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Coexpression cluster:C2965

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Full id: C2965_smooth_thalamus_globus_spinal_locus_substantia_medulla



Phase1 CAGE Peaks

Hg19::chr10:100992367..100992392,-p@chr10:100992367..100992392
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Hg19::chr10:100992596..100992612,-p@chr10:100992596..100992612
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Hg19::chr10:100992617..100992648,-p@chr10:100992617..100992648
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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 organism5.17e-69114
neural tube7.95e-5756
neural rod7.95e-5756
future spinal cord7.95e-5756
neural keel7.95e-5756
regional part of nervous system1.20e-5353
regional part of brain1.20e-5353
regional part of forebrain7.08e-4241
forebrain7.08e-4241
anterior neural tube7.08e-4241
future forebrain7.08e-4241
brain4.10e-4168
future brain4.10e-4168
brain grey matter4.55e-4134
gray matter4.55e-4134
telencephalon1.36e-4034
central nervous system1.80e-3981
neural plate2.21e-3982
presumptive neural plate2.21e-3982
neurectoderm5.17e-3786
regional part of telencephalon1.32e-3632
cerebral hemisphere2.16e-3632
nervous system2.02e-3489
ecto-epithelium3.12e-30104
pre-chordal neural plate2.03e-2761
regional part of cerebral cortex2.23e-2622
neocortex5.34e-2620
cerebral cortex8.87e-2325
pallium8.87e-2325
structure with developmental contribution from neural crest1.32e-22132
neural nucleus6.24e-229
nucleus of brain6.24e-229
organ system subdivision5.28e-21223
telencephalic nucleus4.51e-177
basal ganglion1.83e-169
nuclear complex of neuraxis1.83e-169
aggregate regional part of brain1.83e-169
collection of basal ganglia1.83e-169
cerebral subcortex1.83e-169
ectoderm-derived structure2.24e-16171
ectoderm2.24e-16171
presumptive ectoderm2.24e-16171
brainstem1.32e-156
posterior neural tube1.64e-1515
chordal neural plate1.64e-1515
gyrus2.28e-146
anatomical conduit6.61e-13240
tube8.67e-13192
segmental subdivision of hindbrain1.37e-1212
hindbrain1.37e-1212
presumptive hindbrain1.37e-1212
segmental subdivision of nervous system1.70e-1113
anatomical cluster2.46e-11373
multi-tissue structure1.78e-10342
corpus striatum6.90e-104
striatum6.90e-104
ventral part of telencephalon6.90e-104
future corpus striatum6.90e-104
organ part7.42e-09218
pons9.68e-093
medulla oblongata1.48e-083
myelencephalon1.48e-083
future myelencephalon1.48e-083
occipital lobe2.64e-085
parietal lobe2.80e-085
frontal cortex5.65e-083
caudate-putamen7.16e-083
dorsal striatum7.16e-083
regional part of metencephalon6.31e-079
metencephalon6.31e-079
future metencephalon6.31e-079


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
SUZ12#23512350.11578091106297.93834897779404e-060.000220968344587375



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.