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Coexpression cluster:C2336

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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
nervous system8.42e-3689
central nervous system2.24e-3281
neural tube2.89e-3056
neural rod2.89e-3056
future spinal cord2.89e-3056
neural keel2.89e-3056
neurectoderm3.99e-3086
regional part of nervous system1.61e-2853
regional part of brain1.61e-2853
neural plate4.79e-2882
presumptive neural plate4.79e-2882
brain2.14e-2568
future brain2.14e-2568
regional part of forebrain1.23e-2441
forebrain1.23e-2441
anterior neural tube1.23e-2441
future forebrain1.23e-2441
pre-chordal neural plate2.59e-2361
ectoderm-derived structure1.25e-20171
ectoderm1.25e-20171
presumptive ectoderm1.25e-20171
brain grey matter2.36e-2034
gray matter2.36e-2034
telencephalon2.53e-2034
anatomical cluster1.39e-19373
cerebral hemisphere1.81e-1932
regional part of telencephalon2.49e-1932
ecto-epithelium2.87e-19104
structure with developmental contribution from neural crest2.75e-18132
adult organism6.16e-18114
cerebral cortex1.42e-1525
pallium1.42e-1525
organ system subdivision2.98e-15223
regional part of cerebral cortex3.63e-1422
neocortex4.57e-1320
tube9.60e-13192
anatomical conduit1.15e-11240
epithelium8.50e-09306
cell layer1.44e-08309
multi-tissue structure2.72e-08342
posterior neural tube5.86e-0715
chordal neural plate5.86e-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.