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Coexpression cluster:C1024

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Full id: C1024_Pericytes_cerebellum_neuroblastoma_HES3GFP_iPS_extraskeletal_teratocarcinoma



Phase1 CAGE Peaks

Hg19::chr13:100623360..100623373,-p2@ZIC5
Hg19::chr13:100623375..100623425,-p1@ZIC5
Hg19::chr13:100633445..100633468,+p1@AK298232
Hg19::chr13:100633480..100633490,+p3@AK298232
Hg19::chr13:100634031..100634045,+p1@ZIC2
Hg19::chr13:100634809..100634826,+p11@ZIC2
Hg19::chr13:100638100..100638115,+p4@ZIC2
Hg19::chr13:100638124..100638136,+p7@ZIC2


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>disease_data<br>


Cell Type
Ontology termp-valuen
neural cell6.09e-1125
neurectodermal cell9.34e-0859
neuron3.95e-076
neuroblast3.95e-076
electrically signaling cell3.95e-076
embryonic stem cell5.80e-075
neuronal stem cell7.64e-078
Uber Anatomy
Ontology termp-valuen
central nervous system2.38e-4381
nervous system1.30e-4189
brain1.17e-3368
future brain1.17e-3368
neural tube7.80e-3256
neural rod7.80e-3256
future spinal cord7.80e-3256
neural keel7.80e-3256
neurectoderm4.56e-3086
regional part of nervous system8.79e-3053
regional part of brain8.79e-3053
neural plate1.38e-2682
presumptive neural plate1.38e-2682
ectoderm-derived structure1.83e-23171
ectoderm1.83e-23171
presumptive ectoderm1.83e-23171
regional part of forebrain7.44e-2041
forebrain7.44e-2041
anterior neural tube7.44e-2041
future forebrain7.44e-2041
telencephalon9.01e-2034
brain grey matter2.72e-1934
gray matter2.72e-1934
pre-chordal neural plate3.48e-1961
cerebral hemisphere2.52e-1832
ecto-epithelium2.62e-18104
regional part of telencephalon2.81e-1832
cerebral cortex1.12e-1725
pallium1.12e-1725
organ system subdivision1.64e-16223
regional part of cerebral cortex1.67e-1522
neocortex7.97e-1420
posterior neural tube1.25e-1315
chordal neural plate1.25e-1315
structure with developmental contribution from neural crest1.96e-12132
segmental subdivision of hindbrain1.01e-1112
hindbrain1.01e-1112
presumptive hindbrain1.01e-1112
segmental subdivision of nervous system1.66e-1013
regional part of metencephalon1.48e-099
metencephalon1.48e-099
future metencephalon1.48e-099
cerebellum5.48e-086
rhombic lip5.48e-086
Disease
Ontology termp-valuen
cell type cancer8.40e-22143
cancer1.33e-20235
disease of cellular proliferation1.77e-19239
carcinoma1.56e-15106
germ cell and embryonal cancer2.50e-0822
germ cell cancer2.50e-0822
adenocarcinoma1.07e-0725
organ system cancer7.90e-07137


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
E2F6#187653.135722332310870.01024880501420960.0381472948743376
EGR1#195853.117611934256340.01051390990388360.0389204351345726
ZNF263#1012755.138651023131670.001082531249033560.00763805439250206



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.