Coexpression cluster:C978

Full id: C978_skeletal_amygdala_insula_occipital_medial_frontal_cerebral

Phase1 CAGE Peaks

Hg19::chr10:3147130..3147141,+	p14@PFKP
Hg19::chr12:49393148..49393164,-	p1@DDN
Hg19::chr14:89757957..89757974,-	p1@ENST00000557743
Hg19::chr1:162458011..162458031,-	p@chr1:162458011..162458031 -
Hg19::chr1:162458051..162458067,-	p@chr1:162458051..162458067 -
Hg19::chr1:40137922..40137962,-	p2@NT5C1A
Hg19::chr6:17393807..17393833,+	p2@CAP2
Hg19::chr6:17393888..17393954,+	p1@CAP2

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:0008253	5'-nucleotidase activity	0.0275670551604664
GO:0008252	nucleotidase activity	0.0275670551604664
GO:0000287	magnesium ion binding	0.0275670551604664
GO:0005829	cytosol	0.0275670551604664
GO:0005945	6-phosphofructokinase complex	0.0275670551604664
GO:0003872	6-phosphofructokinase activity	0.0275670551604664
GO:0007190	adenylate cyclase activation	0.0275670551604664
GO:0031281	positive regulation of cyclase activity	0.0275670551604664
GO:0051349	positive regulation of lyase activity	0.0275670551604664
GO:0045762	positive regulation of adenylate cyclase activity	0.0275670551604664
GO:0008443	phosphofructokinase activity	0.0275670551604664
GO:0007163	establishment and/or maintenance of cell polarity	0.0275670551604664
GO:0007189	G-protein signaling, adenylate cyclase activating pathway	0.0281659660913172
GO:0030425	dendrite	0.0281659660913172
GO:0045761	regulation of adenylate cyclase activity	0.0281659660913172
GO:0031279	regulation of cyclase activity	0.0281659660913172
GO:0051339	regulation of lyase activity	0.0281659660913172
GO:0009116	nucleoside metabolic process	0.0329202640965178
GO:0019200	carbohydrate kinase activity	0.0353750131089477
GO:0043005	neuron projection	0.0449943136693105
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0449943136693105
GO:0019933	cAMP-mediated signaling	0.0449943136693105

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	2.09e-08	180

Uber Anatomy

Ontology term	p-value	n
organism subdivision	2.62e-26	365
regional part of nervous system	1.92e-25	94
nervous system	1.92e-25	94
central nervous system	1.81e-24	82
head	5.37e-24	123
brain	1.43e-23	69
future brain	1.43e-23	69
multi-tissue structure	2.55e-23	347
ectoderm-derived structure	5.11e-23	169
anterior region of body	1.03e-22	129
craniocervical region	1.03e-22	129
ectoderm	3.69e-22	173
presumptive ectoderm	3.69e-22	173
neural plate	8.07e-22	86
presumptive neural plate	8.07e-22	86
neural tube	3.51e-21	57
neural rod	3.51e-21	57
future spinal cord	3.51e-21	57
neural keel	3.51e-21	57
adult organism	7.66e-21	115
regional part of brain	1.35e-20	59
neurectoderm	2.04e-20	90
cerebral hemisphere	1.40e-18	32
regional part of forebrain	3.27e-18	41
forebrain	3.27e-18	41
future forebrain	3.27e-18	41
telencephalon	3.89e-18	34
multi-cellular organism	5.38e-18	659
gray matter	6.66e-18	34
brain grey matter	6.66e-18	34
anterior neural tube	8.36e-18	42
regional part of telencephalon	1.86e-17	33
pre-chordal neural plate	8.02e-17	61
anatomical cluster	1.47e-16	286
epithelium	2.34e-15	309
cell layer	3.60e-15	312
regional part of cerebral cortex	7.59e-15	22
cerebral cortex	8.27e-15	25
pallium	8.27e-15	25
anatomical conduit	1.23e-14	241
neocortex	1.35e-13	20
anatomical system	1.62e-13	625
anatomical group	3.25e-13	626
tube	5.77e-13	194
organ	3.50e-12	511
organ part	4.61e-12	219
embryo	2.94e-11	612
embryonic structure	2.07e-10	605
developing anatomical structure	2.07e-10	605
germ layer	3.75e-10	604
embryonic tissue	3.75e-10	604
presumptive structure	3.75e-10	604
epiblast (generic)	3.75e-10	604

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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No analysis results for this cluster

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.