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Coexpression cluster:C2934

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Full id: C2934_heart_left_Mast_Whole_skeletal_tongue_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr9:100263912..100263988,+p1@TMOD1
Hg19::chr9:100263992..100264003,+p2@TMOD1
Hg19::chr9:100264007..100264012,+p5@TMOD1
Hg19::chr9:100264015..100264024,+p3@TMOD1


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 organism1.93e-76114
neural tube3.27e-2956
neural rod3.27e-2956
future spinal cord3.27e-2956
neural keel3.27e-2956
central nervous system1.38e-2781
nervous system5.45e-2789
regional part of nervous system9.57e-2753
regional part of brain9.57e-2753
brain2.03e-2468
future brain2.03e-2468
organ system subdivision1.96e-22223
regional part of forebrain4.39e-2241
forebrain4.39e-2241
anterior neural tube4.39e-2241
future forebrain4.39e-2241
neural plate1.31e-1982
presumptive neural plate1.31e-1982
telencephalon2.02e-1834
brain grey matter2.19e-1834
gray matter2.19e-1834
neurectoderm8.36e-1886
regional part of cerebral cortex9.60e-1822
cerebral hemisphere3.30e-1732
regional part of telencephalon4.99e-1732
neocortex2.31e-1620
cerebral cortex1.14e-1425
pallium1.14e-1425
structure with developmental contribution from neural crest3.36e-13132
ecto-epithelium7.39e-13104
pre-chordal neural plate2.01e-1261
ectoderm-derived structure8.78e-11171
ectoderm8.78e-11171
presumptive ectoderm8.78e-11171
anatomical cluster9.83e-11373
posterior neural tube2.92e-0815
chordal neural plate2.92e-0815
anatomical conduit1.67e-07240
multi-tissue structure2.28e-07342
tube3.91e-07192
developing anatomical structure8.40e-07581
organ9.41e-07503
germ layer9.42e-07560
germ layer / neural crest9.42e-07560
embryonic tissue9.42e-07560
presumptive structure9.42e-07560
germ layer / neural crest derived structure9.42e-07560
epiblast (generic)9.42e-07560


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
CCNT2#90546.336201576962630.0006203100587215640.00513959240165184
CTCF#1066445.360256373075030.001211145381643620.00820569656266483
E2F1#186944.907389214879320.001724022357361790.0106870353146075
ELF1#199744.258097958807540.003041525565781240.0161343909266877
HDAC2#3066413.41562023662633.0859005065161e-050.000629100845207954
PAX5#507946.669565531177830.0005052774169483260.00445134273712916
RAD21#5885410.35503389545638.6948481184721e-050.0013017219648009
SPI1#668848.204323508522730.000220661881527680.00249980542844879
TCF7L2#6934410.77017656313737.42969445082454e-050.00115882595392722



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.