Coexpression cluster:C2599

Full id: C2599_pineal_pituitary_cerebellum_spinal_thalamus_parietal_hippocampus

Phase1 CAGE Peaks

Hg19::chr1:78470530..78470551,+	p7@DNAJB4
Hg19::chr4:186317034..186317083,-	p1@LRP2BP
Hg19::chr4:331318..331341,-	p@chr4:331318..331341 -
Hg19::chr7:95174494..95174520,+	p@chr7:95174494..95174520 +

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:0009408	response to heat	0.0137736177222909
GO:0009266	response to temperature stimulus	0.0153592627850831
GO:0006986	response to unfolded protein	0.0156171759566238
GO:0051789	response to protein stimulus	0.0156171759566238
GO:0031072	heat shock protein binding	0.0215856666907313
GO:0009628	response to abiotic stimulus	0.0290713032697566
GO:0051082	unfolded protein binding	0.030188354377766
GO:0009607	response to biotic stimulus	0.0381192540324227
GO:0006457	protein folding	0.0404160150686843

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	3.81e-45	115
neural tube	3.67e-26	57
neural rod	3.67e-26	57
future spinal cord	3.67e-26	57
neural keel	3.67e-26	57
regional part of brain	3.38e-22	59
anterior neural tube	3.49e-22	42
regional part of forebrain	9.46e-22	41
forebrain	9.46e-22	41
future forebrain	9.46e-22	41
central nervous system	3.23e-21	82
brain	3.40e-21	69
future brain	3.40e-21	69
neural plate	1.83e-19	86
presumptive neural plate	1.83e-19	86
regional part of nervous system	5.58e-19	94
nervous system	5.58e-19	94
neurectoderm	3.10e-18	90
gray matter	2.86e-17	34
brain grey matter	2.86e-17	34
telencephalon	3.45e-17	34
regional part of telencephalon	1.28e-16	33
cerebral hemisphere	6.00e-16	32
pre-chordal neural plate	1.44e-14	61
regional part of cerebral cortex	6.81e-14	22
neocortex	1.28e-12	20
cerebral cortex	9.33e-12	25
pallium	9.33e-12	25
anterior region of body	1.46e-11	129
craniocervical region	1.46e-11	129
head	7.95e-11	123
ectoderm-derived structure	1.26e-08	169
ectoderm	3.04e-08	173
presumptive ectoderm	3.04e-08	173
nucleus of brain	3.58e-07	9
basal ganglion	3.58e-07	9
neural nucleus	3.58e-07	9
nuclear complex of neuraxis	3.58e-07	9
aggregate regional part of brain	3.58e-07	9
collection of basal ganglia	3.58e-07	9
cerebral subcortex	3.58e-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)
{{{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
BCLAF1#9774	2	10.8263238050609	0.0120220381643258	0.0436583206594117
GTF2B#2959	2	15.9719149671621	0.00563658572353722	0.0254751331305394
JUN#3725	3	9.38462189425225	0.00191899450203047	0.0112866963337028
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0386999087893225
KAT2A#2648	1	154.0225	0.00647681994931104	0.0281260955794634
POLR3A#11128	1	84.7830275229358	0.0117428417771162	0.0428650048009589
RFX5#5993	3	9.03593312039632	0.00214456119132407	0.0123853033765038

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.