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Coexpression cluster:C1082

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Full id: C1082_acute_CD4_thymus_small_non_chronic_lymphangiectasia



Phase1 CAGE Peaks

Hg19::chr4:108971419..108971431,-p@chr4:108971419..108971431
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Hg19::chr4:108978060..108978063,-p@chr4:108978060..108978063
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Hg19::chr4:109010390..109010401,-p@chr4:109010390..109010401
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Hg19::chr4:109089901..109089930,-p3@LEF1
Hg19::chr4:109089966..109089977,-p15@LEF1
Hg19::chr4:109089996..109090012,-p5@LEF1
Hg19::chr4:109090026..109090031,-p20@LEF1
Hg19::chr4:109090106..109090124,-p10@LEF1


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


No GOStat results

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>


Uber Anatomy
Ontology termp-valuen
adult organism4.83e-20115
neural tube2.15e-1257
neural rod2.15e-1257
future spinal cord2.15e-1257
neural keel2.15e-1257
central nervous system3.14e-1082
blood3.71e-1015
haemolymphatic fluid3.71e-1015
organism substance3.71e-1015
brain4.23e-1069
future brain4.23e-1069
regional part of brain4.82e-1059
anterior neural tube9.51e-1042
regional part of forebrain1.98e-0941
forebrain1.98e-0941
future forebrain1.98e-0941
regional part of nervous system1.61e-0894
nervous system1.61e-0894
telencephalon1.84e-0834
gray matter3.61e-0834
brain grey matter3.61e-0834
regional part of telencephalon4.51e-0833
cerebral hemisphere7.88e-0832
anterior region of body8.13e-08129
craniocervical region8.13e-08129
neural plate2.68e-0786
presumptive neural plate2.68e-0786
regional part of cerebral cortex9.65e-0722


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
CTBP2#1488539.19812521208015.52610241698922e-083.46839309091308e-06
E2F1#186953.067118259299580.01129732364974160.0414444197075893
E2F6#187653.135722332310870.01024880501420960.0381527338042786
ZNF263#1012755.138651023131670.001082531249033560.00763908656201456



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.