Coexpression cluster:C2237

Full id: C2237_lung_heart_adipose_breast_left_MCF7_retina

Phase1 CAGE Peaks

Hg19::chr12:71003739..71003750,-	p8@PTPRB
Hg19::chr12:71003751..71003810,-	p2@PTPRB
Hg19::chr12:71003811..71003822,-	p9@PTPRB
Hg19::chr7:45197383..45197437,+	p1@RAMP3

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:0015027	coreceptor, soluble ligand activity	0.0046508889673849
GO:0015026	coreceptor activity	0.0206544549269588
GO:0019198	transmembrane receptor protein phosphatase activity	0.0206544549269588
GO:0005001	transmembrane receptor protein tyrosine phosphatase activity	0.0206544549269588
GO:0005887	integral to plasma membrane	0.0206544549269588
GO:0031226	intrinsic to plasma membrane	0.0206544549269588
GO:0008277	regulation of G-protein coupled receptor protein signaling pathway	0.023821772926169
GO:0006898	receptor-mediated endocytosis	0.023821772926169
GO:0044459	plasma membrane part	0.0396951492407639

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
adult organism	2.15e-67	114
neural tube	6.88e-28	56
neural rod	6.88e-28	56
future spinal cord	6.88e-28	56
neural keel	6.88e-28	56
regional part of nervous system	5.83e-26	53
regional part of brain	5.83e-26	53
anatomical cluster	8.80e-25	373
neural plate	2.52e-24	82
presumptive neural plate	2.52e-24	82
neurectoderm	1.43e-23	86
tube	6.50e-23	192
anatomical conduit	7.25e-23	240
regional part of forebrain	7.73e-22	41
forebrain	7.73e-22	41
anterior neural tube	7.73e-22	41
future forebrain	7.73e-22	41
structure with developmental contribution from neural crest	1.88e-20	132
brain	3.05e-20	68
future brain	3.05e-20	68
central nervous system	4.14e-19	81
nervous system	9.59e-18	89
telencephalon	1.16e-17	34
brain grey matter	1.51e-17	34
gray matter	1.51e-17	34
pre-chordal neural plate	1.04e-16	61
ecto-epithelium	1.58e-16	104
cerebral hemisphere	2.73e-16	32
regional part of telencephalon	2.93e-16	32
multi-tissue structure	6.29e-15	342
regional part of cerebral cortex	1.45e-14	22
organ system subdivision	2.27e-14	223
neocortex	1.89e-13	20
epithelium	1.07e-12	306
cell layer	3.26e-12	309
multi-cellular organism	4.04e-12	656
cerebral cortex	6.76e-12	25
pallium	6.76e-12	25
splanchnic layer of lateral plate mesoderm	7.80e-10	83
embryonic structure	1.91e-09	564
germ layer	1.93e-09	560
germ layer / neural crest	1.93e-09	560
embryonic tissue	1.93e-09	560
presumptive structure	1.93e-09	560
germ layer / neural crest derived structure	1.93e-09	560
epiblast (generic)	1.93e-09	560
anatomical system	1.97e-09	624
anatomical group	2.55e-09	625
ectoderm-derived structure	4.70e-09	171
ectoderm	4.70e-09	171
presumptive ectoderm	4.70e-09	171
vessel	6.91e-09	68
embryo	1.07e-08	592
developing anatomical structure	1.68e-08	581
epithelial tube open at both ends	1.70e-08	59
blood vessel	1.70e-08	59
blood vasculature	1.70e-08	59
vascular cord	1.70e-08	59
vasculature	3.99e-08	78
vascular system	3.99e-08	78
circulatory system	7.02e-08	112
organ	1.91e-07	503
neural nucleus	2.54e-07	9
nucleus of brain	2.54e-07	9
posterior neural tube	2.89e-07	15
chordal neural plate	2.89e-07	15
basal ganglion	5.48e-07	9
nuclear complex of neuraxis	5.48e-07	9
aggregate regional part of brain	5.48e-07	9
collection of basal ganglia	5.48e-07	9
cerebral subcortex	5.48e-07	9

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)
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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
CCNT2#905	3	4.75215118272197	0.0138620699668949	0.0487093979299015
SPI1#6688	3	6.15324263139204	0.00658038711305903	0.0280934084004731

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.