Coexpression cluster:C2346

Full id: C2346_optic_testis_brain_medulla_spinal_duodenum_caudate

Phase1 CAGE Peaks

Hg19::chr15:69278159..69278160,+	p@chr15:69278159..69278160 +
Hg19::chr18:74692220..74692236,+	p@chr18:74692220..74692236 +
Hg19::chr6:52268150..52268166,+	p6@PAQR8
Hg19::chr8:22411901..22411915,+	p45@SORBS3

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:0051496	positive regulation of stress fiber formation	0.00553339899145803
GO:0051495	positive regulation of cytoskeleton organization and biogenesis	0.00553339899145803
GO:0032233	positive regulation of actin filament bundle formation	0.00553339899145803
GO:0017166	vinculin binding	0.00553339899145803
GO:0032231	regulation of actin filament bundle formation	0.00553339899145803
GO:0051492	regulation of stress fiber formation	0.00553339899145803
GO:0043149	stress fiber formation	0.00553339899145803
GO:0043410	positive regulation of MAPKKK cascade	0.00553339899145803
GO:0051130	positive regulation of cellular component organization and biogenesis	0.00829924324777567
GO:0043408	regulation of MAPKKK cascade	0.00829924324777567
GO:0051017	actin filament bundle formation	0.00955614159098618
GO:0005925	focal adhesion	0.0151172769961849
GO:0005924	cell-substrate adherens junction	0.0151172769961849
GO:0030055	cell-matrix junction	0.0151172769961849
GO:0007015	actin filament organization	0.0151172769961849
GO:0005912	adherens junction	0.0172028556795746
GO:0051493	regulation of cytoskeleton organization and biogenesis	0.0172028556795746
GO:0033043	regulation of organelle organization and biogenesis	0.0172028556795746
GO:0005200	structural constituent of cytoskeleton	0.0223717054781359
GO:0005496	steroid binding	0.0223717054781359
GO:0016323	basolateral plasma membrane	0.0223717054781359
GO:0051128	regulation of cellular component organization and biogenesis	0.0247453519321812
GO:0031589	cell-substrate adhesion	0.0247453519321812
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0292296123884345
GO:0000165	MAPKKK cascade	0.0324924248843825
GO:0009967	positive regulation of signal transduction	0.0324924248843825
GO:0045892	negative regulation of transcription, DNA-dependent	0.0414835460253769
GO:0005886	plasma membrane	0.0423490121090567
GO:0030036	actin cytoskeleton organization and biogenesis	0.0469634907591985
GO:0030029	actin filament-based process	0.0477782347950747

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><br>

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Uber Anatomy

Ontology term	p-value	n
neural tube	2.05e-67	56
neural rod	2.05e-67	56
future spinal cord	2.05e-67	56
neural keel	2.05e-67	56
regional part of nervous system	2.14e-63	53
regional part of brain	2.14e-63	53
central nervous system	5.32e-57	81
nervous system	3.44e-53	89
regional part of forebrain	7.75e-53	41
forebrain	7.75e-53	41
anterior neural tube	7.75e-53	41
future forebrain	7.75e-53	41
brain	8.03e-53	68
future brain	8.03e-53	68
brain grey matter	1.37e-51	34
gray matter	1.37e-51	34
telencephalon	2.17e-51	34
neural plate	2.22e-48	82
presumptive neural plate	2.22e-48	82
neurectoderm	3.92e-48	86
regional part of telencephalon	2.90e-46	32
cerebral hemisphere	5.47e-46	32
adult organism	1.78e-40	114
ecto-epithelium	4.92e-38	104
pre-chordal neural plate	5.93e-36	61
regional part of cerebral cortex	2.25e-29	22
cerebral cortex	8.74e-29	25
pallium	8.74e-29	25
neocortex	2.37e-28	20
ectoderm-derived structure	4.34e-28	171
ectoderm	4.34e-28	171
presumptive ectoderm	4.34e-28	171
structure with developmental contribution from neural crest	9.80e-28	132
neural nucleus	1.06e-26	9
nucleus of brain	1.06e-26	9
telencephalic nucleus	4.99e-21	7
basal ganglion	6.37e-21	9
nuclear complex of neuraxis	6.37e-21	9
aggregate regional part of brain	6.37e-21	9
collection of basal ganglia	6.37e-21	9
cerebral subcortex	6.37e-21	9
organ system subdivision	8.49e-21	223
tube	7.56e-19	192
brainstem	3.45e-18	6
posterior neural tube	3.34e-15	15
chordal neural plate	3.34e-15	15
anatomical conduit	1.03e-14	240
segmental subdivision of nervous system	5.20e-14	13
gyrus	1.88e-12	6
corpus striatum	2.81e-12	4
striatum	2.81e-12	4
ventral part of telencephalon	2.81e-12	4
future corpus striatum	2.81e-12	4
segmental subdivision of hindbrain	1.38e-11	12
hindbrain	1.38e-11	12
presumptive hindbrain	1.38e-11	12
anatomical cluster	5.80e-11	373
temporal lobe	8.11e-11	6
medulla oblongata	5.20e-10	3
myelencephalon	5.20e-10	3
future myelencephalon	5.20e-10	3
pons	6.82e-10	3
epithelium	7.24e-10	306
parietal lobe	8.97e-10	5
cell layer	1.15e-09	309
caudate-putamen	1.20e-09	3
dorsal striatum	1.20e-09	3
organ part	4.20e-09	218
multi cell component structure	1.38e-07	2
neuron projection bundle	1.38e-07	2
globus pallidus	1.67e-07	2
pallidum	1.67e-07	2
multi-tissue structure	1.70e-07	342
dorsal plus ventral thalamus	1.72e-07	2
thalamic complex	1.72e-07	2
locus ceruleus	2.28e-07	2
brainstem nucleus	2.28e-07	2
hindbrain nucleus	2.28e-07	2
caudate nucleus	5.49e-07	2
future caudate nucleus	5.49e-07	2
middle temporal gyrus	5.66e-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.