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Coexpression cluster:C3272

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Full id: C3272_endometrial_lung_lymphangiectasia_rhabdomyosarcoma_pineal_meningioma_spinal



Phase1 CAGE Peaks

Hg19::chr12:26277994..26278001,-p6@BHLHE41
Hg19::chr12:26278008..26278024,-p4@BHLHE41
Hg19::chr12:26278030..26278039,-p7@BHLHE41


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
adult organism3.03e-37114
neural plate7.60e-2582
presumptive neural plate7.60e-2582
neural tube2.67e-2456
neural rod2.67e-2456
future spinal cord2.67e-2456
neural keel2.67e-2456
neurectoderm4.06e-2486
regional part of nervous system2.55e-2253
regional part of brain2.55e-2253
brain1.10e-1868
future brain1.10e-1868
central nervous system2.97e-1881
nervous system1.10e-1789
ecto-epithelium1.42e-17104
structure with developmental contribution from neural crest3.12e-17132
pre-chordal neural plate1.86e-1661
regional part of forebrain1.79e-1541
forebrain1.79e-1541
anterior neural tube1.79e-1541
future forebrain1.79e-1541
ectoderm-derived structure6.38e-13171
ectoderm6.38e-13171
presumptive ectoderm6.38e-13171
telencephalon2.17e-1134
brain grey matter2.58e-1134
gray matter2.58e-1134
organ3.15e-11503
posterior neural tube2.01e-1015
chordal neural plate2.01e-1015
cerebral hemisphere3.44e-1032
regional part of telencephalon3.67e-1032
segmental subdivision of nervous system3.56e-0913
segmental subdivision of hindbrain1.92e-0812
hindbrain1.92e-0812
presumptive hindbrain1.92e-0812
anatomical cluster2.07e-08373
organ system subdivision2.39e-08223
regional part of cerebral cortex2.39e-0822
anatomical conduit4.81e-08240
multi-tissue structure9.01e-08342
tube9.43e-08192
neocortex2.37e-0720
cerebral cortex4.49e-0725
pallium4.49e-0725
multi-cellular organism8.06e-07656


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
JUND#372736.994663941871030.002921845042734990.0156305165403985
MAX#414936.452555509007120.003721913834265510.0185978163215566
SUZ12#23512350.11578091106297.93834897779404e-060.000221558853258106
TRIM28#10155318.59052504526250.0001555969297255280.00196593125376293
USF1#739136.361499277207960.00388404057290560.018967797315706



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.