Coexpression cluster:C1005

Full id: C1005_nonsmall_cerebellum_spinal_medulla_locus_small_thalamus

Phase1 CAGE Peaks

Hg19::chr11:82556854..82556872,-	p3@PRCP
Hg19::chr12:41221946..41221953,+	p16@CNTN1
Hg19::chr12:41221975..41221996,+	p2@CNTN1
Hg19::chr12:41222004..41222020,+	p4@CNTN1
Hg19::chr18:32073253..32073339,+	p2@DTNA
Hg19::chr18:32073350..32073378,+	p6@DTNA
Hg19::chr18:32073391..32073409,+	p9@DTNA
Hg19::chr18:32073414..32073417,+	p18@DTNA

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:0008322	Pro-X carboxypeptidase activity	0.0027375485694101
GO:0004188	serine-type Pro-X carboxypeptidase activity	0.0027375485694101
GO:0007274	neuromuscular synaptic transmission	0.0150520853554045
GO:0004185	serine carboxypeptidase activity	0.0150520853554045
GO:0006941	striated muscle contraction	0.0404727979551289
GO:0007219	Notch signaling pathway	0.0455600295114098

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	6.92e-84	56
neural rod	6.92e-84	56
future spinal cord	6.92e-84	56
neural keel	6.92e-84	56
central nervous system	1.50e-81	81
nervous system	6.07e-80	89
regional part of nervous system	1.99e-77	53
regional part of brain	1.99e-77	53
brain	3.65e-70	68
future brain	3.65e-70	68
adult organism	1.77e-66	114
neural plate	6.04e-65	82
presumptive neural plate	6.04e-65	82
regional part of forebrain	6.54e-63	41
forebrain	6.54e-63	41
anterior neural tube	6.54e-63	41
future forebrain	6.54e-63	41
neurectoderm	3.41e-61	86
brain grey matter	1.33e-53	34
gray matter	1.33e-53	34
telencephalon	2.83e-53	34
ecto-epithelium	7.87e-52	104
cerebral hemisphere	2.48e-49	32
regional part of telencephalon	2.52e-49	32
pre-chordal neural plate	7.97e-46	61
ectoderm-derived structure	4.52e-45	171
ectoderm	4.52e-45	171
presumptive ectoderm	4.52e-45	171
regional part of cerebral cortex	1.34e-41	22
structure with developmental contribution from neural crest	9.98e-41	132
neocortex	1.87e-37	20
organ system subdivision	3.86e-36	223
cerebral cortex	5.52e-36	25
pallium	5.52e-36	25
tube	7.29e-24	192
anatomical cluster	7.11e-23	373
posterior neural tube	5.29e-21	15
chordal neural plate	5.29e-21	15
anatomical conduit	3.26e-19	240
neural nucleus	3.75e-19	9
nucleus of brain	3.75e-19	9
basal ganglion	5.04e-19	9
nuclear complex of neuraxis	5.04e-19	9
aggregate regional part of brain	5.04e-19	9
collection of basal ganglia	5.04e-19	9
cerebral subcortex	5.04e-19	9
segmental subdivision of nervous system	7.73e-17	13
segmental subdivision of hindbrain	3.88e-15	12
hindbrain	3.88e-15	12
presumptive hindbrain	3.88e-15	12
telencephalic nucleus	6.44e-15	7
epithelium	8.01e-15	306
brainstem	1.46e-14	6
cell layer	1.65e-14	309
multi-tissue structure	1.20e-13	342
gyrus	2.29e-13	6
organ part	1.30e-12	218
limbic system	9.17e-12	5
embryo	2.45e-11	592
temporal lobe	2.78e-11	6
parietal lobe	3.77e-11	5
diencephalon	8.97e-11	7
future diencephalon	8.97e-11	7
developing anatomical structure	9.84e-11	581
occipital lobe	1.07e-10	5
germ layer	3.26e-10	560
germ layer / neural crest	3.26e-10	560
embryonic tissue	3.26e-10	560
presumptive structure	3.26e-10	560
germ layer / neural crest derived structure	3.26e-10	560
epiblast (generic)	3.26e-10	560
embryonic structure	5.50e-10	564
organ	1.19e-09	503
regional part of metencephalon	2.73e-09	9
metencephalon	2.73e-09	9
future metencephalon	2.73e-09	9
regional part of diencephalon	2.86e-09	4
corpus striatum	3.38e-09	4
striatum	3.38e-09	4
ventral part of telencephalon	3.38e-09	4
future corpus striatum	3.38e-09	4
multi-cellular organism	3.93e-09	656
anatomical system	4.99e-09	624
anatomical group	5.61e-09	625
medulla oblongata	3.45e-08	3
myelencephalon	3.45e-08	3
future myelencephalon	3.45e-08	3
pons	4.74e-08	3
spinal cord	7.41e-08	3
dorsal region element	7.41e-08	3
dorsum	7.41e-08	3
frontal cortex	1.70e-07	3
caudate-putamen	2.56e-07	3
dorsal striatum	2.56e-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

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

TF	#promoters	Enrichment	p-value	q-value
EBF1#1879	4	4.4532334232845	0.00765188499674898	0.0315149151027473
FOS#2353	4	4.4989776544472	0.00737448991622712	0.0304794155827632
GATA2#2624	4	6.372465866777	0.00204874075705145	0.0118937429641855
GATA3#2625	4	13.618258178603	0.000112839652281084	0.00154656961215015
JUN#3725	4	6.25641459616817	0.002194211754114	0.0126454740860784
MAFF#23764	3	21.1182586837294	0.000293010169114186	0.00310771697492805
MAFK#7975	3	10.1627749266862	0.00244557310713952	0.01376742182711
TRIM28#10155	4	9.29526252263126	0.000491498033342148	0.00439332104623593
USF2#7392	4	6.4960986925348	0.00190676081592817	0.0112204300684428

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.