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Coexpression cluster:C3067: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000481!5.83e-22!347;UBERON:0007023!1.99e-19!115;UBERON:0001017!3.43e-19!82;UBERON:0005743!1.35e-18!86;UBERON:0000073!2.69e-17!94;UBERON:0001016!2.69e-17!94;UBERON:0000955!2.10e-16!69;UBERON:0006238!2.10e-16!69;UBERON:0000477!4.48e-15!286;UBERON:0001049!3.78e-14!57;UBERON:0005068!3.78e-14!57;UBERON:0006241!3.78e-14!57;UBERON:0007135!3.78e-14!57;UBERON:0002616!4.06e-14!59;UBERON:0000475!1.07e-13!365;UBERON:0000119!1.23e-13!312;UBERON:0000483!1.76e-13!309;UBERON:0000153!2.39e-13!129;UBERON:0007811!2.39e-13!129;UBERON:0000033!4.95e-13!123;UBERON:0004111!5.52e-13!241;UBERON:0003075!6.78e-13!86;UBERON:0007284!6.78e-13!86;UBERON:0000025!3.10e-12!194;UBERON:0004121!3.38e-12!169;UBERON:0000468!1.36e-11!659;UBERON:0000922!1.38e-11!612;UBERON:0000062!3.45e-11!511;UBERON:0003080!3.50e-11!42;UBERON:0002346!3.82e-11!90;UBERON:0000924!4.96e-11!173;UBERON:0006601!4.96e-11!173;UBERON:0002780!1.05e-10!41;UBERON:0001890!1.05e-10!41;UBERON:0006240!1.05e-10!41;UBERON:0000467!3.09e-10!625;UBERON:0000480!5.88e-10!626;UBERON:0003056!2.82e-09!61;UBERON:0002050!3.56e-09!605;UBERON:0005423!3.56e-09!605;UBERON:0000923!7.46e-09!604;UBERON:0005291!7.46e-09!604;UBERON:0006598!7.46e-09!604;UBERON:0002532!7.46e-09!604;UBERON:0002020!8.91e-09!34;UBERON:0003528!8.91e-09!34;UBERON:0001893!1.10e-08!34;UBERON:0002791!1.34e-08!33;UBERON:0001869!4.44e-08!32;UBERON:0003104!4.45e-08!238;UBERON:0009142!4.45e-08!238;UBERON:0000064!9.93e-08!219;UBERON:0001007!3.52e-07!155;UBERON:0001555!3.52e-07!155;UBERON:0007026!3.52e-07!155
|ontology_enrichment_uberon=UBERON:0000481!5.83e-22!347;UBERON:0007023!1.99e-19!115;UBERON:0001017!3.43e-19!82;UBERON:0005743!1.35e-18!86;UBERON:0000073!2.69e-17!94;UBERON:0001016!2.69e-17!94;UBERON:0000955!2.10e-16!69;UBERON:0006238!2.10e-16!69;UBERON:0000477!4.48e-15!286;UBERON:0001049!3.78e-14!57;UBERON:0005068!3.78e-14!57;UBERON:0006241!3.78e-14!57;UBERON:0007135!3.78e-14!57;UBERON:0002616!4.06e-14!59;UBERON:0000475!1.07e-13!365;UBERON:0000119!1.23e-13!312;UBERON:0000483!1.76e-13!309;UBERON:0000153!2.39e-13!129;UBERON:0007811!2.39e-13!129;UBERON:0000033!4.95e-13!123;UBERON:0004111!5.52e-13!241;UBERON:0003075!6.78e-13!86;UBERON:0007284!6.78e-13!86;UBERON:0000025!3.10e-12!194;UBERON:0004121!3.38e-12!169;UBERON:0000468!1.36e-11!659;UBERON:0000922!1.38e-11!612;UBERON:0000062!3.45e-11!511;UBERON:0003080!3.50e-11!42;UBERON:0002346!3.82e-11!90;UBERON:0000924!4.96e-11!173;UBERON:0006601!4.96e-11!173;UBERON:0002780!1.05e-10!41;UBERON:0001890!1.05e-10!41;UBERON:0006240!1.05e-10!41;UBERON:0000467!3.09e-10!625;UBERON:0000480!5.88e-10!626;UBERON:0003056!2.82e-09!61;UBERON:0002050!3.56e-09!605;UBERON:0005423!3.56e-09!605;UBERON:0000923!7.46e-09!604;UBERON:0005291!7.46e-09!604;UBERON:0006598!7.46e-09!604;UBERON:0002532!7.46e-09!604;UBERON:0002020!8.91e-09!34;UBERON:0003528!8.91e-09!34;UBERON:0001893!1.10e-08!34;UBERON:0002791!1.34e-08!33;UBERON:0001869!4.44e-08!32;UBERON:0003104!4.45e-08!238;UBERON:0009142!4.45e-08!238;UBERON:0000064!9.93e-08!219;UBERON:0001007!3.52e-07!155;UBERON:0001555!3.52e-07!155;UBERON:0007026!3.52e-07!155
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}}
}}

Revision as of 14:27, 5 September 2012


Full id: C3067_medulloblastoma_lung_placenta_renal_retina_gall_rectum



Phase1 CAGE Peaks

Hg19::chr11:100557931..100557947,+p4@ARHGAP42
Hg19::chr11:100557958..100558008,+p2@ARHGAP42
Hg19::chr11:100558010..100558029,+p1@ARHGAP42


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
multi-tissue structure5.83e-22347
adult organism1.99e-19115
central nervous system3.43e-1982
regional part of nervous system2.69e-1794
nervous system2.69e-1794
brain2.10e-1669
future brain2.10e-1669
anatomical cluster4.48e-15286
neural tube3.78e-1457
neural rod3.78e-1457
future spinal cord3.78e-1457
neural keel3.78e-1457
regional part of brain4.06e-1459
organism subdivision1.07e-13365
cell layer1.23e-13312
epithelium1.76e-13309
anterior region of body2.39e-13129
craniocervical region2.39e-13129
head4.95e-13123
anatomical conduit5.52e-13241
neural plate6.78e-1386
presumptive neural plate6.78e-1386
tube3.10e-12194
ectoderm-derived structure3.38e-12169
multi-cellular organism1.36e-11659
embryo1.38e-11612
organ3.45e-11511
anterior neural tube3.50e-1142
neurectoderm3.82e-1190
ectoderm4.96e-11173
presumptive ectoderm4.96e-11173
regional part of forebrain1.05e-1041
forebrain1.05e-1041
future forebrain1.05e-1041
anatomical system3.09e-10625
anatomical group5.88e-10626
pre-chordal neural plate2.82e-0961
embryonic structure3.56e-09605
developing anatomical structure3.56e-09605
germ layer7.46e-09604
embryonic tissue7.46e-09604
presumptive structure7.46e-09604
epiblast (generic)7.46e-09604
gray matter8.91e-0934
brain grey matter8.91e-0934
telencephalon1.10e-0834
regional part of telencephalon1.34e-0833
cerebral hemisphere4.44e-0832
mesenchyme4.45e-08238
entire embryonic mesenchyme4.45e-08238
organ part9.93e-08219
digestive system3.52e-07155
digestive tract3.52e-07155
primitive gut3.52e-07155


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
E2F1#186934.907389214879320.008460985347239390.0323541611262571
EGR1#195834.988179094810140.008056488137383440.0319030698635091
ELF1#199734.258097958807540.01295179875054610.0460030237283459
GABPB1#255337.067683836182170.002832212825417420.0153635005076492
MEF2A#4205318.74323090964410.0001518243905622470.00194748065904329
SIN3A#2594235.408884726815140.006318961977991520.027536763332198
TCF12#6938310.63446490218640.0008313523990202070.00627624788212168



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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