Coexpression cluster:C3729

Full id: C3729_medial_hippocampus_cerebral_middle_parietal_globus_olfactory

Phase1 CAGE Peaks

Hg19::chr18:55030190..55030203,+	p@chr18:55030190..55030203 +
Hg19::chr3:48016734..48016748,-	p49@MAP4
Hg19::chr7:98460933..98460941,-	p19@TMEM130

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:0007026	negative regulation of microtubule depolymerization	0.0169474033792886
GO:0031114	regulation of microtubule depolymerization	0.0169474033792886
GO:0007019	microtubule depolymerization	0.0169474033792886
GO:0031111	negative regulation of microtubule polymerization or depolymerization	0.0169474033792886
GO:0031110	regulation of microtubule polymerization or depolymerization	0.0169474033792886
GO:0031109	microtubule polymerization or depolymerization	0.0169474033792886
GO:0051261	protein depolymerization	0.0206485650106885
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0206485650106885
GO:0051128	regulation of cellular component organization and biogenesis	0.0300112721168847
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0300112721168847
GO:0051248	negative regulation of protein metabolic process	0.0300112721168847
GO:0005875	microtubule associated complex	0.0475606955091801

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	6.19e-92	56
neural rod	6.19e-92	56
future spinal cord	6.19e-92	56
neural keel	6.19e-92	56
regional part of nervous system	4.20e-91	53
regional part of brain	4.20e-91	53
regional part of forebrain	3.07e-76	41
forebrain	3.07e-76	41
anterior neural tube	3.07e-76	41
future forebrain	3.07e-76	41
brain	9.38e-74	68
future brain	9.38e-74	68
brain grey matter	2.64e-71	34
gray matter	2.64e-71	34
central nervous system	5.71e-70	81
cerebral hemisphere	9.61e-69	32
telencephalon	1.49e-64	34
nervous system	1.61e-62	89
regional part of telencephalon	2.43e-62	32
neural plate	3.04e-61	82
presumptive neural plate	3.04e-61	82
neurectoderm	3.80e-58	86
regional part of cerebral cortex	8.71e-58	22
cerebral cortex	1.02e-50	25
pallium	1.02e-50	25
pre-chordal neural plate	6.11e-50	61
neocortex	4.84e-48	20
ecto-epithelium	3.95e-47	104
adult organism	5.28e-46	114
structure with developmental contribution from neural crest	1.41e-38	132
ectoderm-derived structure	4.34e-30	171
ectoderm	4.34e-30	171
presumptive ectoderm	4.34e-30	171
organ system subdivision	3.12e-23	223
gyrus	3.35e-23	6
tube	8.42e-23	192
regional part of diencephalon	4.37e-22	4
neural nucleus	1.32e-21	9
nucleus of brain	1.32e-21	9
limbic system	2.33e-18	5
occipital lobe	2.07e-17	5
anatomical conduit	5.33e-17	240
pons	7.92e-17	3
posterior neural tube	9.05e-17	15
chordal neural plate	9.05e-17	15
segmental subdivision of hindbrain	1.18e-15	12
hindbrain	1.18e-15	12
presumptive hindbrain	1.18e-15	12
basal ganglion	2.37e-15	9
nuclear complex of neuraxis	2.37e-15	9
aggregate regional part of brain	2.37e-15	9
collection of basal ganglia	2.37e-15	9
cerebral subcortex	2.37e-15	9
regional part of metencephalon	5.30e-15	9
metencephalon	5.30e-15	9
future metencephalon	5.30e-15	9
segmental subdivision of nervous system	2.07e-14	13
brainstem	2.11e-14	6
temporal lobe	2.73e-13	6
corpus striatum	4.66e-13	4
striatum	4.66e-13	4
ventral part of telencephalon	4.66e-13	4
future corpus striatum	4.66e-13	4
telencephalic nucleus	6.95e-13	7
middle temporal gyrus	9.14e-13	2
diencephalon	1.07e-12	7
future diencephalon	1.07e-12	7
Ammon's horn	1.15e-12	2
lobe parts of cerebral cortex	1.15e-12	2
hippocampal formation	1.15e-12	2
limbic lobe	1.15e-12	2
organ part	1.55e-12	218
locus ceruleus	5.23e-12	2
brainstem nucleus	5.23e-12	2
hindbrain nucleus	5.23e-12	2
dorsal plus ventral thalamus	5.53e-12	2
thalamic complex	5.53e-12	2
epithelium	5.70e-12	306
pineal body	7.28e-12	2
regional part of epithalamus	7.28e-12	2
secretory circumventricular organ	7.28e-12	2
circumventricular organ	7.28e-12	2
epithalamus	7.28e-12	2
cell layer	8.59e-12	309
anatomical cluster	2.36e-11	373
parietal lobe	2.24e-10	5
multi-tissue structure	5.16e-10	342
caudate-putamen	1.64e-08	3
dorsal striatum	1.64e-08	3
frontal cortex	2.95e-08	3
olfactory region	4.69e-07	1
primary subdivision of skull	4.69e-07	1
cranium	4.69e-07	1
neurocranium	4.69e-07	1
chondrocranium	4.69e-07	1
cartilaginous neurocranium	4.69e-07	1
head paraxial mesoderm	4.69e-07	1
putamen	4.97e-07	1

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.