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Coexpression cluster:C3382: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3382_Hodgkin_acute_chronic_CD19_CD133_thymus_granulocyte
|full_id=C3382_Hodgkin_acute_chronic_CD19_CD133_thymus_granulocyte
|id=C3382
|id=C3382

Revision as of 16:17, 12 September 2012


Full id: C3382_Hodgkin_acute_chronic_CD19_CD133_thymus_granulocyte



Phase1 CAGE Peaks

Hg19::chr13:51483881..51483935,+p1@RNASEH2B
Hg19::chr13:51484119..51484151,+p3@RNASEH2B
Hg19::chr13:51484154..51484216,+p2@RNASEH2B


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><br>disease_data<br>


Disease
Ontology termp-valuen
hematologic cancer1.38e-2051
immune system cancer1.38e-2051
leukemia1.68e-1639
myeloid leukemia4.25e-1331


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#90536.336201576962630.003930750035764890.0189539499970104
CTCF#1066435.360256373075030.0064925092527670.027876631057792
CTCFL#140690319.74647435897440.0001298372005551160.00171407753618706
E2F1#186934.907389214879320.008460985347239390.0324230149218586
E2F4#1874312.66806031528440.0004917987006298980.00436203520128119
E2F6#187635.017155731697390.00791769806886330.0321145080824115
EBF1#187938.9064668465690.00141523283560980.00913394525511385
ELF1#199734.258097958807540.01295179875054610.0460876630224287
HMGN3#932438.178547723350590.001827766942164210.0108478804155645
MYC#460935.22228187160940.007020843755740150.0293711156020727
NANOG#79923329.24477848101273.99627955670032e-050.000735838223946095
NFKB1#479035.488063424193840.006049381815655430.0269019113240467
PAX5#507936.669565531177830.003370290999677260.0172560947992594
RXRA#6256320.07461713913330.0001235730348432220.00164994172666726
SIN3A#2594235.408884726815140.006318961977991520.0275874120064985
TFAP2A#7020211.01242291536330.01054990655215560.0389997766671592
TFAP2C#7022310.80922860986020.0007916746575753130.00614003487022933
YY1#752834.911170749853860.008441455341808260.0328483607602039
ZBTB7A#5134137.35190930787590.002516255860282270.0139807014838548
ZEB1#6935316.88843201754390.0002075486917327580.00242300221505449
ZNF263#1012738.221841637010680.001799043925565870.0109105364695531



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.