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Coexpression cluster:C4284

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Full id: C4284_neuroblastoma_occipital_duodenum_temporal_brain_parietal_Neural



Phase1 CAGE Peaks

Hg19::chr3:132757184..132757209,+p2@TMEM108
Hg19::chr3:132757215..132757247,+p1@TMEM108
Hg19::chr8:1012255..1012307,+p@chr8:1012255..1012307
+


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
neural cell6.20e-0925
neuronal stem cell3.51e-088
Uber Anatomy
Ontology termp-valuen
central nervous system3.18e-5281
nervous system2.77e-4989
neural tube9.01e-4456
neural rod9.01e-4456
future spinal cord9.01e-4456
neural keel9.01e-4456
adult organism3.48e-43114
regional part of nervous system6.15e-4253
regional part of brain6.15e-4253
brain1.08e-4168
future brain1.08e-4168
neural plate2.19e-3982
presumptive neural plate2.19e-3982
neurectoderm3.41e-3686
regional part of forebrain1.30e-3341
forebrain1.30e-3341
anterior neural tube1.30e-3341
future forebrain1.30e-3341
ectoderm-derived structure6.08e-31171
ectoderm6.08e-31171
presumptive ectoderm6.08e-31171
ecto-epithelium2.08e-29104
pre-chordal neural plate6.40e-2961
telencephalon1.87e-2834
brain grey matter3.54e-2834
gray matter3.54e-2834
cerebral hemisphere2.65e-2732
structure with developmental contribution from neural crest4.23e-27132
regional part of telencephalon7.57e-2732
organ system subdivision1.76e-26223
cerebral cortex1.12e-2225
pallium1.12e-2225
regional part of cerebral cortex1.06e-2022
neocortex3.83e-1920
anatomical cluster1.63e-17373
multi-tissue structure9.15e-16342
embryo4.89e-12592
tube2.07e-11192
posterior neural tube4.47e-1115
chordal neural plate4.47e-1115
cell layer7.66e-11309
epithelium4.06e-10306
developing anatomical structure5.19e-10581
organ part7.02e-10218
segmental subdivision of hindbrain2.19e-0912
hindbrain2.19e-0912
presumptive hindbrain2.19e-0912
germ layer4.43e-09560
germ layer / neural crest4.43e-09560
embryonic tissue4.43e-09560
presumptive structure4.43e-09560
germ layer / neural crest derived structure4.43e-09560
epiblast (generic)4.43e-09560
embryonic structure4.82e-09564
multi-cellular organism1.02e-08656
anatomical conduit1.17e-08240
segmental subdivision of nervous system2.41e-0813
anatomical system3.87e-08624
anatomical group4.90e-08625
organ5.41e-08503
regional part of metencephalon1.80e-079
metencephalon1.80e-079
future metencephalon1.80e-079
basal ganglion2.66e-079
nuclear complex of neuraxis2.66e-079
aggregate regional part of brain2.66e-079
collection of basal ganglia2.66e-079
cerebral subcortex2.66e-079
temporal lobe3.73e-076
neural nucleus5.23e-079
nucleus of brain5.23e-079


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
ATF3#467214.97544968400580.005768294540793880.0259636647651585
NFYA#4800212.28372046655370.008516011403724430.0324860733068002
NFYB#4801211.17319550235760.01025467135054530.0381460187056417
SP1#666735.69838137814090.005403962701712170.0247244254875418



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.