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Coexpression cluster:C2761

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Full id: C2761_Wilms_duodenum_amygdala_cerebellum_hippocampus_neuroblastoma_temporal



Phase1 CAGE Peaks

Hg19::chr3:96532496..96532521,+p@chr3:96532496..96532521
+
Hg19::chr3:96533374..96533391,+p4@EPHA6
Hg19::chr3:96533397..96533411,+p2@EPHA6
Hg19::chr3:96533413..96533443,+p1@EPHA6


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
neural tube1.19e-4656
neural rod1.19e-4656
future spinal cord1.19e-4656
neural keel1.19e-4656
adult organism2.20e-44114
regional part of nervous system2.24e-4353
regional part of brain2.24e-4353
nervous system2.61e-4289
central nervous system1.29e-4181
brain3.77e-3768
future brain3.77e-3768
cerebral hemisphere1.65e-3632
telencephalon3.59e-3634
brain grey matter4.65e-3634
gray matter4.65e-3634
regional part of forebrain4.23e-3541
forebrain4.23e-3541
anterior neural tube4.23e-3541
future forebrain4.23e-3541
regional part of telencephalon1.07e-3332
neural plate2.52e-3282
presumptive neural plate2.52e-3282
neurectoderm2.02e-3186
regional part of cerebral cortex3.61e-3122
neocortex4.15e-2820
organ system subdivision6.33e-28223
cerebral cortex1.25e-2625
pallium1.25e-2625
pre-chordal neural plate3.16e-2561
ecto-epithelium1.36e-24104
ectoderm-derived structure2.74e-21171
ectoderm2.74e-21171
presumptive ectoderm2.74e-21171
structure with developmental contribution from neural crest1.74e-20132
anatomical cluster4.70e-16373
posterior neural tube2.33e-1215
chordal neural plate2.33e-1215
basal ganglion1.71e-119
nuclear complex of neuraxis1.71e-119
aggregate regional part of brain1.71e-119
collection of basal ganglia1.71e-119
cerebral subcortex1.71e-119
tube8.14e-11192
neural nucleus8.90e-119
nucleus of brain8.90e-119
multi-tissue structure1.59e-10342
gyrus5.14e-106
organ part8.14e-10218
anatomical conduit1.14e-09240
segmental subdivision of hindbrain2.39e-0912
hindbrain2.39e-0912
presumptive hindbrain2.39e-0912
limbic system3.31e-095
temporal lobe8.09e-096
brainstem1.01e-086
occipital lobe1.07e-085
telencephalic nucleus1.72e-087
segmental subdivision of nervous system1.86e-0813
parietal lobe3.16e-085
embryo3.19e-08592
corpus striatum1.53e-074
striatum1.53e-074
ventral part of telencephalon1.53e-074
future corpus striatum1.53e-074
organ1.97e-07503
epithelium4.29e-07306
cell layer7.32e-07309


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
CTCF#1066445.360256373075030.001211145381643620.00818922779447613
MYC#460945.22228187160940.001344309395272740.00888878309166758
ZNF263#1012736.166381227758010.006539814347975980.0279853999298641



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.