Coexpression cluster:C1736

Full id: C1736_retinoblastoma_eye_pituitary_Wilms_pineal_small_retina

Phase1 CAGE Peaks

Hg19::chr15:35043922..35043932,-	p@chr15:35043922..35043932 -
Hg19::chr15:35044153..35044155,-	p@chr15:35044153..35044155 -
Hg19::chr15:35047190..35047204,-	p1@GJD2
Hg19::chr19:48343614..48343629,+	p2@CRX
Hg19::chr19:48344846..48344850,+	p@chr19:48344846..48344850 +

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:0046534	positive regulation of photoreceptor cell differentiation	0.00113328623572354
GO:0046532	regulation of photoreceptor cell differentiation	0.00113328623572354
GO:0046530	photoreceptor cell differentiation	0.00755524157149024
GO:0007623	circadian rhythm	0.0164326504179913
GO:0045597	positive regulation of cell differentiation	0.0213057812316025
GO:0051094	positive regulation of developmental process	0.0256878213430668
GO:0003682	chromatin binding	0.0362651595431532
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0362651595431532
GO:0045595	regulation of cell differentiation	0.0362651595431532
GO:0005667	transcription factor complex	0.0382079359472507
GO:0007601	visual perception	0.0382079359472507
GO:0050953	sensory perception of light stimulus	0.0382079359472507
GO:0045893	positive regulation of transcription, DNA-dependent	0.0382079359472507
GO:0050793	regulation of developmental process	0.0382079359472507
GO:0045941	positive regulation of transcription	0.0409399652655128
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0409399652655128
GO:0009887	organ morphogenesis	0.0459610528932323
GO:0031325	positive regulation of cellular metabolic process	0.0459610528932323
GO:0009893	positive regulation of metabolic process	0.0466436755966214
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0479380077711056
GO:0044451	nucleoplasm part	0.048785274147337

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
neuronal stem cell	1.19e-07	8

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	1.95e-61	94
nervous system	1.95e-61	94
central nervous system	1.80e-56	82
neural tube	5.83e-52	57
neural rod	5.83e-52	57
future spinal cord	5.83e-52	57
neural keel	5.83e-52	57
neural plate	2.67e-51	86
presumptive neural plate	2.67e-51	86
neurectoderm	4.34e-48	90
brain	2.63e-46	69
future brain	2.63e-46	69
regional part of brain	2.78e-45	59
regional part of forebrain	9.06e-43	41
forebrain	9.06e-43	41
future forebrain	9.06e-43	41
anterior neural tube	1.88e-41	42
pre-chordal neural plate	5.75e-39	61
adult organism	1.67e-37	115
ectoderm-derived structure	2.31e-35	169
ectoderm	5.68e-34	173
presumptive ectoderm	5.68e-34	173
gray matter	1.33e-33	34
brain grey matter	1.33e-33	34
telencephalon	1.66e-33	34
regional part of telencephalon	3.88e-32	33
cerebral hemisphere	1.08e-31	32
head	1.29e-29	123
anterior region of body	1.98e-29	129
craniocervical region	1.98e-29	129
neocortex	5.84e-28	20
regional part of cerebral cortex	2.34e-27	22
cerebral cortex	2.61e-23	25
pallium	2.61e-23	25
tube	1.64e-13	194
nucleus of brain	8.36e-12	9
neural nucleus	8.36e-12	9
segmental subdivision of nervous system	1.07e-11	13
basal ganglion	1.16e-11	9
nuclear complex of neuraxis	1.16e-11	9
aggregate regional part of brain	1.16e-11	9
collection of basal ganglia	1.16e-11	9
cerebral subcortex	1.16e-11	9
temporal lobe	1.27e-11	7
posterior neural tube	1.88e-11	15
chordal neural plate	1.88e-11	15
organ part	2.62e-11	219
diencephalon	9.59e-11	7
future diencephalon	9.59e-11	7
segmental subdivision of hindbrain	1.73e-10	12
hindbrain	1.73e-10	12
presumptive hindbrain	1.73e-10	12
epithelium	1.77e-10	309
cell layer	3.57e-10	312
telencephalic nucleus	2.30e-09	7
regional part of metencephalon	2.77e-09	9
metencephalon	2.77e-09	9
future metencephalon	2.77e-09	9
gyrus	3.13e-09	6
anatomical conduit	1.79e-08	241
organism subdivision	3.61e-08	365
parietal lobe	6.01e-08	5
retina	6.46e-08	5
photoreceptor array	6.46e-08	5
posterior segment of eyeball	6.46e-08	5
occipital lobe	8.87e-08	5
gland of diencephalon	9.89e-08	4
neuroendocrine gland	9.89e-08	4
anatomical cluster	7.31e-07	286

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.