Coexpression cluster:C573

Full id: C573_Lens_small_retina_Ciliary_Retinal_eye_putamen

Phase1 CAGE Peaks

Hg19::chr2:45165994..45166012,-	p1@ENST00000444871
Hg19::chr2:45166274..45166281,-	p5@ENST00000437916
Hg19::chr2:45166354..45166379,-	p1@ENST00000437916
Hg19::chr2:45168617..45168631,-	p1@ENST00000456467
Hg19::chr2:45168834..45168847,+	p2@SIX3
Hg19::chr2:45168856..45168867,+	p7@SIX3
Hg19::chr2:45168875..45168916,+	p1@SIX3
Hg19::chr2:45169039..45169058,-	p1@ENST00000419364
Hg19::chr2:45169143..45169167,+	p5@SIX3
Hg19::chr2:45169172..45169177,+	p11@SIX3
Hg19::chr2:45169179..45169190,+	p8@SIX3
Hg19::chr2:45169193..45169219,+	p3@SIX3
Hg19::chr2:45169233..45169244,+	p10@SIX3
Hg19::chr2:45169905..45169915,+	p@chr2:45169905..45169915 +
Hg19::chr2:45171888..45171968,+	p@chr2:45171888..45171968 +
Hg19::chr8:99076582..99076599,+	p6@C8orf47

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:0030178	negative regulation of Wnt receptor signaling pathway	0.0165135994348287
GO:0030111	regulation of Wnt receptor signaling pathway	0.0165135994348287
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0165135994348287
GO:0043010	camera-type eye development	0.0165135994348287
GO:0001654	eye development	0.0182620981985164
GO:0007423	sensory organ development	0.027846461792064
GO:0009968	negative regulation of signal transduction	0.0288641065751627
GO:0007420	brain development	0.0313002865104596
GO:0016055	Wnt receptor signaling pathway	0.0313002865104596
GO:0016564	transcription repressor activity	0.0351194196125316
GO:0007601	visual perception	0.0351194196125316
GO:0050953	sensory perception of light stimulus	0.0351194196125316
GO:0007417	central nervous system development	0.0351194196125316
GO:0003702	RNA polymerase II transcription factor activity	0.0376898622394913
GO:0016481	negative regulation of transcription	0.0376898622394913
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0387341045566937
GO:0031324	negative regulation of cellular metabolic process	0.0435410476447732
GO:0009892	negative regulation of metabolic process	0.0470583617881392

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
neurectoderm	6.65e-29	90
regional part of nervous system	1.12e-28	94
nervous system	1.12e-28	94
neural plate	1.22e-27	86
presumptive neural plate	1.22e-27	86
pre-chordal neural plate	6.58e-25	61
central nervous system	9.45e-23	82
regional part of brain	9.36e-21	59
neural tube	3.54e-20	57
neural rod	3.54e-20	57
future spinal cord	3.54e-20	57
neural keel	3.54e-20	57
brain	1.35e-19	69
future brain	1.35e-19	69
regional part of forebrain	2.91e-19	41
forebrain	2.91e-19	41
future forebrain	2.91e-19	41
ectoderm	1.32e-18	173
presumptive ectoderm	1.32e-18	173
anterior neural tube	1.81e-18	42
ectoderm-derived structure	1.65e-17	169
gray matter	2.57e-14	34
brain grey matter	2.57e-14	34
telencephalon	3.49e-14	34
regional part of telencephalon	5.44e-14	33
head	7.16e-14	123
anterior region of body	3.48e-13	129
craniocervical region	3.48e-13	129
cerebral hemisphere	5.28e-13	32
pigment epithelium of eye	8.25e-12	11
adult organism	4.63e-11	115
visual system	5.78e-09	21
basal ganglion	1.02e-08	9
nuclear complex of neuraxis	1.02e-08	9
aggregate regional part of brain	1.02e-08	9
collection of basal ganglia	1.02e-08	9
cerebral subcortex	1.02e-08	9
eye	2.16e-08	20
cerebral cortex	2.40e-08	25
pallium	2.40e-08	25
nucleus of brain	2.71e-08	9
neural nucleus	2.71e-08	9
sensory system	5.45e-08	24
entire sense organ system	5.45e-08	24
camera-type eye	1.36e-07	19
simple eye	1.36e-07	19
ocular region	1.36e-07	19
optic cup	1.36e-07	19
eye primordium	1.36e-07	19
optic vesicle	1.36e-07	19
sense organ	1.89e-07	23
telencephalic nucleus	2.18e-07	7
diencephalon	5.44e-07	7
future diencephalon	5.44e-07	7

Disease

Ontology term	p-value	n
cell type cancer	1.02e-12	143
carcinoma	1.41e-09	106

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.