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>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
neuronal stem cell	3.20e-11	8
neuron	7.14e-08	6
neuroblast	7.14e-08	6
electrically signaling cell	7.14e-08	6

Uber Anatomy

Ontology term	p-value	n
central nervous system	2.05e-66	81
nervous system	3.73e-65	89
neural tube	9.48e-60	56
neural rod	9.48e-60	56
future spinal cord	9.48e-60	56
neural keel	9.48e-60	56
regional part of nervous system	7.73e-55	53
regional part of brain	7.73e-55	53
regional part of forebrain	1.51e-53	41
forebrain	1.51e-53	41
anterior neural tube	1.51e-53	41
future forebrain	1.51e-53	41
cerebral hemisphere	5.62e-52	32
telencephalon	9.98e-52	34
brain grey matter	1.45e-51	34
gray matter	1.45e-51	34
brain	1.23e-48	68
future brain	1.23e-48	68
regional part of telencephalon	3.52e-48	32
regional part of cerebral cortex	2.58e-41	22
neural plate	2.47e-40	82
presumptive neural plate	2.47e-40	82
ectoderm-derived structure	3.71e-40	171
ectoderm	3.71e-40	171
presumptive ectoderm	3.71e-40	171
neurectoderm	6.76e-40	86
cerebral cortex	8.64e-39	25
pallium	8.64e-39	25
neocortex	1.98e-37	20
pre-chordal neural plate	1.42e-36	61
ecto-epithelium	3.67e-32	104
adult organism	3.58e-29	114
organ system subdivision	5.05e-27	223
structure with developmental contribution from neural crest	2.52e-23	132
anatomical cluster	2.91e-16	373
basal ganglion	1.23e-14	9
nuclear complex of neuraxis	1.23e-14	9
aggregate regional part of brain	1.23e-14	9
collection of basal ganglia	1.23e-14	9
cerebral subcortex	1.23e-14	9
neural nucleus	5.79e-14	9
nucleus of brain	5.79e-14	9
tube	2.40e-13	192
gyrus	8.78e-13	6
limbic system	1.84e-11	5
temporal lobe	3.06e-11	6
parietal lobe	4.65e-11	5
occipital lobe	5.05e-11	5
anatomical conduit	6.44e-11	240
telencephalic nucleus	1.00e-10	7
organ part	2.37e-10	218
corpus striatum	1.93e-09	4
striatum	1.93e-09	4
ventral part of telencephalon	1.93e-09	4
future corpus striatum	1.93e-09	4
embryo	7.98e-09	592
posterior neural tube	9.45e-09	15
chordal neural plate	9.45e-09	15
brainstem	4.43e-08	6
caudate-putamen	1.68e-07	3
dorsal striatum	1.68e-07	3
multi-tissue structure	2.03e-07	342
frontal cortex	3.46e-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
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.