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Coexpression cluster:C3706: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3706_temporal_duodenum_occipital_Neural_mucinous_parietal_Neurons
|full_id=C3706_temporal_duodenum_occipital_Neural_mucinous_parietal_Neurons
|id=C3706
|id=C3706

Revision as of 16:40, 12 September 2012


Full id: C3706_temporal_duodenum_occipital_Neural_mucinous_parietal_Neurons



Phase1 CAGE Peaks

Hg19::chr18:12657866..12657958,-p2@SPIRE1
Hg19::chr18:12657964..12657987,-p3@SPIRE1
Hg19::chr18:12657988..12658128,-p1@SPIRE1


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
neural tube5.22e-2757
neural rod5.22e-2757
future spinal cord5.22e-2757
neural keel5.22e-2757
regional part of nervous system1.14e-2694
nervous system1.14e-2694
central nervous system5.69e-2682
regional part of brain2.89e-2359
brain2.93e-2369
future brain2.93e-2369
anatomical system1.43e-22625
neural plate1.67e-2286
presumptive neural plate1.67e-2286
anatomical group2.33e-22626
anterior neural tube2.56e-2242
regional part of forebrain4.47e-2241
forebrain4.47e-2241
future forebrain4.47e-2241
multi-cellular organism3.16e-21659
organ1.10e-20511
neurectoderm3.94e-2090
telencephalon2.73e-1934
gray matter2.85e-1934
brain grey matter2.85e-1934
regional part of telencephalon1.27e-1833
ectoderm-derived structure2.48e-18169
cerebral hemisphere4.39e-1832
embryonic structure4.79e-18605
developing anatomical structure4.79e-18605
germ layer5.75e-18604
embryonic tissue5.75e-18604
presumptive structure5.75e-18604
epiblast (generic)5.75e-18604
embryo4.13e-17612
ectoderm5.77e-17173
presumptive ectoderm5.77e-17173
adult organism1.16e-16115
pre-chordal neural plate1.97e-1661
head2.88e-16123
cerebral cortex2.60e-1425
pallium2.60e-1425
anterior region of body4.82e-14129
craniocervical region4.82e-14129
regional part of cerebral cortex6.54e-1422
tube5.32e-13194
neocortex8.38e-1320
anatomical conduit1.25e-12241
organism subdivision1.32e-10365
anatomical cluster1.54e-10286
epithelium2.40e-09309
cell layer2.51e-09312
multi-tissue structure7.79e-07347


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
CTCF#1066435.360256373075030.0064925092527670.0279236986307183
E2F1#186934.907389214879320.008460985347239390.0325053098650114
E2F6#187635.017155731697390.00791769806886330.0321895156920866
ELF1#199734.258097958807540.01295179875054610.0461883804448639
JUND#372736.994663941871030.002921845042734990.0156650192206468
REST#597839.650028716128020.001112636247114590.00766963349035712
TFAP2A#7020316.5186343730450.0002218033880766340.0024815130206037
TFAP2C#7022310.80922860986020.0007916746575753130.00615557694777458
YY1#752834.911170749853860.008441455341808260.0329084417485298
ZBTB7A#5134137.35190930787590.002516255860282270.014007528692075



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.