Coexpression cluster:C2506

Full id: C2506_putamen_caudate_nucleus_temporal_amygdala_insula_frontal

Phase1 CAGE Peaks

Hg19::chr19:7989858..7989889,-	p2@CTXN1
Hg19::chr19:7990008..7990044,-	p4@CTXN1
Hg19::chr19:7990260..7990308,+	p@chr19:7990260..7990308 +
Hg19::chr19:7990991..7991059,-	p1@CTXN1

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

---

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>

---

Cell Type

Ontology term	p-value	n
embryonic cell	4.76e-15	250
epithelial cell	1.55e-14	253
neurectodermal cell	2.19e-11	59
lining cell	1.18e-09	58
barrier cell	1.18e-09	58
ectodermal cell	3.43e-09	72
mesodermal cell	1.80e-08	121
neural cell	6.60e-08	25
squamous epithelial cell	6.56e-07	63

Uber Anatomy

Ontology term	p-value	n
anatomical cluster	1.67e-24	373
central nervous system	1.24e-23	81
nervous system	2.41e-23	89
pre-chordal neural plate	3.54e-19	61
brain	3.88e-19	68
future brain	3.88e-19	68
cerebral hemisphere	5.79e-19	32
brain grey matter	7.83e-19	34
gray matter	7.83e-19	34
telencephalon	9.07e-19	34
neurectoderm	1.09e-18	86
regional part of telencephalon	3.11e-18	32
regional part of nervous system	4.58e-18	53
regional part of brain	4.58e-18	53
neural plate	7.85e-18	82
presumptive neural plate	7.85e-18	82
regional part of forebrain	8.27e-18	41
forebrain	8.27e-18	41
anterior neural tube	8.27e-18	41
future forebrain	8.27e-18	41
neural tube	1.83e-17	56
neural rod	1.83e-17	56
future spinal cord	1.83e-17	56
neural keel	1.83e-17	56
tube	3.87e-16	192
cell layer	9.12e-16	309
epithelium	1.45e-15	306
anatomical conduit	7.95e-15	240
cerebral cortex	1.36e-14	25
pallium	1.36e-14	25
ectoderm-derived structure	1.52e-14	171
ectoderm	1.52e-14	171
presumptive ectoderm	1.52e-14	171
ecto-epithelium	6.51e-14	104
organ system subdivision	1.06e-13	223
regional part of cerebral cortex	2.83e-13	22
structure with developmental contribution from neural crest	7.32e-13	132
multi-tissue structure	1.92e-12	342
neocortex	5.11e-12	20
embryo	3.86e-09	592
multi-cellular organism	1.28e-08	656
organ part	3.44e-08	218
developing anatomical structure	1.49e-07	581

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
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00512211908782586
CTCFL#140690	3	14.8098557692308	0.000499629176756334	0.00440939425310586
E2F4#1874	3	9.50104523646333	0.00185075103472827	0.0109283986722443
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466221995448671
NANOG#79923	2	14.6223892405063	0.00669875771536376	0.0284916129926644
NRF1#4899	4	12.2102794477109	4.49717228915276e-05	0.00079391510599531
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.043494736779617
RAD21#5885	3	7.76627542159225	0.003341119385872	0.0172684301252579
SETDB1#9869	3	30.2400196335079	5.98509618524166e-05	0.000984684090249612
SMC3#9126	3	11.2836996336996	0.00111580236686805	0.00765709201612016
ZBTB7A#51341	4	7.3519093078759	0.00034222354001599	0.00346600895032292
ZNF143#7702	3	10.1256574141709	0.00153486161068818	0.0097666125485081

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.