Coexpression cluster:C1482

Full id: C1482_caudate_anaplastic_putamen_thalamus_small_diencephalon_nucleus

Phase1 CAGE Peaks

Hg19::chr20:60795296..60795309,-	p2@HRH3
Hg19::chr20:60795316..60795323,-	p3@HRH3
Hg19::chr20:60795326..60795340,-	p1@HRH3
Hg19::chr2:242089628..242089643,-	p5@PASK
Hg19::chr3:58810185..58810229,+	p1@ENST00000463703 p1@ENST00000482372 p1@uc003dku.1
Hg19::chr4:72102152..72102166,+	p16@SLC4A4

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0008510	sodium:bicarbonate symporter activity	0.0323188318986822
GO:0004969	histamine receptor activity	0.0475105037576734
GO:0015106	bicarbonate transmembrane transporter activity	0.0475105037576734
GO:0005452	inorganic anion exchanger activity	0.0475105037576734
GO:0015380	anion exchanger activity	0.0475105037576734
GO:0015301	anion:anion antiporter activity	0.0475105037576734
GO:0015108	chloride transmembrane transporter activity	0.0475105037576734
GO:0015296	anion:cation symporter activity	0.0475105037576734
GO:0007269	neurotransmitter secretion	0.0475105037576734
GO:0005887	integral to plasma membrane	0.0475105037576734
GO:0031226	intrinsic to plasma membrane	0.0475105037576734
GO:0045055	regulated secretory pathway	0.0475105037576734

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>

---

Cell Type

Ontology term	p-value	n
embryonic stem cell	1.74e-07	5

Uber Anatomy

Ontology term	p-value	n
neural tube	8.76e-80	56
neural rod	8.76e-80	56
future spinal cord	8.76e-80	56
neural keel	8.76e-80	56
regional part of nervous system	1.97e-73	53
regional part of brain	1.97e-73	53
nervous system	6.51e-71	89
central nervous system	1.12e-70	81
brain	2.79e-63	68
future brain	2.79e-63	68
regional part of forebrain	2.87e-62	41
forebrain	2.87e-62	41
anterior neural tube	2.87e-62	41
future forebrain	2.87e-62	41
telencephalon	4.00e-62	34
brain grey matter	4.47e-62	34
gray matter	4.47e-62	34
cerebral hemisphere	4.76e-62	32
regional part of telencephalon	1.57e-57	32
neural plate	4.82e-56	82
presumptive neural plate	4.82e-56	82
neurectoderm	7.35e-53	86
regional part of cerebral cortex	6.49e-51	22
neocortex	3.71e-46	20
ecto-epithelium	8.83e-46	104
cerebral cortex	2.87e-44	25
pallium	2.87e-44	25
pre-chordal neural plate	3.21e-44	61
adult organism	4.64e-39	114
ectoderm-derived structure	5.62e-35	171
ectoderm	5.62e-35	171
presumptive ectoderm	5.62e-35	171
structure with developmental contribution from neural crest	7.45e-35	132
organ system subdivision	6.74e-28	223
tube	1.02e-19	192
basal ganglion	2.29e-19	9
nuclear complex of neuraxis	2.29e-19	9
aggregate regional part of brain	2.29e-19	9
collection of basal ganglia	2.29e-19	9
cerebral subcortex	2.29e-19	9
neural nucleus	6.24e-19	9
nucleus of brain	6.24e-19	9
posterior neural tube	6.78e-18	15
chordal neural plate	6.78e-18	15
gyrus	5.44e-16	6
telencephalic nucleus	1.59e-14	7
anatomical conduit	4.83e-14	240
limbic system	6.86e-14	5
temporal lobe	2.18e-13	6
anatomical cluster	2.33e-13	373
parietal lobe	3.49e-13	5
occipital lobe	4.28e-13	5
segmental subdivision of hindbrain	2.62e-12	12
hindbrain	2.62e-12	12
presumptive hindbrain	2.62e-12	12
epithelium	2.69e-12	306
corpus striatum	3.35e-12	4
striatum	3.35e-12	4
ventral part of telencephalon	3.35e-12	4
future corpus striatum	3.35e-12	4
cell layer	4.81e-12	309
organ part	1.84e-11	218
segmental subdivision of nervous system	3.01e-11	13
brainstem	2.32e-10	6
regional part of metencephalon	1.02e-09	9
metencephalon	1.02e-09	9
future metencephalon	1.02e-09	9
caudate-putamen	1.40e-09	3
dorsal striatum	1.40e-09	3
frontal cortex	4.59e-09	3
pons	3.02e-08	3
spinal cord	8.30e-08	3
dorsal region element	8.30e-08	3
dorsum	8.30e-08	3
embryo	1.15e-07	592
multi-tissue structure	2.64e-07	342
caudate nucleus	6.27e-07	2
future caudate nucleus	6.27e-07	2
dorsal plus ventral thalamus	9.22e-07	2
thalamic complex	9.22e-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

---

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ETS1#2113	4	6.48584061480156	0.00141047406846322	0.00917067180702423
HDAC2#3066	3	6.70781011831313	0.00697394002796266	0.0294902956749693
SIN3A#25942	4	3.60592315121009	0.0127389384448714	0.0459470228016273

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

---

This analysis result is provided for C0 - C305 clusters.