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Coexpression cluster:C987

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Full id: C987_skeletal_heart_left_mature_spinal_kidney_substantia



Phase1 CAGE Peaks

Hg19::chr11:111779473..111779528,+p@chr11:111779473..111779528
+
Hg19::chr11:111779507..111779528,-p15@CRYAB
Hg19::chr11:111779539..111779572,-p11@CRYAB
Hg19::chr11:111779550..111779574,+p@chr11:111779550..111779574
+
Hg19::chr11:111779604..111779626,+p@chr11:111779604..111779626
+
Hg19::chr11:111779606..111779681,-p5@CRYAB
Hg19::chr11:111781142..111781160,-p@chr11:111781142..111781160
-
Hg19::chr11:111782484..111782501,-p1@CRYAB


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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
fat cell1.10e-1215
Uber Anatomy
Ontology termp-valuen
adult organism9.77e-53114
neural tube9.84e-2756
neural rod9.84e-2756
future spinal cord9.84e-2756
neural keel9.84e-2756
regional part of nervous system5.07e-2453
regional part of brain5.07e-2453
central nervous system2.87e-2281
neural plate7.29e-2182
presumptive neural plate7.29e-2182
nervous system2.37e-2089
regional part of forebrain1.37e-1941
forebrain1.37e-1941
anterior neural tube1.37e-1941
future forebrain1.37e-1941
neurectoderm5.46e-1986
brain8.78e-1968
future brain8.78e-1968
brain grey matter6.81e-1734
gray matter6.81e-1734
telencephalon1.13e-1634
structure with developmental contribution from neural crest1.84e-16132
regional part of telencephalon2.30e-1532
ecto-epithelium4.46e-15104
cerebral hemisphere6.02e-1532
pre-chordal neural plate1.25e-1361
ectoderm-derived structure6.59e-13171
ectoderm6.59e-13171
presumptive ectoderm6.59e-13171
cerebral cortex2.19e-1025
pallium2.19e-1025
regional part of cerebral cortex2.92e-1022
neocortex5.28e-0920
neural nucleus1.36e-089
nucleus of brain1.36e-089
posterior neural tube2.62e-0815
chordal neural plate2.62e-0815
basal ganglion2.82e-089
nuclear complex of neuraxis2.82e-089
aggregate regional part of brain2.82e-089
collection of basal ganglia2.82e-089
cerebral subcortex2.82e-089
telencephalic nucleus5.65e-077
organ system subdivision8.46e-07223
omentum9.05e-076
peritoneum9.05e-076
abdominal cavity9.05e-076
visceral peritoneum9.05e-076


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
FOXA1#316945.540709874692730.003444272925946160.0175240619726648



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.