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Coexpression cluster:C3873: Difference between revisions

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|ontology_enrichment_disease=DOID:162!2.88e-43!235;DOID:14566!3.27e-43!239;DOID:0050686!9.62e-22!137;DOID:0050687!2.89e-21!143;DOID:305!1.61e-17!106;DOID:2531!2.19e-14!51;DOID:0060083!2.19e-14!51;DOID:1240!9.76e-12!39;DOID:8692!5.40e-09!31;DOID:3095!8.19e-07!22;DOID:2994!8.19e-07!22
|ontology_enrichment_disease=DOID:162!2.88e-43!235;DOID:14566!3.27e-43!239;DOID:0050686!9.62e-22!137;DOID:0050687!2.89e-21!143;DOID:305!1.61e-17!106;DOID:2531!2.19e-14!51;DOID:0060083!2.19e-14!51;DOID:1240!9.76e-12!39;DOID:8692!5.40e-09!31;DOID:3095!8.19e-07!22;DOID:2994!8.19e-07!22
|ontology_enrichment_uberon=UBERON:0000487!5.04e-09!22;UBERON:0001986!2.32e-08!18;UBERON:0004638!2.32e-08!18;UBERON:0004852!2.32e-08!18;UBERON:0006914!3.56e-08!25;UBERON:0000055!4.27e-07!69;UBERON:0000490!5.42e-07!138;UBERON:0001737!5.73e-07!9;UBERON:0000072!8.58e-07!46
|ontology_enrichment_uberon=UBERON:0000487!5.04e-09!22;UBERON:0001986!2.32e-08!18;UBERON:0004638!2.32e-08!18;UBERON:0004852!2.32e-08!18;UBERON:0006914!3.56e-08!25;UBERON:0000055!4.27e-07!69;UBERON:0000490!5.42e-07!138;UBERON:0001737!5.73e-07!9;UBERON:0000072!8.58e-07!46
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}}
}}

Revision as of 11:53, 5 September 2012


Full id: C3873_neuroblastoma_nonsmall_teratocarcinoma_acute_neuroectodermal_medulloblastoma_small



Phase1 CAGE Peaks

Hg19::chr1:153643418..153643429,-p2@ILF2
Hg19::chr1:153643442..153643475,-p1@ILF2
Hg19::chr1:156308018..156308101,-p1@CCT3


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>


Uber Anatomy
Ontology termp-valuen
simple squamous epithelium5.04e-0922
endothelium2.32e-0818
blood vessel endothelium2.32e-0818
cardiovascular system endothelium2.32e-0818
squamous epithelium3.56e-0825
vessel4.27e-0769
unilaminar epithelium5.42e-07138
larynx5.73e-079
segment of respiratory tract8.58e-0746
Disease
Ontology termp-valuen
cancer2.88e-43235
disease of cellular proliferation3.27e-43239
organ system cancer9.62e-22137
cell type cancer2.89e-21143
carcinoma1.61e-17106
hematologic cancer2.19e-1451
immune system cancer2.19e-1451
leukemia9.76e-1239
myeloid leukemia5.40e-0931
germ cell and embryonal cancer8.19e-0722
germ cell cancer8.19e-0722


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
BDP1#558142700.1022727272732.7031542867596e-069.4199109294256e-05
BRCA1#672213.45615376214920.007119807716084560.0296261045483946
BRF1#297221184.788461538469.40380308868135e-074.02674780967114e-05
CEBPB#105137.971147625824820.001974187055288560.0115237045532798
CHD2#1106310.34402283411690.0009033701102746880.00660508757679769
CTCF#1066435.360256373075030.0064925092527670.0279524764551791
E2F1#186934.907389214879320.008460985347239390.0325460148311419
E2F6#187635.017155731697390.00791769806886330.0322321757401681
EP300#203336.77394172622320.003216880500103790.0167481446934367
FOS#235338.99795530889440.001372499272417130.00897741914648792
FOSL2#2355211.28680040304110.0100534586973120.0376753085108387
GATA2#2624312.7449317335540.0004829527704283790.0043692917871422
GATA3#2625218.15767757147070.003944546819279620.0189504818647934
GTF2B#2959221.29588662288280.002878180589911410.0155812929001533
GTF2F1#2962312.73966087675770.0004835525047438590.00434012891396905
HSF1#32973164.2906666666672.24910326529255e-071.1911465310542e-05
IRF1#365937.63716375356390.002244692747297240.0128119721190828
IRF3#3661346.98195221148969.63568551583244e-060.000253550355149414
MAX#414936.452555509007120.003721913834265510.0186585205652981
MEF2A#4205318.74323090964410.0001518243905622470.00195035516924114
MYC#460935.22228187160940.007020843755740150.0294596183610183
NFKB1#479035.488063424193840.006049381815655430.0269662122773161
NFYA#4800318.42558069983050.0001598135507814160.0019972199868446
NFYB#4801316.75979325353650.0002123649923296180.00245916259384776
PAX5#507936.669565531177830.003370290999677260.0172976471431173
POLR3A#111282226.0880733944952.5985838218527e-050.000561426346235983
POLR3G#1062221449.623529411766.26846128533636e-072.86257904756993e-05
PPARGC1A#108911116.6837121212120.008545763211786680.0325686383037436
RFX5#5993312.04791082719510.0005717246050312580.00484661899552431
RXRA#6256213.38307809275550.007196434429465730.0298308559388359
SIN3A#2594235.408884726815140.006318961977991520.0276857855442991
SP1#666735.69838137814090.005403962701712170.0246596085377777
STAT1#6772320.70658749719920.0001125992441046670.00154896634023278
TAF7#6879311.43306940492390.0006690181981945830.00543156029238527
TCF12#6938310.63446490218640.0008313523990202070.006294447817984
THAP1#55145220.91276306856750.002983447413736940.0158690228899044
TRIM28#10155212.39368336350830.008368344129438470.0329108861475533
USF1#739136.361499277207960.00388404057290560.0190327646691544
YY1#752834.911170749853860.008441455341808260.0329514914761021



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.