Coexpression cluster:C624

Full id: C624_pituitary_cerebellum_occipital_parietal_middle_medial_hippocampus

Phase1 CAGE Peaks

Hg19::chr12:117996926..117996946,-	p@chr12:117996926..117996946 -
Hg19::chr12:118406727..118406753,-	p2@KSR2
Hg19::chr12:118406887..118406903,-	p8@KSR2
Hg19::chr12:118406915..118406926,-	p9@KSR2
Hg19::chr12:118406929..118406949,-	p4@KSR2
Hg19::chr12:130924535..130924559,-	p@chr12:130924535..130924559 -
Hg19::chr13:108333449..108333463,-	p@chr13:108333449..108333463 -
Hg19::chr14:93897199..93897215,+	p7@UNC79
Hg19::chr17:3794021..3794042,-	p4@CAMKK1
Hg19::chr1:50489500..50489513,-	p4@AGBL4
Hg19::chr1:50489522..50489544,-	p3@AGBL4
Hg19::chr1:50489547..50489616,-	p1@AGBL4
Hg19::chr7:19813192..19813256,-	p1@TMEM196
Hg19::chrX:139791917..139791938,+	p1@RP1-177G6.2

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:0004674	protein serine/threonine kinase activity	0.0255729724364849
GO:0004683	calmodulin-dependent protein kinase activity	0.0255729724364849
GO:0004672	protein kinase activity	0.0255729724364849
GO:0006468	protein amino acid phosphorylation	0.0255729724364849
GO:0004182	carboxypeptidase A activity	0.0255729724364849
GO:0004181	metallocarboxypeptidase activity	0.0255729724364849
GO:0044267	cellular protein metabolic process	0.0255729724364849
GO:0044260	cellular macromolecule metabolic process	0.0255729724364849
GO:0016310	phosphorylation	0.0255729724364849
GO:0016773	phosphotransferase activity, alcohol group as acceptor	0.0255729724364849
GO:0019538	protein metabolic process	0.0255729724364849
GO:0019992	diacylglycerol binding	0.0255729724364849
GO:0004180	carboxypeptidase activity	0.0266709895222861
GO:0006793	phosphorus metabolic process	0.0266709895222861
GO:0006796	phosphate metabolic process	0.0266709895222861
GO:0016301	kinase activity	0.0266709895222861
GO:0016772	transferase activity, transferring phosphorus-containing groups	0.0331628902417336
GO:0008235	metalloexopeptidase activity	0.0331628902417336
GO:0005737	cytoplasm	0.0331628902417336
GO:0005516	calmodulin binding	0.0348677178207337
GO:0043687	post-translational protein modification	0.0348677178207337
GO:0008238	exopeptidase activity	0.0440444315224427
GO:0006464	protein modification process	0.0441479240308551
GO:0005524	ATP binding	0.0441479240308551
GO:0043412	biopolymer modification	0.0441479240308551
GO:0032559	adenyl ribonucleotide binding	0.0441479240308551
GO:0030554	adenyl nucleotide binding	0.0461000830774222

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>

---

Uber Anatomy

Ontology term	p-value	n
neural tube	8.03e-89	56
neural rod	8.03e-89	56
future spinal cord	8.03e-89	56
neural keel	8.03e-89	56
regional part of nervous system	6.74e-83	53
regional part of brain	6.74e-83	53
regional part of forebrain	1.31e-73	41
forebrain	1.31e-73	41
anterior neural tube	1.31e-73	41
future forebrain	1.31e-73	41
central nervous system	1.12e-72	81
brain	7.85e-70	68
future brain	7.85e-70	68
nervous system	4.27e-69	89
adult organism	2.26e-64	114
neural plate	2.57e-61	82
presumptive neural plate	2.57e-61	82
neurectoderm	3.85e-60	86
brain grey matter	4.94e-59	34
gray matter	4.94e-59	34
telencephalon	5.47e-59	34
cerebral hemisphere	1.71e-55	32
regional part of telencephalon	6.13e-55	32
pre-chordal neural plate	3.85e-51	61
ecto-epithelium	1.63e-49	104
regional part of cerebral cortex	3.83e-47	22
neocortex	1.21e-42	20
cerebral cortex	7.06e-41	25
pallium	7.06e-41	25
structure with developmental contribution from neural crest	5.53e-39	132
ectoderm-derived structure	1.42e-35	171
ectoderm	1.42e-35	171
presumptive ectoderm	1.42e-35	171
organ system subdivision	6.38e-30	223
tube	5.51e-20	192
basal ganglion	8.82e-20	9
nuclear complex of neuraxis	8.82e-20	9
aggregate regional part of brain	8.82e-20	9
collection of basal ganglia	8.82e-20	9
cerebral subcortex	8.82e-20	9
neural nucleus	1.92e-19	9
nucleus of brain	1.92e-19	9
anatomical conduit	4.28e-17	240
anatomical cluster	1.84e-16	373
posterior neural tube	2.68e-16	15
chordal neural plate	2.68e-16	15
diencephalon	1.08e-15	7
future diencephalon	1.08e-15	7
telencephalic nucleus	1.77e-15	7
gyrus	6.74e-15	6
brainstem	2.18e-13	6
epithelium	8.21e-13	306
limbic system	1.24e-12	5
cell layer	1.55e-12	309
parietal lobe	1.64e-12	5
occipital lobe	2.99e-12	5
temporal lobe	3.01e-12	6
organ part	4.16e-12	218
multi-tissue structure	1.80e-11	342
segmental subdivision of hindbrain	2.84e-11	12
hindbrain	2.84e-11	12
presumptive hindbrain	2.84e-11	12
corpus striatum	2.70e-10	4
striatum	2.70e-10	4
ventral part of telencephalon	2.70e-10	4
future corpus striatum	2.70e-10	4
segmental subdivision of nervous system	2.77e-10	13
gland of diencephalon	2.83e-10	4
neuroendocrine gland	2.83e-10	4
organ	4.56e-10	503
embryo	8.79e-10	592
regional part of diencephalon	2.70e-09	4
frontal cortex	1.72e-08	3
developing anatomical structure	3.99e-08	581
germ layer	4.10e-08	560
germ layer / neural crest	4.10e-08	560
embryonic tissue	4.10e-08	560
presumptive structure	4.10e-08	560
germ layer / neural crest derived structure	4.10e-08	560
epiblast (generic)	4.10e-08	560
caudate-putamen	4.43e-08	3
dorsal striatum	4.43e-08	3
embryonic structure	6.41e-08	564
pons	1.13e-07	3
medulla oblongata	2.22e-07	3
myelencephalon	2.22e-07	3
future myelencephalon	2.22e-07	3
multi-cellular organism	2.58e-07	656
spinal cord	3.59e-07	3
dorsal region element	3.59e-07	3
dorsum	3.59e-07	3
male genital duct	7.44e-07	3
internal male genitalia	7.44e-07	3

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
E2F1#1869	7	2.45369460743966	0.0128734132000325	0.0463120940097894
PBX3#5090	4	6.26128933906975	0.00299894388765468	0.0159392722993775
YY1#7528	7	2.45558537492693	0.0128187546389251	0.0461186370779117
ZBTB33#10009	3	6.78529822071025	0.00882369911046179	0.0335068287604086
ZEB1#6935	4	4.82526629072682	0.00760737063368616	0.031350123569094

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.