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Coexpression cluster:C3617: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3617_testis_trachea_putamen_pituitary_lung_caudate_epididymis
|full_id=C3617_testis_trachea_putamen_pituitary_lung_caudate_epididymis
|id=C3617
|id=C3617

Revision as of 16:34, 12 September 2012


Full id: C3617_testis_trachea_putamen_pituitary_lung_caudate_epididymis



Phase1 CAGE Peaks

Hg19::chr17:260097..260196,+p1@C17orf97
Hg19::chr1:36916011..36916057,-p1@OSCP1
Hg19::chr9:135753649..135753688,-p1@AK8


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
non-terminally differentiated cell9.45e-07180
Uber Anatomy
Ontology termp-valuen
organism subdivision2.54e-35365
neurectoderm3.47e-2890
neural plate1.04e-2786
presumptive neural plate1.04e-2786
ectoderm8.97e-26173
presumptive ectoderm8.97e-26173
multi-tissue structure1.09e-25347
neural tube1.15e-2557
neural rod1.15e-2557
future spinal cord1.15e-2557
neural keel1.15e-2557
ectoderm-derived structure4.31e-25169
epithelium7.54e-24309
head7.74e-24123
anterior region of body8.18e-24129
craniocervical region8.18e-24129
cell layer9.14e-24312
regional part of brain1.19e-2359
central nervous system2.17e-2382
brain2.20e-2369
future brain2.20e-2369
regional part of nervous system5.53e-2394
nervous system5.53e-2394
pre-chordal neural plate1.32e-2161
anatomical cluster5.22e-21286
adult organism6.58e-20115
multi-cellular organism7.52e-20659
regional part of forebrain8.53e-2041
forebrain8.53e-2041
future forebrain8.53e-2041
organ part8.76e-19219
anterior neural tube9.31e-1942
anatomical conduit1.55e-18241
tube4.46e-18194
telencephalon3.03e-1634
gray matter4.01e-1634
brain grey matter4.01e-1634
cerebral hemisphere9.04e-1632
regional part of telencephalon1.23e-1533
organ1.02e-14511
anatomical system1.23e-14625
anatomical group2.34e-14626
embryo2.71e-14612
embryonic structure5.14e-14605
developing anatomical structure5.14e-14605
germ layer9.82e-14604
embryonic tissue9.82e-14604
presumptive structure9.82e-14604
epiblast (generic)9.82e-14604
regional part of cerebral cortex1.93e-1222
cerebral cortex4.14e-1225
pallium4.14e-1225
neocortex1.78e-1120
posterior neural tube4.32e-0815
chordal neural plate4.32e-0815
organ segment1.63e-0797
trunk3.09e-07216
segmental subdivision of nervous system3.50e-0713
segmental subdivision of hindbrain6.11e-0712
hindbrain6.11e-0712
presumptive hindbrain6.11e-0712


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
ELF1#199734.258097958807540.01295179875054610.0461678866073341
MXI1#460139.96157162875930.001011470541259020.00719597900943808
SIN3A#2594235.408884726815140.006318961977991520.0276301473736427
SIX5#147912211.3911435703060.009873820081429030.0370699509484638
THAP1#55145220.91276306856750.002983447413736940.0158657907451129



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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