Coexpression cluster:C1726

Full id: C1726_acute_Lens_pituitary_Ciliary_eye_H9_retina

Phase1 CAGE Peaks

Hg19::chr14:60975644..60975673,+	p3@SIX6
Hg19::chr14:60975858..60975869,+	p2@SIX6
Hg19::chr14:60975871..60975880,+	p4@SIX6
Hg19::chr14:60975883..60975911,+	p1@SIX6
Hg19::chr14:60975914..60975925,+	p5@SIX6

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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No GOStat results

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
embryonic stem cell	8.80e-16	5
ciliated cell	5.63e-11	3
multi-ciliated epithelial cell	5.63e-11	3
ciliated epithelial cell	5.63e-11	3
non-pigmented ciliary epithelial cell	5.63e-11	3
columnar/cuboidal epithelial cell	2.26e-08	27
crystallin accumulating cell	2.93e-08	4
vertebrate lens cell	2.93e-08	4
lens epithelial cell	2.93e-08	4

Uber Anatomy

Ontology term	p-value	n
visual system	5.50e-20	21
pigment epithelium of eye	3.24e-18	11
eye	1.13e-17	20
sensory system	4.09e-17	24
entire sense organ system	4.09e-17	24
camera-type eye	2.32e-15	19
simple eye	2.32e-15	19
ocular region	2.32e-15	19
optic cup	2.32e-15	19
eye primordium	2.32e-15	19
optic vesicle	2.32e-15	19
sense organ	5.02e-15	23
atypical epithelium	6.16e-14	4
face	1.10e-13	21
pre-chordal neural plate	2.24e-13	61
ciliary epithelium	5.63e-11	3
ciliary body	5.63e-11	3
anterior segment of eyeball	6.09e-11	14
neural plate	2.23e-10	86
presumptive neural plate	2.23e-10	86
neurectoderm	1.07e-09	90
ectoderm-derived structure	2.47e-09	169
ectodermal placode	2.65e-09	29
vasculature of eye	2.87e-09	6
uvea	2.87e-09	6
ectoderm	5.92e-09	173
presumptive ectoderm	5.92e-09	173
regional part of nervous system	1.68e-08	94
nervous system	1.68e-08	94
cuboidal epithelium	2.93e-08	4
transparent eye structure	2.93e-08	4
simple cuboidal epithelium	2.93e-08	4
cranial placode	2.93e-08	4
lens of camera-type eye	2.93e-08	4
epithelium of lens	2.93e-08	4
lens placode	2.93e-08	4
lens vesicle	2.93e-08	4
gland of diencephalon	4.18e-08	4
neuroendocrine gland	4.18e-08	4
pituitary gland	6.69e-08	2
vasculature of head	2.40e-07	11
vasculature of organ	2.40e-07	11
meninx	5.67e-07	2
membrane organ	5.67e-07	2
future meninx	5.67e-07	2
multi cell component structure	6.21e-07	2
neuron projection bundle	6.21e-07	2
globus pallidus	7.22e-07	2
pallidum	7.22e-07	2

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CTBP2#1488	5	62.7170003393281	1.02712351233917e-09	9.50990713698493e-08
CTCF#10664	4	4.28820509846002	0.00515201558824328	0.0239323647209242
REST#5978	5	9.65002871612802	1.19441074361324e-05	0.000301457379536546
SIN3A#25942	5	5.40888472681514	0.000215952267165727	0.00247926116637588
SUZ12#23512	5	50.1157809110629	3.15480790456198e-09	2.61911750989308e-07

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.