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Coexpression cluster:C644

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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
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Hg19::chr11:33903432..33903464,-p@chr11:33903432..33903464
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Hg19::chr11:33903469..33903500,-p@chr11:33903469..33903500
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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
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Hg19::chr19:12997072..12997102,-p@chr19:12997072..12997102
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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


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


GO IDGO nameFDR corrected p-value
GO:0045199maintenance of epithelial cell polarity0.00214879681956168
GO:0030507spectrin binding0.00214879681956168
GO:0030011maintenance of cell polarity0.00214879681956168
GO:0035090maintenance of apical/basal cell polarity0.00214879681956168
GO:0045197establishment and/or maintenance of epithelial cell polarity0.00552490824291214
GO:0008093cytoskeletal adaptor activity0.00552490824291214
GO:0035088establishment and/or maintenance of apical/basal cell polarity0.00552490824291214
GO:0016528sarcoplasm0.0119337188304714
GO:0016529sarcoplasmic reticulum0.0119337188304714
GO:0007163establishment and/or maintenance of cell polarity0.0124580687034563
GO:0060090molecular adaptor activity0.0234214083346067
GO:0005200structural constituent of cytoskeleton0.0280653228297728
GO:0016323basolateral plasma membrane0.0280653228297728
GO:0006887exocytosis0.0340191124462199



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>


Uber Anatomy
Ontology termp-valuen
adult organism2.17e-25115
neural tube8.82e-1657
neural rod8.82e-1657
future spinal cord8.82e-1657
neural keel8.82e-1657
regional part of nervous system1.93e-1594
nervous system1.93e-1594
central nervous system2.27e-1582
neural plate3.03e-1386
presumptive neural plate3.03e-1386
neurectoderm3.14e-1390
regional part of brain3.15e-1259
brain4.34e-1269
future brain4.34e-1269
gray matter7.40e-1234
brain grey matter7.40e-1234
telencephalon1.35e-1134
regional part of telencephalon3.25e-1133
regional part of forebrain4.35e-1141
forebrain4.35e-1141
future forebrain4.35e-1141
cerebral hemisphere8.84e-1132
anterior neural tube1.42e-1042
pre-chordal neural plate7.72e-0961
anterior region of body6.92e-08129
craniocervical region6.92e-08129
regional part of cerebral cortex7.39e-0822
cerebral cortex1.35e-0725
pallium1.35e-0725
ectoderm3.74e-07173
presumptive ectoderm3.74e-07173
head5.06e-07123
ectoderm-derived structure5.13e-07169
Disease
Ontology termp-valuen
myeloid leukemia1.50e-0831


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


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
GATA1#262366.258603758677130.0001749511264227230.00212808300634321
SMARCA4#6597224.11783127813660.003026596196368890.0160690702126262
TAL1#688649.190343593058530.0007038605141735960.00565857041334587



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


This analysis result is provided for C0 - C305 clusters.