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Coexpression cluster:C4707: Difference between revisions

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|ontology_enrichment_disease=DOID:2531!1.94e-21!51;DOID:0060083!1.94e-21!51;DOID:1240!1.18e-18!39;DOID:8692!1.65e-16!31;DOID:162!3.06e-11!235;DOID:14566!6.20e-11!239;DOID:0050686!1.39e-10!137
|ontology_enrichment_disease=DOID:2531!1.94e-21!51;DOID:0060083!1.94e-21!51;DOID:1240!1.18e-18!39;DOID:8692!1.65e-16!31;DOID:162!3.06e-11!235;DOID:14566!6.20e-11!239;DOID:0050686!1.39e-10!137
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tf_chipseq_enrich=BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.00139526811629907!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191172395913779!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324357287445679!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322528198627794!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465011829113508!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00765312818392953!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109229887658897!REST#5978;3:9.65002871612802:0.00111263624711459:0.00771495266315235!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278305600311836!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00545786530239369!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331285568331246!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140931648947294!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243771680340503
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}}
}}

Revision as of 13:59, 5 September 2012


Full id: C4707_lymphoma_granulocyte_acute_rhabdomyosarcoma_Hodgkin_CD34_Keratinocyte



Phase1 CAGE Peaks

Hg19::chr7:92465854..92465865,-p6@CDK6
Hg19::chr7:92465868..92465922,-p1@CDK6
Hg19::chr7:92465924..92465939,-p5@CDK6


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>

Cell Type
Ontology termp-valuen
animal cell7.69e-08679
eukaryotic cell7.69e-08679
native cell2.22e-07722
Disease
Ontology termp-valuen
hematologic cancer1.94e-2151
immune system cancer1.94e-2151
leukemia1.18e-1839
myeloid leukemia1.65e-1631
cancer3.06e-11235
disease of cellular proliferation6.20e-11239
organ system cancer1.39e-10137


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
BCLAF1#9774321.65264761012189.8473954032885e-050.00139526811629907
CCNT2#90536.336201576962630.003930750035764890.0191172395913779
E2F6#187635.017155731697390.00791769806886330.0324357287445679
EGR1#195834.988179094810140.008056488137383440.0322528198627794
ELF1#199734.258097958807540.01295179875054610.0465011829113508
ETS1#211339.728760922202340.001085840092584840.00765312818392953
HMGN3#932438.178547723350590.001827766942164210.0109229887658897
REST#597839.650028716128020.001112636247114590.00771495266315235
SIN3A#2594235.408884726815140.006318961977991520.0278305600311836
TAF7#6879311.43306940492390.0006690181981945830.00545786530239369
YY1#752834.911170749853860.008441455341808260.0331285568331246
ZBTB7A#5134137.35190930787590.002516255860282270.0140931648947294
ZEB1#6935316.88843201754390.0002075486917327580.00243771680340503



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.

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