Personal tools

Coexpression cluster:C4439

From FANTOM5_SSTAR

Revision as of 07:44, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4439_ductus_seminal_pons_mesothelioma_medulla_rectal_brain



Phase1 CAGE Peaks

Hg19::chr4:89079686..89079698,-p9@ABCG2
Hg19::chr4:89079714..89079746,-p4@ABCG2
Hg19::chr4:89079757..89079802,-p2@ABCG2


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 organism7.26e-51114
neural tube2.94e-4056
neural rod2.94e-4056
future spinal cord2.94e-4056
neural keel2.94e-4056
regional part of nervous system3.26e-3753
regional part of brain3.26e-3753
regional part of forebrain2.48e-3341
forebrain2.48e-3341
anterior neural tube2.48e-3341
future forebrain2.48e-3341
central nervous system1.48e-3081
brain2.30e-3068
future brain2.30e-3068
telencephalon1.32e-2634
brain grey matter2.19e-2634
gray matter2.19e-2634
nervous system1.78e-2589
neural plate7.38e-2582
presumptive neural plate7.38e-2582
cerebral hemisphere1.96e-2432
regional part of telencephalon2.24e-2432
neurectoderm8.04e-2386
regional part of cerebral cortex1.72e-2122
pre-chordal neural plate3.54e-2161
neocortex9.88e-2020
organ system subdivision2.83e-19223
cerebral cortex5.21e-1825
pallium5.21e-1825
ecto-epithelium2.45e-17104
structure with developmental contribution from neural crest2.08e-15132
anatomical cluster2.50e-13373
anatomical conduit4.43e-13240
tube3.45e-12192
neural nucleus5.37e-109
nucleus of brain5.37e-109
ectoderm-derived structure6.77e-10171
ectoderm6.77e-10171
presumptive ectoderm6.77e-10171
basal ganglion8.02e-109
nuclear complex of neuraxis8.02e-109
aggregate regional part of brain8.02e-109
collection of basal ganglia8.02e-109
cerebral subcortex8.02e-109
organ1.02e-09503
multi-tissue structure3.11e-09342
posterior neural tube2.66e-0815
chordal neural plate2.66e-0815
diencephalon3.53e-087
future diencephalon3.53e-087
telencephalic nucleus5.45e-087
brainstem5.72e-086
gyrus1.05e-076
organ part2.97e-07218


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
CCNT2#90536.336201576962630.003930750035764890.0190790353202235
E2F1#186934.907389214879320.008460985347239390.0326977557328523
EGR1#195834.988179094810140.008056488137383440.0321960497658295
FOS#235338.99795530889440.001372499272417130.00900731755133672
FOSL2#2355316.93020060456170.0002060162053171620.00243864065137924
GATA1#2623313.56030814380040.0004009615963782630.00389001655031579
JUN#3725312.51282919233630.0005103313992726250.0044578873376241
JUND#372736.994663941871030.002921845042734990.0157385411531384
TAL1#6886219.91241111829350.003287176608740550.017019107566937



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.