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Coexpression cluster:C2525: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2525_neuroblastoma_nonsmall_Neurons_Neural_temporal_duodenum_brain
|full_id=C2525_neuroblastoma_nonsmall_Neurons_Neural_temporal_duodenum_brain
|id=C2525
|id=C2525

Revision as of 15:16, 12 September 2012


Full id: C2525_neuroblastoma_nonsmall_Neurons_Neural_temporal_duodenum_brain



Phase1 CAGE Peaks

Hg19::chr1:151032739..151032748,+p6@MLLT11
Hg19::chr1:151032782..151032801,+p4@MLLT11
Hg19::chr1:151032833..151032850,+p3@MLLT11
Hg19::chr1:151032860..151032918,+p1@MLLT11


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>

Uber Anatomy
Ontology termp-valuen
central nervous system2.47e-3082
cell layer3.06e-30312
regional part of nervous system6.76e-3094
nervous system6.76e-3094
epithelium2.35e-29309
brain6.12e-2769
future brain6.12e-2769
tube5.51e-26194
ectoderm-derived structure1.08e-24169
ectoderm2.15e-24173
presumptive ectoderm2.15e-24173
neural plate2.67e-2486
presumptive neural plate2.67e-2486
regional part of brain1.27e-2359
neurectoderm1.53e-2390
neural tube4.54e-2357
neural rod4.54e-2357
future spinal cord4.54e-2357
neural keel4.54e-2357
head3.58e-22123
anatomical conduit2.79e-20241
anterior region of body3.52e-20129
craniocervical region3.52e-20129
organism subdivision5.95e-20365
regional part of forebrain1.55e-1841
forebrain1.55e-1841
future forebrain1.55e-1841
pre-chordal neural plate1.72e-1861
anterior neural tube2.83e-1742
gray matter3.24e-1734
brain grey matter3.24e-1734
cerebral hemisphere3.33e-1732
telencephalon1.06e-1634
regional part of telencephalon4.75e-1633
anatomical cluster1.07e-15286
vasculature3.92e-1579
vascular system3.92e-1579
cerebral cortex2.37e-1425
pallium2.37e-1425
regional part of cerebral cortex7.96e-1422
multi-tissue structure3.52e-13347
neocortex8.10e-1320
blood vessel1.54e-1260
epithelial tube open at both ends1.54e-1260
blood vasculature1.54e-1260
vascular cord1.54e-1260
splanchnic layer of lateral plate mesoderm2.04e-1284
artery2.27e-1242
arterial blood vessel2.27e-1242
arterial system2.27e-1242
vessel1.29e-1169
circulatory system2.61e-11113
cardiovascular system9.26e-11110
skeletal muscle tissue1.26e-1061
striated muscle tissue1.26e-1061
myotome1.26e-1061
systemic artery4.19e-1033
systemic arterial system4.19e-1033
muscle tissue6.17e-1063
musculature6.17e-1063
musculature of body6.17e-1063
somite7.89e-1083
paraxial mesoderm7.89e-1083
presomitic mesoderm7.89e-1083
presumptive segmental plate7.89e-1083
trunk paraxial mesoderm7.89e-1083
presumptive paraxial mesoderm7.89e-1083
multilaminar epithelium9.97e-1082
organ part2.32e-09219
dermomyotome6.21e-0970
epithelial tube9.78e-09118
multi-cellular organism2.48e-07659
embryo2.76e-07612
posterior neural tube5.16e-0715
chordal neural plate5.16e-0715
anatomical system5.45e-07625
anatomical group8.26e-07626
germ layer8.71e-07604
embryonic tissue8.71e-07604
presumptive structure8.71e-07604
epiblast (generic)8.71e-07604
embryonic structure8.79e-07605
developing anatomical structure8.79e-07605


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
CTBP2#1488462.71700033932816.45042639894877e-083.95814384653238e-06
EGR1#195844.988179094810140.001615011500076050.0101467957682995
ELF1#199744.258097958807540.003041525565781240.0160935195341284
EP300#203346.77394172622320.0004748459821442640.00434449754964212
HEY1#2346244.040111043105710.00375304636917980.0186135630045954
MAFK#7975427.10073313782991.85228494563408e-066.85266693011258e-05
REST#597849.650028716128020.0001152825614219170.00157077565979695
SIN3A#2594245.408884726815140.001168172384885160.00796622629481037
SP1#666745.69838137814090.0009482606065333980.00684466027270313
TAF1#687243.343046285745290.008005664898701650.0322346995279321
TBP#690843.706770687096390.005296377814784350.02443127081835
USF1#739146.361499277207960.0006105011399140830.00508089318284221
YY1#752844.911170749853860.00171871838055440.0106890507322528
ZBTB7A#5134147.35190930787590.000342223540015990.00346668130899418



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.

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