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Coexpression cluster:C2408

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Full id: C2408_Alveolar_Renal_Mesenchymal_Mammary_chronic_Smooth_Trabecular



Phase1 CAGE Peaks

Hg19::chr17:40761660..40761748,+p1@TUBG1
Hg19::chr17:76183121..76183140,-p1@TK1
Hg19::chr17:79849438..79849493,-p1@ALYREF
Hg19::chr2:242626195..242626243,-p1@DTYMK


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


p.valueFDRnGenesnPathwayName
3.63651983036618e-050.01150958526310892100Pyrimidine metabolism (KEGG):00240
2.15074464693702e-050.0115095852631089277Metabolism of nucleotides (Reactome):REACT_1698



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:0000212meiotic spindle organization and biogenesis0.00482736289747114
GO:0005827polar microtubule0.00482736289747114
GO:0005816spindle pole body0.00482736289747114
GO:0004797thymidine kinase activity0.0055165801495387
GO:0000242pericentriolar material0.0055165801495387
GO:0019136deoxynucleoside kinase activity0.0055165801495387
GO:0005881cytoplasmic microtubule0.0055165801495387
GO:0000930gamma-tubulin complex0.00603358190524557
GO:0019206nucleoside kinase activity0.00750801537250585
GO:0005876spindle microtubule0.00833620862192411
GO:0007051spindle organization and biogenesis0.00833620862192411
GO:0044450microtubule organizing center part0.00924972184269641
GO:0000794condensed nuclear chromosome0.010684755395396
GO:0000922spindle pole0.010684755395396
GO:0000793condensed chromosome0.0167227884531008
GO:0051321meiotic cell cycle0.0213999825167229
GO:0005819spindle0.0221246261206918
GO:0005200structural constituent of cytoskeleton0.0223487963212117
GO:0019205nucleobase, nucleoside, nucleotide kinase activity0.0223487963212117
GO:0051258protein polymerization0.0223487963212117
GO:0000228nuclear chromosome0.0223487963212117
GO:0000226microtubule cytoskeleton organization and biogenesis0.0223487963212117
GO:0005813centrosome0.0270249962186935
GO:0005815microtubule organizing center0.0295049287144001
GO:0032553ribonucleotide binding0.0336590258312562
GO:0032555purine ribonucleotide binding0.0336590258312562
GO:0017076purine nucleotide binding0.0348772877197093
GO:0000166nucleotide binding0.0454283255281328
GO:0003924GTPase activity0.0454283255281328
GO:0005874microtubule0.0477435948549856
GO:0007017microtubule-based process0.0488269739331223



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>disease_data<br>


Cell Type
Ontology termp-valuen
animal cell2.16e-27679
eukaryotic cell2.16e-27679
epithelial cell8.31e-26254
embryonic cell7.51e-23248
non-terminally differentiated cell5.41e-15180
native cell1.39e-14722
mesodermal cell5.67e-13119
somatic cell6.84e-10591
squamous epithelial cell7.75e-0962
migratory neural crest cell5.08e-0841
lining cell5.50e-0857
barrier cell5.50e-0857
meso-epithelial cell6.70e-0844
epithelial cell of nephron2.09e-0716
endothelial cell3.34e-0735
ectodermal cell4.81e-0771
kidney cell5.01e-0718
kidney epithelial cell5.01e-0718
Uber Anatomy
Ontology termp-valuen
mesenchyme2.52e-11238
entire embryonic mesenchyme2.52e-11238
trunk mesenchyme5.94e-09143
epithelial tube6.55e-09118
unilaminar epithelium8.89e-09138
trunk1.02e-08216
segment of respiratory tract1.50e-0746
simple squamous epithelium1.99e-0722
nephron epithelium2.09e-0716
nephron2.09e-0716
uriniferous tubule2.09e-0716
metanephric mesenchyme2.09e-0716
nephrogenic mesenchyme2.09e-0716
Disease
Ontology termp-valuen
cancer3.33e-26235
disease of cellular proliferation1.63e-25239
cell type cancer8.00e-14143
organ system cancer4.63e-12137
carcinoma1.25e-11106
hematologic cancer5.06e-1051
immune system cancer5.06e-1051
leukemia2.95e-0839


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


No analysis results for this cluster

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.