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Coexpression cluster:C4057

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Full id: C4057_prostate_smallcell_Mammary_mucinous_pituitary_Keratinocyte_bile



Phase1 CAGE Peaks

Hg19::chr20:58411012..58411026,+p7@PHACTR3
Hg19::chr20:58411027..58411085,+p3@PHACTR3
Hg19::chr20:58411232..58411249,+p15@PHACTR3


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
respiratory epithelial cell1.23e-0713
endo-epithelial cell3.89e-0742
Uber Anatomy
Ontology termp-valuen
neural tube1.62e-4956
neural rod1.62e-4956
future spinal cord1.62e-4956
neural keel1.62e-4956
regional part of nervous system1.28e-4453
regional part of brain1.28e-4453
regional part of forebrain1.23e-3641
forebrain1.23e-3641
anterior neural tube1.23e-3641
future forebrain1.23e-3641
brain1.22e-3568
future brain1.22e-3568
adult organism1.44e-35114
central nervous system2.49e-3581
nervous system8.26e-3489
neural plate3.32e-3382
presumptive neural plate3.32e-3382
neurectoderm4.79e-3186
ecto-epithelium3.96e-29104
telencephalon5.65e-2834
brain grey matter5.95e-2834
gray matter5.95e-2834
regional part of telencephalon5.73e-2532
pre-chordal neural plate5.84e-2561
cerebral hemisphere8.10e-2532
ectoderm-derived structure2.38e-20171
ectoderm2.38e-20171
presumptive ectoderm2.38e-20171
organ system subdivision2.77e-20223
structure with developmental contribution from neural crest4.97e-20132
regional part of cerebral cortex1.68e-1722
basal ganglion6.52e-179
nuclear complex of neuraxis6.52e-179
aggregate regional part of brain6.52e-179
collection of basal ganglia6.52e-179
cerebral subcortex6.52e-179
neural nucleus1.46e-169
nucleus of brain1.46e-169
cerebral cortex5.87e-1525
pallium5.87e-1525
neocortex2.84e-1420
posterior neural tube1.33e-1315
chordal neural plate1.33e-1315
tube1.76e-13192
telencephalic nucleus2.69e-137
anatomical conduit2.20e-12240
anatomical cluster9.84e-12373
brainstem1.80e-116
epithelium2.68e-11306
organ part4.96e-11218
cell layer5.06e-11309
segmental subdivision of nervous system1.26e-1013
limbic system1.52e-105
diencephalon2.36e-107
future diencephalon2.36e-107
multi-tissue structure7.63e-10342
segmental subdivision of hindbrain4.18e-0912
hindbrain4.18e-0912
presumptive hindbrain4.18e-0912
organ3.17e-08503
gyrus5.26e-086
corpus striatum7.65e-084
striatum7.65e-084
ventral part of telencephalon7.65e-084
future corpus striatum7.65e-084
developing anatomical structure3.87e-07581
embryo4.82e-07592
medulla oblongata5.04e-073
myelencephalon5.04e-073
future myelencephalon5.04e-073
temporal lobe5.55e-076
spinal cord9.24e-073
dorsal region element9.24e-073
dorsum9.24e-073


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
ZNF263#1012738.221841637010680.001799043925565870.0109595396956471



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.