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Coexpression cluster:C4068: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4068_myeloma_Astrocyte_pineal_hippocampus_caudate_cervix_thalamus
|full_id=C4068_myeloma_Astrocyte_pineal_hippocampus_caudate_cervix_thalamus
|id=C4068
|id=C4068

Revision as of 17:06, 12 September 2012


Full id: C4068_myeloma_Astrocyte_pineal_hippocampus_caudate_cervix_thalamus



Phase1 CAGE Peaks

Hg19::chr21:17566852..17566866,+p5@LINC00478
Hg19::chr21:17566867..17566899,+p2@LINC00478
Hg19::chr21:17566902..17566923,+p8@LINC00478


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 organism5.45e-32115
central nervous system8.28e-3082
neural tube1.33e-2957
neural rod1.33e-2957
future spinal cord1.33e-2957
neural keel1.33e-2957
regional part of brain2.39e-2859
brain6.46e-2869
future brain6.46e-2869
regional part of nervous system6.97e-2694
nervous system6.97e-2694
neural plate8.44e-2486
presumptive neural plate8.44e-2486
anterior region of body1.54e-23129
craniocervical region1.54e-23129
regional part of forebrain4.14e-2341
forebrain4.14e-2341
future forebrain4.14e-2341
anterior neural tube6.07e-2342
neurectoderm7.32e-2390
head3.34e-22123
telencephalon2.10e-1834
gray matter2.35e-1834
brain grey matter2.35e-1834
regional part of telencephalon7.65e-1833
pre-chordal neural plate1.90e-1761
cerebral hemisphere4.28e-1732
ectoderm-derived structure9.64e-16169
ectoderm1.88e-15173
presumptive ectoderm1.88e-15173
cerebral cortex6.38e-1325
pallium6.38e-1325
regional part of cerebral cortex2.66e-1122
anatomical cluster8.14e-11286
organism subdivision1.70e-10365
neocortex4.91e-1020
multi-tissue structure1.98e-09347
organ2.83e-08511
posterior neural tube8.24e-0815
chordal neural plate8.24e-0815
tissue3.09e-07787
nucleus of brain5.35e-079
neural nucleus5.35e-079
anatomical conduit6.08e-07241
basal ganglion7.96e-079
nuclear complex of neuraxis7.96e-079
aggregate regional part of brain7.96e-079
collection of basal ganglia7.96e-079
cerebral subcortex7.96e-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
CTCF#1066435.360256373075030.0064925092527670.0279940208838962
EBF1#187938.9064668465690.00141523283560980.0091622552763608
ESR1#2099220.51240219743630.003099741577095180.0163139442940054
RAD21#5885310.35503389545630.0009004912073565420.00665155960146473
RFX5#5993312.04791082719510.0005717246050312580.00485331594122243
SMC3#9126315.04493284493280.0002935825420371870.00309586703431156
TFAP2A#7020316.5186343730450.0002218033880766340.00248604035708688
TFAP2C#7022310.80922860986020.0007916746575753130.00616705523700366
TRIM28#10155318.59052504526250.0001555969297255280.00197309224667367



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.