Personal tools

Coexpression cluster:C1272

From FANTOM5_SSTAR

Revision as of 14:47, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1272_medulloblastoma_neuroblastoma_colon_Osteoblast_normal_Ciliary_pons



Phase1 CAGE Peaks

Hg19::chr4:151502879..151502889,-p8@LRBA
Hg19::chr4:151502911..151502924,-p5@LRBA
Hg19::chr4:151502958..151502978,-p6@LRBA
Hg19::chr4:151503105..151503132,+p2@MAB21L2
Hg19::chr4:151503215..151503245,+p4@MAB21L2
Hg19::chr4:151503507..151503518,+p6@MAB21L2
Hg19::chr4:151513323..151513325,+p@chr4:151513323..151513325
+


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
pigment epithelium of eye3.21e-2311
intestine1.01e-2017
eye8.06e-1721
visual system8.06e-1721
face2.99e-1622
subdivision of head6.12e-1649
camera-type eye9.53e-1520
simple eye9.53e-1520
immature eye9.53e-1520
ocular region9.53e-1520
eyeball of camera-type eye9.53e-1520
optic cup9.53e-1520
optic vesicle9.53e-1520
eye primordium9.53e-1520
sense organ2.03e-1424
sensory system2.03e-1424
entire sense organ system2.03e-1424
large intestine2.51e-1411
atypical epithelium8.25e-144
gastrointestinal system1.38e-1325
head2.05e-1356
colon4.75e-139
brainstem1.61e-126
anterior region of body1.03e-1162
craniocervical region1.03e-1162
ciliary epithelium3.61e-113
ciliary body3.61e-113
pigmented layer of retina1.09e-103
presumptive retinal pigmented epithelium1.09e-103
organ segment1.31e-1098
pons9.50e-103
vasculature of eye3.24e-096
uvea3.24e-096
vasculature of head3.24e-096
retina5.07e-096
photoreceptor array5.07e-096
posterior segment of eyeball5.07e-096
ectodermal placode8.53e-0931
layer of retina4.08e-084
anterior segment of eyeball4.35e-0814
ectoderm-derived structure4.90e-08171
ectoderm4.90e-08171
presumptive ectoderm4.90e-08171
neural plate2.96e-0782
presumptive neural plate2.96e-0782
sympathetic nervous system3.94e-075
autonomic nervous system3.94e-075
locus ceruleus5.85e-072
brainstem nucleus5.85e-072
hindbrain nucleus5.85e-072
posterior neural tube8.06e-0715
chordal neural plate8.06e-0715
small intestine8.93e-074
neurectoderm9.39e-0786
anatomical cluster9.40e-07373


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
EP300#203354.838529804445140.001132708190785470.00775781433126394
YY1#752853.507979107038470.005072570672808980.0236168958852308



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.