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Coexpression cluster:C3595

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Full id: C3595_acute_Mast_parietal_chronic_placenta_choriocarcinoma_Neutrophils



Phase1 CAGE Peaks

Hg19::chr16:85589286..85589316,+p@chr16:85589286..85589316
+
Hg19::chr16:85589318..85589348,+p@chr16:85589318..85589348
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Hg19::chr16:85589349..85589370,+p@chr16:85589349..85589370
+


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
hematopoietic system1.97e-1998
blood island1.97e-1998
hemolymphoid system9.47e-15108
bone marrow2.21e-1376
bone element7.95e-1382
immune system4.13e-1093
skeletal element4.98e-1090
adult organism1.92e-07114
skeletal system3.12e-07100
blood6.45e-0715
haemolymphatic fluid6.45e-0715
organism substance6.45e-0715
Disease
Ontology termp-valuen
myeloid leukemia1.42e-0831
leukemia1.81e-0739


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#90536.336201576962630.003930750035764890.0189767301338348
CEBPB#105137.971147625824820.001974187055288560.0115114802002837
CHD2#1106310.34402283411690.0009033701102746880.00659723592384995
EP300#203336.77394172622320.003216880500103790.0167297969599811
FOS#235338.99795530889440.001372499272417130.00896562744007834
GATA2#2624312.7449317335540.0004829527704283790.00436702202517485
GTF2B#2959331.94382993432423.06634405746243e-050.000627441040394434
HDAC2#3066313.41562023662630.0004140761399857210.00390762609415096
HMGN3#932438.178547723350590.001827766942164210.0108602236828064
JUN#3725312.51282919233630.0005103313992726250.00443747406615883
JUNB#3726330.61063265982113.4847716247536e-050.000679891768573961
JUND#372736.994663941871030.002921845042734990.0156521632344173
RAD21#5885310.35503389545630.0009004912073565420.00663326288652207
SMARCA4#65973156.7659033078882.58908533335753e-071.33994788469042e-05
SMARCB1#6598318.25271578115740.000164397760679890.00202877676091776
SMARCC1#6599343.66335931963151.20046018043203e-050.000301526841712701
STAT2#6773365.26377118644073.59360517547754e-060.000118245913963988
TAL1#6886219.91241111829350.003287176608740550.0170115176572149
YY1#752834.911170749853860.008441455341808260.0328838923701273



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.