Coexpression cluster:C369

Full id: C369_Lens_eye_Ciliary_retina_H9_Retinal_Renal

Phase1 CAGE Peaks

Hg19::chr11:31671561..31671580,+	p@chr11:31671561..31671580 +
Hg19::chr13:104778247..104778293,+	p@chr13:104778247..104778293 +
Hg19::chr13:36052713..36052724,-	p@chr13:36052713..36052724 -
Hg19::chr15:79501729..79501736,+	p1@MIR184
Hg19::chr15:95888661..95888665,+	p@chr15:95888661..95888665 +
Hg19::chr19:40920692..40920700,-	p@chr19:40920692..40920700 -
Hg19::chr19:51891222..51891233,-	p1@LIM2
Hg19::chr1:147374915..147374932,+	p1@GJA8
Hg19::chr20:35861148..35861151,+	p@chr20:35861148..35861151 +
Hg19::chr22:25595823..25595826,+	p1@CRYBB3
Hg19::chr22:25615541..25615544,+	p2@CRYBB2
Hg19::chr2:45162900..45162914,-	p1@ENST00000432125
Hg19::chr2:45162929..45162943,-	p2@ENST00000432125
Hg19::chr2:45166428..45166437,-	p4@ENST00000437916
Hg19::chr2:63196015..63196016,+	p@chr2:63196015..63196016 +
Hg19::chr2:66670833..66670853,+	p@chr2:66670833..66670853 +
Hg19::chr3:150690508..150690520,-	p1@CLRN1
Hg19::chr3:150690540..150690556,-	p2@CLRN1
Hg19::chr3:150690809..150690822,-	p3@CLRN1
Hg19::chr3:62358596..62358618,-	p3@FEZF2
Hg19::chr3:62358748..62358751,-	p7@FEZF2
Hg19::chr3:98705008..98705016,-	p@chr3:98705008..98705016 -
Hg19::chr3:98705040..98705081,-	p@chr3:98705040..98705081 -
Hg19::chr4:8873531..8873542,-	p4@HMX1
Hg19::chr4:8873545..8873583,-	p1@HMX1
Hg19::chr6:80543084..80543091,-	p@chr6:80543084..80543091 -
Hg19::chr8:123875589..123875604,+	p24@ZHX2
Hg19::chr8:123875629..123875640,+	p21@ZHX2
Hg19::chr8:36807609..36807626,-	p@chr8:36807609..36807626 -
Hg19::chr9:75848662..75848671,-	p@chr9:75848662..75848671 -

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:0005212	structural constituent of eye lens	1.27415068449798e-06
GO:0007601	visual perception	4.62678414592927e-06
GO:0050953	sensory perception of light stimulus	4.62678414592927e-06
GO:0007600	sensory perception	0.0010352899857421
GO:0032501	multicellular organismal process	0.0010352899857421
GO:0050877	neurological system process	0.0022444358804151
GO:0003008	system process	0.00405747896702666
GO:0050957	equilibrioception	0.0263556467090979
GO:0007043	intercellular junction assembly	0.0364949867660109
GO:0045494	photoreceptor cell maintenance	0.0364949867660109
GO:0050885	neuromuscular process controlling balance	0.0364949867660109
GO:0045216	intercellular junction assembly and maintenance	0.0364949867660109
GO:0030054	cell junction	0.0364949867660109
GO:0050905	neuromuscular process	0.0420995890852978
GO:0007028	cytoplasm organization and biogenesis	0.0420995890852978
GO:0005922	connexon complex	0.0448624819908534
GO:0006402	mRNA catabolic process	0.0448624819908534
GO:0005921	gap junction	0.0470365975887916
GO:0043010	camera-type eye development	0.0470365975887916

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
ciliated cell	9.82e-67	3
ciliated epithelial cell	9.82e-67	3
multi-ciliated epithelial cell	9.82e-67	3
non-pigmented ciliary epithelial cell	9.82e-67	3
columnar/cuboidal epithelial cell	2.19e-29	27
pigment cell (sensu Vertebrata)	4.10e-23	1
iris pigment epithelial cell	4.10e-23	1
crystallin accumulating cell	5.75e-23	4
vertebrate lens cell	5.75e-23	4
lens epithelial cell	5.75e-23	4
neurecto-epithelial cell	4.07e-18	20
ecto-epithelial cell	7.76e-11	34
pigment cell	3.24e-07	14

Uber Anatomy

Ontology term	p-value	n
atypical epithelium	5.61e-88	4
pigment epithelium of eye	1.20e-71	11
ciliary epithelium	9.82e-67	3
ciliary body	9.82e-67	3
eye	2.15e-66	21
visual system	2.15e-66	21
vasculature of eye	6.44e-59	6
uvea	6.44e-59	6
vasculature of head	6.44e-59	6
sense organ	4.06e-58	24
sensory system	4.06e-58	24
entire sense organ system	4.06e-58	24
anterior segment of eyeball	2.24e-56	14
camera-type eye	1.74e-53	20
simple eye	1.74e-53	20
immature eye	1.74e-53	20
ocular region	1.74e-53	20
eyeball of camera-type eye	1.74e-53	20
optic cup	1.74e-53	20
optic vesicle	1.74e-53	20
eye primordium	1.74e-53	20
face	1.22e-48	22
ectodermal placode	1.45e-34	31
vasculature of organ	1.90e-32	11
iris epithelium	4.10e-23	1
iris	4.10e-23	1
cuboidal epithelium	5.75e-23	4
transparent eye structure	5.75e-23	4
simple cuboidal epithelium	5.75e-23	4
cranial placode	5.75e-23	4
lens of camera-type eye	5.75e-23	4
epithelium of lens	5.75e-23	4
lens placode	5.75e-23	4
lens vesicle	5.75e-23	4
subdivision of head	6.84e-22	49
head	3.73e-19	56
anterior region of body	2.68e-17	62
craniocervical region	2.68e-17	62
pre-chordal neural plate	2.68e-17	61
neural plate	6.68e-13	82
presumptive neural plate	6.68e-13	82
neurectoderm	2.65e-12	86
external ectoderm	5.22e-12	8
organ segment	6.62e-11	98
ecto-epithelium	3.62e-10	104
structure with developmental contribution from neural crest	5.53e-08	132

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	3	6.27170003393281	0.0119266470001682	0.0433903607500111
SUZ12#23512	4	6.68210412147505	0.00286620885512734	0.0155317795164554

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.