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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4852_gastric_ductal_adrenal_chronic_clear_bronchogenic_fibrosarcoma
|full_id=C4852_gastric_ductal_adrenal_chronic_clear_bronchogenic_fibrosarcoma
|id=C4852
|id=C4852

Revision as of 18:00, 12 September 2012


Full id: C4852_gastric_ductal_adrenal_chronic_clear_bronchogenic_fibrosarcoma



Phase1 CAGE Peaks

Hg19::chrX:134975521..134975551,-p1@CT45A5
Hg19::chrX:134975562..134975599,-p2@CT45A5
Hg19::chrX:134975858..134975877,+p1@SAGE1


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>


Cell Type
Ontology termp-valuen
bone matrix secreting cell7.82e-082
osteocyte7.82e-082
osteoclast7.82e-082
Uber Anatomy
Ontology termp-valuen
pons7.29e-103
brainstem nucleus9.34e-103
brainstem2.27e-098
locus ceruleus4.09e-072
hindbrain nucleus4.09e-072
Disease
Ontology termp-valuen
chronic leukemia5.73e-118
cancer2.42e-08235
disease of cellular proliferation5.30e-08239
clear cell adenocarcinoma5.59e-082
giant cell tumor7.82e-082
bone giant cell tumor7.82e-082
organ system cancer1.17e-07137


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#90536.336201576962630.003930750035764890.0191457701233677
CEBPB#105137.971147625824820.001974187055288560.0115910794843311
CTCF#1066435.360256373075030.0064925092527670.0281825093038127
CTCFL#140690319.74647435897440.0001298372005551160.00172519941333026
E2F6#187635.017155731697390.00791769806886330.0324841478870998
ELF1#199734.258097958807540.01295179875054610.046547588083561
ETS1#211339.728760922202340.001085840092584840.00765984825595864
GABPB1#255337.067683836182170.002832212825417420.0154963052846694
HDAC2#3066313.41562023662630.0004140761399857210.00394110070026143
IRF1#365937.63716375356390.002244692747297240.0128866241114213
SETDB1#9869340.32002617801051.52461559299059e-050.000360410429869498
SIN3A#2594235.408884726815140.006318961977991520.0278658138757529
SIRT6#515483153.6384039900252.75057764221434e-071.40610659997662e-05
SPI1#668838.204323508522730.001810593189410520.0109494233994699
YY1#752834.911170749853860.008441455341808260.0331622025368859



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.