Coexpression cluster:C2246

Full id: C2246_carcinoid_Fibroblast_neuroblastoma_salivary_anaplastic_epitheloid_melanoma

Phase1 CAGE Peaks

Hg19::chr12:85285909..85285928,-	p3@SLC6A15
Hg19::chr12:85306494..85306558,-	p1@SLC6A15
Hg19::chr12:85306562..85306591,-	p2@SLC6A15
Hg19::chr12:85306594..85306622,-	p4@SLC6A15

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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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>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	7.96e-11	180
ectodermal cell	4.07e-10	71
embryonic cell	1.22e-09	248
electrically responsive cell	3.61e-09	60
electrically active cell	3.61e-09	60
muscle precursor cell	1.51e-08	57
myoblast	1.51e-08	57
multi-potent skeletal muscle stem cell	1.51e-08	57
muscle cell	6.80e-08	54
contractile cell	9.11e-08	59
neurectodermal cell	1.87e-07	59

Uber Anatomy

Ontology term	p-value	n
ectoderm	7.89e-37	173
presumptive ectoderm	7.89e-37	173
ectoderm-derived structure	2.98e-35	169
head	1.40e-29	123
regional part of nervous system	1.66e-29	94
nervous system	1.66e-29	94
anterior region of body	3.97e-27	129
craniocervical region	3.97e-27	129
organism subdivision	5.77e-26	365
neurectoderm	2.70e-25	90
central nervous system	7.27e-24	82
neural plate	7.38e-24	86
presumptive neural plate	7.38e-24	86
regional part of brain	2.11e-23	59
pre-chordal neural plate	4.31e-23	61
neural tube	7.25e-23	57
neural rod	7.25e-23	57
future spinal cord	7.25e-23	57
neural keel	7.25e-23	57
brain	7.15e-22	69
future brain	7.15e-22	69
cell layer	2.31e-21	312
epithelium	6.45e-21	309
multi-tissue structure	7.64e-19	347
regional part of forebrain	1.25e-18	41
forebrain	1.25e-18	41
future forebrain	1.25e-18	41
anterior neural tube	1.87e-18	42
multi-cellular organism	5.02e-16	659
embryo	6.91e-16	612
gray matter	7.77e-16	34
brain grey matter	7.77e-16	34
telencephalon	2.17e-15	34
organ part	2.53e-15	219
regional part of telencephalon	6.70e-15	33
cerebral hemisphere	1.26e-14	32
embryonic structure	1.82e-14	605
developing anatomical structure	1.82e-14	605
germ layer	2.11e-14	604
embryonic tissue	2.11e-14	604
presumptive structure	2.11e-14	604
epiblast (generic)	2.11e-14	604
anatomical system	1.31e-13	625
anatomical group	1.38e-13	626
anatomical cluster	1.56e-13	286
anatomical conduit	1.34e-12	241
regional part of cerebral cortex	3.35e-12	22
cerebral cortex	1.83e-11	25
pallium	1.83e-11	25
neocortex	3.75e-11	20
tube	1.98e-09	194
multilaminar epithelium	2.18e-09	82
somite	2.57e-09	83
paraxial mesoderm	2.57e-09	83
presomitic mesoderm	2.57e-09	83
presumptive segmental plate	2.57e-09	83
trunk paraxial mesoderm	2.57e-09	83
presumptive paraxial mesoderm	2.57e-09	83
dermomyotome	6.46e-09	70
subdivision of head	1.70e-07	48
skeletal muscle tissue	2.68e-07	61
striated muscle tissue	2.68e-07	61
myotome	2.68e-07	61
organ segment	4.52e-07	97
sensory system	4.80e-07	24
entire sense organ system	4.80e-07	24
ectodermal placode	5.17e-07	29
muscle tissue	5.77e-07	63
musculature	5.77e-07	63
musculature of body	5.77e-07	63
surface structure	7.15e-07	95
sense organ	7.57e-07	23

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
ATF3#467	3	16.8473808945066	0.000340998682365564	0.00346334351722038
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466048061517861
REST#5978	3	7.23752153709602	0.00410469730419261	0.0195731203430085
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0482862447851121
USF2#7392	3	9.7441480388022	0.00171834184841007	0.0107167027532605

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.