Coexpression cluster:C3334

Full id: C3334_cerebellum_pineal_occipital_Dendritic_parietal_medial_pituitary

Phase1 CAGE Peaks

Hg19::chr12:77158021..77158045,+	p1@ZDHHC17
Hg19::chr16:2723378..2723446,-	p1@ERVK13-1
Hg19::chr6:83777374..83777456,+	p1@DOPEY1

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:0042953	lipoprotein transport	0.00255108298212802
GO:0019706	protein-cysteine S-palmitoleyltransferase activity	0.00255108298212802
GO:0019707	protein-cysteine S-acyltransferase activity	0.00255108298212802
GO:0016417	S-acyltransferase activity	0.00640284617945621
GO:0015031	protein transport	0.00640284617945621
GO:0016409	palmitoyltransferase activity	0.00640284617945621
GO:0045184	establishment of protein localization	0.00640284617945621
GO:0008104	protein localization	0.00640284617945621
GO:0033036	macromolecule localization	0.00640284617945621
GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB cascade	0.0308358649373065
GO:0030659	cytoplasmic vesicle membrane	0.0308358649373065
GO:0044433	cytoplasmic vesicle part	0.0308358649373065
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.0308358649373065
GO:0012506	vesicle membrane	0.0308358649373065
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.035388549833398
GO:0009967	positive regulation of signal transduction	0.036510769983116
GO:0006810	transport	0.0481393143616867
GO:0008415	acyltransferase activity	0.0481393143616867
GO:0016747	transferase activity, transferring groups other than amino-acyl groups	0.0481393143616867
GO:0051234	establishment of localization	0.0481393143616867

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
leukocyte	1.35e-11	136
hematopoietic stem cell	2.79e-10	168
angioblastic mesenchymal cell	2.79e-10	168
hematopoietic lineage restricted progenitor cell	5.15e-10	120
hematopoietic oligopotent progenitor cell	5.93e-09	161
hematopoietic multipotent progenitor cell	5.93e-09	161
hematopoietic cell	1.70e-08	177
nongranular leukocyte	1.79e-08	115

Uber Anatomy

Ontology term	p-value	n
adult organism	1.41e-38	114
neural tube	1.68e-26	56
neural rod	1.68e-26	56
future spinal cord	1.68e-26	56
neural keel	1.68e-26	56
regional part of nervous system	7.97e-25	53
regional part of brain	7.97e-25	53
central nervous system	8.66e-24	81
nervous system	2.20e-23	89
regional part of forebrain	2.23e-23	41
forebrain	2.23e-23	41
anterior neural tube	2.23e-23	41
future forebrain	2.23e-23	41
brain	1.21e-20	68
future brain	1.21e-20	68
brain grey matter	6.17e-19	34
gray matter	6.17e-19	34
telencephalon	6.79e-19	34
cerebral hemisphere	6.54e-18	32
regional part of telencephalon	6.69e-18	32
neurectoderm	3.34e-15	86
neural plate	1.47e-14	82
presumptive neural plate	1.47e-14	82
regional part of cerebral cortex	1.65e-14	22
cerebral cortex	7.16e-14	25
pallium	7.16e-14	25
neocortex	3.21e-13	20
pre-chordal neural plate	2.28e-11	61
organ system subdivision	1.71e-09	223
ecto-epithelium	3.29e-09	104
ectoderm-derived structure	9.45e-09	171
ectoderm	9.45e-09	171
presumptive ectoderm	9.45e-09	171
basal ganglion	7.95e-07	9
nuclear complex of neuraxis	7.95e-07	9
aggregate regional part of brain	7.95e-07	9
collection of basal ganglia	7.95e-07	9
cerebral subcortex	7.95e-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
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321045334710569
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319551693661536
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275839527698832
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328397956657645

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.