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Coexpression cluster:C2881: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!2.98e-08!375
|ontology_enrichment_uberon=UBERON:0002384!2.98e-08!375
|tf_chipseq_enrich=EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101657537401424!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.0192121259464513!FOS#2353;3:6.7484664816708:0.00503245277631794:0.0234761629223633!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0283150045280375!MXI1#4601;3:7.47117872156947:0.00374131473855096:0.0186439149718257!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00769263702920424!NFYA#4800;3:13.8191855248729:0.000613241180673451:0.00508990667315859!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0435265511116397!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195963833311653!RFX5#5993;3:9.03593312039632:0.00214456119132407:0.0123907848119437!SP2#6668;2:13.0767652469223:0.00833003653661494:0.0328133627219676!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0281140948946931!SREBF1#6720;3:35.2543870803662:3.78704019553645e-05:0.000725315772935322!SREBF2#6721;1:109.235815602837:0.00912320148412682:0.0345173902260803!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162896823555134!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483416937287318!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00613560622276823
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}}
}}

Revision as of 13:15, 5 September 2012


Full id: C2881_immature_migratory_cord_Mast_mycosis_Smooth_acute



Phase1 CAGE Peaks

Hg19::chr7:141286167..141286178,+p@chr7:141286167..141286178
+
Hg19::chr8:126010973..126010985,+p4@SQLE
Hg19::chr8:126010988..126010995,+p5@SQLE
Hg19::chr8:126011002..126011010,+p6@SQLE


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><br>

Uber Anatomy
Ontology termp-valuen
connective tissue2.98e-08375


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
EGR1#195844.988179094810140.001615011500076050.0101657537401424
ETS1#211337.296570691651750.00400857377511390.0192121259464513
FOS#235336.74846648167080.005032452776317940.0234761629223633
HMGN3#932436.133910792512940.006640696683324720.0283150045280375
MXI1#460137.471178721569470.003741314738550960.0186439149718257
NFKB1#479045.488063424193840.001102199566301980.00769263702920424
NFYA#4800313.81918552487290.0006132411806734510.00508990667315859
PAX5#507935.002174148383370.01196533174786410.0435265511116397
REST#597837.237521537096020.004104697304192610.0195963833311653
RFX5#599339.035933120396320.002144561191324070.0123907848119437
SP2#6668213.07676524692230.008330036536614940.0328133627219676
SPI1#668836.153242631392040.006580387113059030.0281140948946931
SREBF1#6720335.25438708036623.78704019553645e-050.000725315772935322
SREBF2#67211109.2358156028370.009123201484126820.0345173902260803
TCF12#693837.975848676639820.003090920396013070.0162896823555134
USF1#739134.771124457905970.01370465887188020.0483416937287318
ZEB1#6935312.66632401315790.000793336075912850.00613560622276823



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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