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Coexpression cluster:C3542

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Full id: C3542_signet_adenocarcinoma_chronic_liver_Hepatocyte_kidney_gastric



Phase1 CAGE Peaks

Hg19::chr16:20775295..20775302,+p4@ACSM3
Hg19::chr16:20775312..20775352,+p1@ACSM3
Hg19::chr16:20775358..20775386,+p2@ACSM3


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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract3.00e-10118
gastrointestinal system3.54e-0825
digestive system3.59e-08145
digestive tract3.59e-08145
primitive gut3.59e-08145
intestine3.02e-0717
endoderm-derived structure3.68e-07160
endoderm3.68e-07160
presumptive endoderm3.68e-07160
Disease
Ontology termp-valuen
hematologic cancer1.30e-0851
immune system cancer1.30e-0851
leukemia5.05e-0839
myeloid leukemia5.81e-0831
chronic leukemia7.14e-078


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#90536.336201576962630.003930750035764890.0189714683204052
E2F6#187635.017155731697390.00791769806886330.0321519681408303
IRF4#3662321.91451268674419.49854535978121e-050.00136453724735927
MAX#414936.452555509007120.003721913834265510.0186272263243653
NFKB1#479035.488063424193840.006049381815655430.02692254601974
NFYB#4801211.17319550235760.01025467135054530.038118864649046
RXRA#6256320.07461713913330.0001235730348432220.00165078590253151
SETDB1#9869340.32002617801051.52461559299059e-050.000358301817993574
SIN3A#2594235.408884726815140.006318961977991520.0276128062769647
SP1#666735.69838137814090.005403962701712170.0246069262558474
SPI1#668838.204323508522730.001810593189410520.0108976799278956
ZNF263#1012738.221841637010680.001799043925565870.0109219524816703



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.