.80e-14	15
brain grey matter	7.98e-14	34
gray matter	7.98e-14	34
medulla oblongata	2.03e-12	3
myelencephalon	2.03e-12	3
future myelencephalon	2.03e-12	3
regional part of cerebral cortex	3.47e-12	22
pons	3.57e-12	3
segmental subdivision of hindbrain	1.55e-11	12
hindbrain	1.55e-11	12
presumptive hindbrain	1.55e-11	12
regional part of telencephalon	2.89e-11	32
cerebral hemisphere	2.94e-11	32
cerebral cortex	9.90e-11	25
pallium	9.90e-11	25
segmental subdivision of nervous system	1.16e-10	13
eye	3.26e-10	21
visual system	3.26e-10	21
corpus callosum	6.31e-10	1
central nervous system cell part cluster	6.31e-10	1
axon tract	6.31e-10	1
intercerebral commissure	6.31e-10	1
dorsal telencephalic commissure	6.31e-10	1
brain white matter	6.31e-10	1
brain commissure	6.31e-10	1
white matter	6.31e-10	1
nervous system commissure	6.31e-10	1
cerebral hemisphere white matter	6.31e-10	1
pulmonary valve	8.91e-10	1
semi-lunar valve	8.91e-10	1
epididymis	1.25e-09	1
substantia nigra	1.36e-09	1
midbrain nucleus	1.36e-09	1
regional part of midbrain	1.36e-09	1
midbrain	1.36e-09	1
presumptive midbrain	1.36e-09	1
midbrain neural tube	1.36e-09	1
paracentral gyrus	1.48e-09	1
neocortex	1.83e-09	20
occipital pole	1.91e-09	1
pole of cerebral hemisphere	1.91e-09	1
insula	2.67e-09	1
sense organ	6.54e-09	24
sensory system	6.54e-09	24
entire sense organ system	6.54e-09	24
tube	4.04e-08	192
organ part	5.24e-08	218
pigment epithelium of eye	1.09e-07	11
epithelium	1.77e-07	306
cell layer	2.26e-07	309
camera-type eye	3.73e-07	20
simple eye	3.73e-07	20
immature eye	3.73e-07	20
ocular region	3.73e-07	20
eyeball of camera-type eye	3.73e-07	20
optic cup	3.73e-07	20
optic vesicle	3.73e-07	20
eye primordium	3.73e-07	20

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)
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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.