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Coexpression cluster:C4531

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Full id: C4531_temporal_duodenum_Mesenchymal_occipital_parietal_Neurons_glioblastoma



Phase1 CAGE Peaks

Hg19::chr5:92919068..92919082,+p5@NR2F1
Hg19::chr5:92919100..92919135,+p3@NR2F1
Hg19::chr5:92919375..92919438,+p6@NR2F1


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 cell2.48e-07180
Uber Anatomy
Ontology termp-valuen
neural plate4.41e-2786
presumptive neural plate4.41e-2786
neurectoderm1.21e-2690
anatomical cluster2.89e-26286
organism subdivision2.34e-25365
central nervous system5.37e-2582
regional part of brain2.72e-2459
neural tube3.25e-2457
neural rod3.25e-2457
future spinal cord3.25e-2457
neural keel3.25e-2457
regional part of nervous system1.11e-2394
nervous system1.11e-2394
cell layer3.45e-23312
brain1.49e-2269
future brain1.49e-2269
multi-tissue structure3.45e-22347
epithelium3.68e-22309
anatomical conduit4.16e-22241
tube3.05e-20194
pre-chordal neural plate1.82e-1961
head4.79e-19123
adult organism2.73e-18115
anterior region of body4.04e-18129
craniocervical region4.04e-18129
anterior neural tube3.68e-1742
regional part of forebrain5.56e-1741
forebrain5.56e-1741
future forebrain5.56e-1741
ectoderm2.15e-16173
presumptive ectoderm2.15e-16173
ectoderm-derived structure2.53e-16169
multi-cellular organism2.65e-16659
gray matter8.89e-1634
brain grey matter8.89e-1634
telencephalon9.51e-1634
regional part of telencephalon2.43e-1533
cerebral hemisphere3.81e-1532
cerebral cortex1.69e-1325
pallium1.69e-1325
organ part2.22e-13219
regional part of cerebral cortex1.93e-1222
embryo2.25e-12612
neocortex1.21e-1120
embryonic structure1.86e-11605
developing anatomical structure1.86e-11605
anatomical system3.62e-11625
germ layer4.10e-11604
embryonic tissue4.10e-11604
presumptive structure4.10e-11604
epiblast (generic)4.10e-11604
anatomical group5.90e-11626
organ3.76e-10511
posterior neural tube2.66e-0815
chordal neural plate2.66e-0815
organ segment8.87e-0897
trunk1.05e-07216
unilaminar epithelium3.74e-07138


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
HDAC2#3066313.41562023662630.0004140761399857210.00393071241446725
HNF4A#3172215.42152690863580.005444210486686610.0246879379540212
HNF4G#3174219.16894835096450.003543986611284220.0179797152285977
JUND#372736.994663941871030.002921845042734990.0157491006615504
MXI1#460139.96157162875930.001011470541259020.00722699403834925
TAL1#6886219.91241111829350.003287176608740550.017020795133379
TRIM28#10155212.39368336350830.008368344129438470.0329406562842765
ZNF263#1012738.221841637010680.001799043925565870.0109973865111018
ZZZ3#260093239.4132124352337.25894005043406e-084.38724791624585e-06



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.