Coexpression cluster:C2556

Full id: C2556_Fibroblast_corpus_medulla_gastrointestinal_occipital_temporal_cerebellum

Phase1 CAGE Peaks

Hg19::chr1:204797749..204797855,+	p1@NFASC
Hg19::chr1:240255166..240255197,+	p1@FMN2
Hg19::chr1:240255198..240255211,+	p3@FMN2
Hg19::chr1:240255217..240255249,+	p2@FMN2

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
fibroblast	1.43e-16	76
skin fibroblast	2.31e-11	23
non-terminally differentiated cell	1.33e-09	106
neurectodermal cell	1.91e-08	59
neural cell	2.17e-07	25

Uber Anatomy

Ontology term	p-value	n
nervous system	7.38e-38	89
central nervous system	2.06e-36	81
neural tube	2.72e-34	56
neural rod	2.72e-34	56
future spinal cord	2.72e-34	56
neural keel	2.72e-34	56
neural plate	6.49e-33	82
presumptive neural plate	6.49e-33	82
regional part of nervous system	2.63e-32	53
regional part of brain	2.63e-32	53
brain	2.67e-31	68
future brain	2.67e-31	68
neurectoderm	1.37e-29	86
ectoderm-derived structure	2.52e-29	171
ectoderm	2.52e-29	171
presumptive ectoderm	2.52e-29	171
structure with developmental contribution from neural crest	3.60e-29	132
ecto-epithelium	1.65e-28	104
regional part of forebrain	6.17e-26	41
forebrain	6.17e-26	41
anterior neural tube	6.17e-26	41
future forebrain	6.17e-26	41
pre-chordal neural plate	3.01e-24	61
brain grey matter	4.21e-22	34
gray matter	4.21e-22	34
telencephalon	4.82e-22	34
cerebral hemisphere	6.10e-21	32
regional part of telencephalon	8.47e-21	32
adult organism	2.08e-17	114
cerebral cortex	1.28e-16	25
pallium	1.28e-16	25
multi-tissue structure	2.65e-16	342
regional part of cerebral cortex	6.26e-16	22
anatomical cluster	4.85e-15	373
organ system subdivision	5.34e-15	223
epithelium	5.42e-15	306
cell layer	1.35e-14	309
neocortex	1.37e-14	20
multi-cellular organism	3.23e-12	656
anatomical system	5.99e-11	624
anatomical group	9.65e-11	625
tube	1.29e-10	192
skin of body	4.36e-10	41
integument	7.25e-10	46
integumental system	7.25e-10	46
anatomical conduit	1.44e-09	240
organ part	1.77e-09	218
posterior neural tube	2.11e-09	15
chordal neural plate	2.11e-09	15
dense mesenchyme tissue	8.31e-08	73
segmental subdivision of nervous system	1.09e-07	13
segmental subdivision of hindbrain	1.46e-07	12
hindbrain	1.46e-07	12
presumptive hindbrain	1.46e-07	12
organ	1.70e-07	503
paraxial mesoderm	1.99e-07	72
presumptive paraxial mesoderm	1.99e-07	72
surface structure	3.78e-07	99
somite	5.10e-07	71
presomitic mesoderm	5.10e-07	71
presumptive segmental plate	5.10e-07	71
dermomyotome	5.10e-07	71
trunk paraxial mesoderm	5.10e-07	71
embryo	5.43e-07	592
basal ganglion	5.99e-07	9
nuclear complex of neuraxis	5.99e-07	9
aggregate regional part of brain	5.99e-07	9
collection of basal ganglia	5.99e-07	9
cerebral subcortex	5.99e-07	9
neural nucleus	6.20e-07	9
nucleus of brain	6.20e-07	9

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.