Coexpression cluster:C644

Full id: C644_chronic_Reticulocytes_acute_CD34_leukemia_liver_schwannoma

Phase1 CAGE Peaks

Hg19::chr10:119184702..119184711,+	p1@ENST00000549104
Hg19::chr11:119994013..119994021,-	p50@TRIM29
Hg19::chr11:13804110..13804121,-	p@chr11:13804110..13804121 -
Hg19::chr11:33903432..33903464,-	p@chr11:33903432..33903464 -
Hg19::chr11:33903469..33903500,-	p@chr11:33903469..33903500 -
Hg19::chr11:5264817..5264828,-	p4@HBBP1
Hg19::chr11:5264837..5264870,-	p1@HBBP1
Hg19::chr11:5264874..5264909,-	p2@HBBP1
Hg19::chr11:5264923..5264932,-	p6@HBBP1
Hg19::chr13:52569530..52569556,-	p@chr13:52569530..52569556 -
Hg19::chr19:12997072..12997102,-	p@chr19:12997072..12997102 -
Hg19::chr19:13189413..13189435,+	p@chr19:13189413..13189435 +
Hg19::chr8:41655080..41655089,-	p10@ANK1

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:0045199	maintenance of epithelial cell polarity	0.00214879681956168
GO:0030507	spectrin binding	0.00214879681956168
GO:0030011	maintenance of cell polarity	0.00214879681956168
GO:0035090	maintenance of apical/basal cell polarity	0.00214879681956168
GO:0045197	establishment and/or maintenance of epithelial cell polarity	0.00552490824291214
GO:0008093	cytoskeletal adaptor activity	0.00552490824291214
GO:0035088	establishment and/or maintenance of apical/basal cell polarity	0.00552490824291214
GO:0016528	sarcoplasm	0.0119337188304714
GO:0016529	sarcoplasmic reticulum	0.0119337188304714
GO:0007163	establishment and/or maintenance of cell polarity	0.0124580687034563
GO:0060090	molecular adaptor activity	0.0234214083346067
GO:0005200	structural constituent of cytoskeleton	0.0280653228297728
GO:0016323	basolateral plasma membrane	0.0280653228297728
GO:0006887	exocytosis	0.0340191124462199

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>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	2.17e-25	115
neural tube	8.82e-16	57
neural rod	8.82e-16	57
future spinal cord	8.82e-16	57
neural keel	8.82e-16	57
regional part of nervous system	1.93e-15	94
nervous system	1.93e-15	94
central nervous system	2.27e-15	82
neural plate	3.03e-13	86
presumptive neural plate	3.03e-13	86
neurectoderm	3.14e-13	90
regional part of brain	3.15e-12	59
brain	4.34e-12	69
future brain	4.34e-12	69
gray matter	7.40e-12	34
brain grey matter	7.40e-12	34
telencephalon	1.35e-11	34
regional part of telencephalon	3.25e-11	33
regional part of forebrain	4.35e-11	41
forebrain	4.35e-11	41
future forebrain	4.35e-11	41
cerebral hemisphere	8.84e-11	32
anterior neural tube	1.42e-10	42
pre-chordal neural plate	7.72e-09	61
anterior region of body	6.92e-08	129
craniocervical region	6.92e-08	129
regional part of cerebral cortex	7.39e-08	22
cerebral cortex	1.35e-07	25
pallium	1.35e-07	25
ectoderm	3.74e-07	173
presumptive ectoderm	3.74e-07	173
head	5.06e-07	123
ectoderm-derived structure	5.13e-07	169

Disease

Ontology term	p-value	n
myeloid leukemia	1.50e-08	31

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
GATA1#2623	6	6.25860375867713	0.000174951126422723	0.00212808300634321
SMARCA4#6597	2	24.1178312781366	0.00302659619636889	0.0160690702126262
TAL1#6886	4	9.19034359305853	0.000703860514173596	0.00565857041334587

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.