Coexpression cluster:C1665

Full id: C1665_kidney_occipital_duodenum_temporal_parietal_Neural_brain

Phase1 CAGE Peaks

Hg19::chr12:15475214..15475223,+	p9@PTPRO
Hg19::chr12:15475249..15475280,+	p4@PTPRO
Hg19::chr12:15475292..15475303,+	p7@PTPRO
Hg19::chr12:15475462..15475483,+	p5@PTPRO
Hg19::chr2:213403858..213403879,-	p2@ERBB4

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:0019198	transmembrane receptor protein phosphatase activity	0.0250990844682031
GO:0005001	transmembrane receptor protein tyrosine phosphatase activity	0.0250990844682031
GO:0005887	integral to plasma membrane	0.0250990844682031
GO:0031226	intrinsic to plasma membrane	0.0250990844682031
GO:0006793	phosphorus metabolic process	0.0266015515049223
GO:0006796	phosphate metabolic process	0.0266015515049223
GO:0004888	transmembrane receptor activity	0.0321580955874543
GO:0043687	post-translational protein modification	0.0321580955874543
GO:0044459	plasma membrane part	0.0321580955874543
GO:0046982	protein heterodimerization activity	0.033791670924434
GO:0006464	protein modification process	0.033791670924434
GO:0004714	transmembrane receptor protein tyrosine kinase activity	0.033791670924434
GO:0043412	biopolymer modification	0.033791670924434
GO:0019199	transmembrane receptor protein kinase activity	0.0341160217542822
GO:0004872	receptor activity	0.0352430259229253
GO:0060089	molecular transducer activity	0.0409379450656799
GO:0004871	signal transducer activity	0.0409379450656799
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0409379450656799
GO:0005886	plasma membrane	0.0409379450656799
GO:0004725	protein tyrosine phosphatase activity	0.0409379450656799
GO:0006470	protein amino acid dephosphorylation	0.044156149366298
GO:0016311	dephosphorylation	0.0469563405358217
GO:0007167	enzyme linked receptor protein signaling pathway	0.0469563405358217
GO:0004713	protein-tyrosine kinase activity	0.0469563405358217
GO:0004721	phosphoprotein phosphatase activity	0.0469563405358217

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
regional part of nervous system	3.08e-43	94
nervous system	3.08e-43	94
central nervous system	9.56e-41	82
neural tube	2.22e-39	57
neural rod	2.22e-39	57
future spinal cord	2.22e-39	57
neural keel	2.22e-39	57
adult organism	3.89e-34	115
regional part of brain	3.79e-33	59
neurectoderm	6.66e-33	90
anterior neural tube	8.96e-33	42
regional part of forebrain	2.77e-32	41
forebrain	2.77e-32	41
future forebrain	2.77e-32	41
brain	6.52e-32	69
future brain	6.52e-32	69
neural plate	8.14e-32	86
presumptive neural plate	8.14e-32	86
ectoderm	8.45e-30	173
presumptive ectoderm	8.45e-30	173
ectoderm-derived structure	1.26e-28	169
telencephalon	1.84e-27	34
gray matter	2.08e-27	34
brain grey matter	2.08e-27	34
regional part of telencephalon	1.48e-26	33
cerebral hemisphere	5.24e-26	32
pre-chordal neural plate	1.65e-25	61
anterior region of body	1.70e-24	129
craniocervical region	1.70e-24	129
head	3.93e-24	123
cerebral cortex	6.22e-20	25
pallium	6.22e-20	25
regional part of cerebral cortex	1.11e-19	22
neocortex	6.72e-18	20
anatomical cluster	2.86e-15	286
organ part	1.16e-12	219
anatomical conduit	2.06e-12	241
multi-tissue structure	4.43e-12	347
organism subdivision	6.02e-12	365
tube	8.29e-12	194
embryo	4.74e-11	612
multi-cellular organism	1.48e-10	659
epithelium	1.47e-09	309
basal ganglion	3.03e-09	9
nuclear complex of neuraxis	3.03e-09	9
aggregate regional part of brain	3.03e-09	9
collection of basal ganglia	3.03e-09	9
cerebral subcortex	3.03e-09	9
cell layer	3.80e-09	312
embryonic structure	5.71e-09	605
developing anatomical structure	5.71e-09	605
nucleus of brain	6.44e-09	9
neural nucleus	6.44e-09	9
germ layer	1.13e-08	604
embryonic tissue	1.13e-08	604
presumptive structure	1.13e-08	604
epiblast (generic)	1.13e-08	604
posterior neural tube	5.53e-08	15
chordal neural plate	5.53e-08	15
anatomical system	8.82e-08	625
anatomical group	1.12e-07	626
telencephalic nucleus	2.23e-07	7
brainstem	3.96e-07	8
organ	4.54e-07	511
gyrus	8.61e-07	6

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
REST#5978	4	7.72002297290242	0.000528636377365057	0.00457152062727741

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.