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Coexpression cluster:C4102: Difference between revisions

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|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321247542982662!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457632438904508
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321247542982662!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457632438904508
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}}
}}

Revision as of 16:33, 26 November 2012


Full id: C4102_cerebellum_caudate_putamen_argyrophil_insula_nucleus_temporal



Phase1 CAGE Peaks

Hg19::chr22:39638219..39638270,+p@chr22:39638219..39638270
+
Hg19::chr5:137071512..137071564,-p2@KLHL3
Hg19::chr5:137071571..137071604,-p5@KLHL3


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
mature alpha-beta T cell8.01e-1218
alpha-beta T cell8.01e-1218
immature T cell8.01e-1218
mature T cell8.01e-1218
immature alpha-beta T cell8.01e-1218
CD8-positive, alpha-beta T cell5.86e-0911
T cell1.43e-0825
pro-T cell1.43e-0825
Uber Anatomy
Ontology termp-valuen
adult organism4.20e-46114
neural tube3.94e-3356
neural rod3.94e-3356
future spinal cord3.94e-3356
neural keel3.94e-3356
regional part of nervous system1.49e-3153
regional part of brain1.49e-3153
regional part of forebrain1.22e-2741
forebrain1.22e-2741
anterior neural tube1.22e-2741
future forebrain1.22e-2741
neural plate9.05e-2782
presumptive neural plate9.05e-2782
neurectoderm2.44e-2686
central nervous system1.96e-2581
telencephalon6.11e-2534
brain grey matter6.96e-2534
gray matter6.96e-2534
brain1.44e-2468
future brain1.44e-2468
cerebral hemisphere4.55e-2432
nervous system9.09e-2489
regional part of telencephalon1.50e-2332
pre-chordal neural plate2.77e-2161
regional part of cerebral cortex3.76e-1922
cerebral cortex4.61e-1825
pallium4.61e-1825
neocortex2.16e-1720
ecto-epithelium3.34e-17104
structure with developmental contribution from neural crest3.26e-15132
ectoderm-derived structure1.18e-10171
ectoderm1.18e-10171
presumptive ectoderm1.18e-10171
tube1.25e-09192
organ system subdivision7.50e-09223
basal ganglion1.01e-089
nuclear complex of neuraxis1.01e-089
aggregate regional part of brain1.01e-089
collection of basal ganglia1.01e-089
cerebral subcortex1.01e-089
neural nucleus2.75e-089
nucleus of brain2.75e-089
anatomical conduit7.32e-08240
anatomical cluster4.62e-07373
telencephalic nucleus5.23e-077
posterior neural tube6.04e-0715
chordal neural plate6.04e-0715
gyrus7.83e-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
EGR1#195834.988179094810140.008056488137383440.0321247542982662
SMC3#9126210.02995522995520.0126656379767470.0457632438904508



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.