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Coexpression cluster:C1708

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Full id: C1708_Mast_placenta_CD14_small_pituitary_non_parotid



Phase1 CAGE Peaks

Hg19::chr13:49550733..49550806,+p3@FNDC3A
Hg19::chr13:49550881..49550897,+p9@FNDC3A
Hg19::chr13:49550907..49550927,+p5@FNDC3A
Hg19::chr13:49550933..49550944,+p7@FNDC3A
Hg19::chr13:49550947..49550962,+p4@FNDC3A


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
bone marrow1.32e-1476
skeletal element4.84e-1290
immune system5.22e-1293
bone element5.37e-1282
organ1.06e-11503
skeletal system1.06e-11100
hematopoietic system6.00e-1198
blood island6.00e-1198
hemolymphoid system4.69e-09108


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
CCNT2#90556.336201576962639.78880505817628e-050.0013894169767204
CTCF#1066455.360256373075030.0002259278299937090.00249610458444017
E2F1#186954.907389214879320.0003512818099256460.00352425753571801
E2F6#187655.017155731697390.0003144978599297790.00322587330516658
EBF1#187947.12517347725520.0007230531046774210.00576934396817214
EGR1#195854.988179094810140.0003237398000590710.00330573533226137
GATA1#2623513.56030814380042.17950082879909e-067.8356243393786e-05
HEY1#2346254.040111043105710.0009288852205177990.00673880546996794
MYC#460955.22228187160940.0002573944848850610.00276308177684355
SPI1#668858.204323508522732.68916109982495e-050.000574224690461292
TAF1#687253.343046285745290.002394600090870310.0135249385587802
TBP#690853.706770687096390.001428755106721120.00918150102084957
TCF7L2#6934510.77017656313736.89693748574565e-060.000199642254455041
TFAP2C#7022510.80922860986026.77323239348459e-060.000197154297085601
YY1#752854.911170749853860.00034993140821360.00352561126205095



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.