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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 organism1.35e-77115
neural tube8.65e-5457
neural rod8.65e-5457
future spinal cord8.65e-5457
neural keel8.65e-5457
regional part of brain7.16e-4459
central nervous system1.13e-4082
anterior neural tube4.51e-3942
brain1.27e-3869
future brain1.27e-3869
neural plate1.66e-3886
presumptive neural plate1.66e-3886
regional part of forebrain7.09e-3841
forebrain7.09e-3841
future forebrain7.09e-3841
neurectoderm4.53e-3690
regional part of nervous system5.02e-3694
nervous system5.02e-3694
gray matter7.83e-3634
brain grey matter7.83e-3634
telencephalon1.43e-3534
regional part of telencephalon4.59e-3433
cerebral hemisphere2.20e-3232
pre-chordal neural plate1.63e-2661
regional part of cerebral cortex9.96e-2622
anterior region of body8.45e-24129
craniocervical region8.45e-24129
head1.44e-23123
neocortex3.39e-2320
cerebral cortex5.28e-2225
pallium5.28e-2225
ectoderm-derived structure9.21e-19169
ectoderm6.08e-18173
presumptive ectoderm6.08e-18173
nucleus of brain3.89e-169
neural nucleus3.89e-169
posterior neural tube2.51e-1515
chordal neural plate2.51e-1515
brainstem1.80e-148
anatomical conduit6.09e-13241
telencephalic nucleus9.89e-137
segmental subdivision of nervous system2.79e-1213
basal ganglion4.33e-129
nuclear complex of neuraxis4.33e-129
aggregate regional part of brain4.33e-129
collection of basal ganglia4.33e-129
cerebral subcortex4.33e-129
tube3.10e-11194
segmental subdivision of hindbrain4.62e-1112
hindbrain4.62e-1112
presumptive hindbrain4.62e-1112
gyrus1.24e-106
anatomical cluster3.09e-09286
parietal lobe6.58e-095
organ part6.84e-09219
organism subdivision1.25e-08365
corpus striatum1.50e-074
striatum1.50e-074
ventral part of telencephalon1.50e-074
future corpus striatum1.50e-074
temporal lobe2.53e-077
multi-tissue structure5.72e-07347
brainstem nucleus8.45e-073
organ8.69e-07511


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.