Coexpression cluster:C4542

Full id: C4542_Astrocyte_eye_caudate_Neural_amygdala_brain_hippocampus

Phase1 CAGE Peaks

Hg19::chr6:108487220..108487236,+	p2@NR2E1
Hg19::chr6:108487245..108487256,+	p3@NR2E1
Hg19::chr6:108487289..108487302,+	p1@NR2E1

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
astrocyte of the cerebral cortex	1.86e-11	3
neuronal stem cell	3.31e-10	8
neural cell	3.48e-10	25
oligodendrocyte	7.01e-08	7
macroglial cell	7.01e-08	7
astrocyte	7.01e-08	7
oligodendrocyte precursor cell	7.01e-08	7

Uber Anatomy

Ontology term	p-value	n
telencephalon	1.12e-93	34
regional part of forebrain	6.71e-92	41
forebrain	6.71e-92	41
anterior neural tube	6.71e-92	41
future forebrain	6.71e-92	41
cerebral hemisphere	3.28e-88	32
regional part of telencephalon	6.81e-88	32
brain grey matter	2.24e-82	34
gray matter	2.24e-82	34
central nervous system	7.16e-79	81
regional part of nervous system	2.42e-77	53
regional part of brain	2.42e-77	53
pre-chordal neural plate	4.42e-74	61
neural tube	9.75e-73	56
neural rod	9.75e-73	56
future spinal cord	9.75e-73	56
neural keel	9.75e-73	56
brain	4.14e-71	68
future brain	4.14e-71	68
nervous system	5.37e-70	89
cerebral cortex	1.55e-67	25
pallium	1.55e-67	25
neural plate	2.16e-58	82
presumptive neural plate	2.16e-58	82
regional part of cerebral cortex	1.03e-57	22
neurectoderm	3.30e-55	86
neocortex	1.20e-51	20
ecto-epithelium	6.99e-44	104
ectoderm-derived structure	2.59e-38	171
ectoderm	2.59e-38	171
presumptive ectoderm	2.59e-38	171
structure with developmental contribution from neural crest	3.24e-34	132
organ system subdivision	5.09e-29	223
basal ganglion	4.74e-27	9
nuclear complex of neuraxis	4.74e-27	9
aggregate regional part of brain	4.74e-27	9
collection of basal ganglia	4.74e-27	9
cerebral subcortex	4.74e-27	9
adult organism	5.72e-27	114
telencephalic nucleus	2.51e-21	7
gyrus	2.57e-19	6
parietal lobe	7.77e-17	5
anatomical cluster	9.21e-17	373
neural nucleus	2.35e-16	9
nucleus of brain	2.35e-16	9
limbic system	2.63e-16	5
temporal lobe	3.13e-16	6
tube	1.56e-15	192
corpus striatum	1.73e-13	4
striatum	1.73e-13	4
ventral part of telencephalon	1.73e-13	4
future corpus striatum	1.73e-13	4
organ part	2.02e-13	218
anatomical conduit	2.55e-11	240
epithelium	7.09e-11	306
frontal cortex	1.11e-10	3
cell layer	1.15e-10	309
multi-tissue structure	1.22e-10	342
caudate-putamen	1.27e-10	3
dorsal striatum	1.27e-10	3
occipital lobe	1.49e-10	5
caudate nucleus	7.11e-08	2
future caudate nucleus	7.11e-08	2
middle frontal gyrus	1.02e-07	2
Ammon's horn	1.06e-07	2
lobe parts of cerebral cortex	1.06e-07	2
hippocampal formation	1.06e-07	2
limbic lobe	1.06e-07	2
middle temporal gyrus	1.33e-07	2
amygdala	2.02e-07	2
dorsal plus ventral thalamus	2.61e-07	2
thalamic complex	2.61e-07	2
globus pallidus	5.37e-07	2
pallidum	5.37e-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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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.