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Coexpression cluster:C2799

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Full id: C2799_hippocampus_cerebellum_pituitary_amygdala_olfactory_middle_medial



Phase1 CAGE Peaks

Hg19::chr5:113697717..113697728,+p6@KCNN2
Hg19::chr5:113697740..113697793,+p1@KCNN2
Hg19::chr5:113697798..113697814,+p3@KCNN2
Hg19::chr5:113697983..113698024,+p4@KCNN2


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 organism9.11e-47114
neural tube3.10e-4056
neural rod3.10e-4056
future spinal cord3.10e-4056
neural keel3.10e-4056
central nervous system4.29e-3981
nervous system5.03e-3889
regional part of nervous system2.11e-3753
regional part of brain2.11e-3753
regional part of forebrain2.27e-3141
forebrain2.27e-3141
anterior neural tube2.27e-3141
future forebrain2.27e-3141
brain1.20e-3068
future brain1.20e-3068
neural plate2.62e-2982
presumptive neural plate2.62e-2982
neurectoderm6.86e-2886
telencephalon1.04e-2434
brain grey matter1.17e-2434
gray matter1.17e-2434
organ system subdivision1.38e-24223
cerebral hemisphere7.00e-2332
regional part of telencephalon8.21e-2332
ecto-epithelium1.67e-22104
ectoderm-derived structure6.18e-21171
ectoderm6.18e-21171
presumptive ectoderm6.18e-21171
pre-chordal neural plate8.46e-2161
regional part of cerebral cortex1.06e-2022
neocortex1.21e-1820
structure with developmental contribution from neural crest2.57e-18132
cerebral cortex2.85e-1725
pallium2.85e-1725
anatomical cluster2.20e-16373
anatomical conduit4.18e-14240
tube6.40e-13192
posterior neural tube6.81e-1015
chordal neural plate6.81e-1015
basal ganglion4.87e-099
nuclear complex of neuraxis4.87e-099
aggregate regional part of brain4.87e-099
collection of basal ganglia4.87e-099
cerebral subcortex4.87e-099
neural nucleus6.24e-099
nucleus of brain6.24e-099
diencephalon3.49e-087
future diencephalon3.49e-087
multi-tissue structure1.14e-07342
brainstem1.51e-076
segmental subdivision of hindbrain2.46e-0712
hindbrain2.46e-0712
presumptive hindbrain2.46e-0712
gyrus2.71e-076
telencephalic nucleus4.31e-077
epithelium8.18e-07306


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
JUND#372735.245997956403270.01043432751748420.0387095315287913
MYC#460945.22228187160940.001344309395272740.00889216093057758
TAF1#687243.343046285745290.008005664898701650.0323056928385882
TAF7#6879411.43306940492395.85061525419808e-050.00097128025199999
TBP#690843.706770687096390.005296377814784350.0244842600300222
ZNF143#7702413.50087655222793.00867915035614e-050.00062160918255993



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.