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Coexpression cluster:C2336: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2336_occipital_parietal_temporal_cerebellum_neuroblastoma_duodenum_pineal
|full_id=C2336_occipital_parietal_temporal_cerebellum_neuroblastoma_duodenum_pineal
|id=C2336
|id=C2336

Revision as of 15:02, 12 September 2012


Full id: C2336_occipital_parietal_temporal_cerebellum_neuroblastoma_duodenum_pineal



Phase1 CAGE Peaks

Hg19::chr15:48470481..48470541,-p1@MYEF2
Hg19::chr15:48470544..48470555,-p2@MYEF2
Hg19::chr15:48470558..48470572,-p3@MYEF2
Hg19::chr15:71185148..71185214,+p1@LRRC49


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
regional part of nervous system2.23e-3794
nervous system2.23e-3794
central nervous system1.44e-3282
neurectoderm2.12e-3190
neural tube1.23e-2957
neural rod1.23e-2957
future spinal cord1.23e-2957
neural keel1.23e-2957
neural plate2.32e-2986
presumptive neural plate2.32e-2986
brain1.00e-2569
future brain1.00e-2569
regional part of forebrain4.10e-2541
forebrain4.10e-2541
future forebrain4.10e-2541
regional part of brain1.01e-2459
anterior neural tube3.15e-2442
pre-chordal neural plate8.27e-2361
ectoderm1.03e-22173
presumptive ectoderm1.03e-22173
ectoderm-derived structure4.80e-21169
adult organism6.38e-21115
telencephalon8.92e-2134
gray matter9.75e-2134
brain grey matter9.75e-2134
regional part of telencephalon3.20e-2033
cerebral hemisphere5.85e-2032
anterior region of body1.20e-18129
craniocervical region1.20e-18129
head1.21e-18123
cerebral cortex6.85e-1625
pallium6.85e-1625
regional part of cerebral cortex1.64e-1422
neocortex2.23e-1320
tube6.42e-13194
anatomical conduit9.68e-13241
epithelium2.01e-10309
anatomical cluster2.68e-10286
cell layer3.92e-10312
organism subdivision6.77e-09365
multi-tissue structure5.25e-08347
posterior neural tube9.83e-0715
chordal neural plate9.83e-0715


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
BRCA1#672315.13817298241780.0004682184421431190.00430081494098375
CHD2#110637.758017125587640.003351522464536340.0172931008682235
ELF1#199744.258097958807540.003041525565781240.016074788146583
JUND#372746.994663941871030.000417684217818580.0039116321758209
TAF1#687243.343046285745290.008005664898701650.0321763954725996
TAF7#6879411.43306940492395.85061525419808e-050.000967895464174233
TBP#690843.706770687096390.005296377814784350.0243828088952774
ZBTB33#10009323.74854377248590.0001229451908818380.00165510090107093



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.