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Coexpression cluster:C2503

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Full id: C2503_medial_merkel_neuroectodermal_chorionic_hepatocellular_pituitary_putamen



Phase1 CAGE Peaks

Hg19::chr19:57326873..57326888,-p3@PEG3
Hg19::chr19:57327230..57327235,-p10@PEG3
Hg19::chr19:57327807..57327832,-p9@PEG3
Hg19::chr19:57327900..57327911,-p14@PEG3


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
chorionic membrane mesenchymal stem cell7.19e-073
Uber Anatomy
Ontology termp-valuen
neural tube4.06e-4957
neural rod4.06e-4957
future spinal cord4.06e-4957
neural keel4.06e-4957
regional part of brain8.91e-4059
anterior neural tube4.60e-3942
regional part of forebrain1.41e-3741
forebrain1.41e-3741
future forebrain1.41e-3741
brain2.03e-3569
future brain2.03e-3569
adult organism3.46e-35115
gray matter6.43e-3534
brain grey matter6.43e-3534
central nervous system1.02e-3482
telencephalon1.48e-3434
regional part of telencephalon4.66e-3333
neurectoderm7.85e-3390
cerebral hemisphere1.03e-3132
neural plate3.61e-3186
presumptive neural plate3.61e-3186
regional part of nervous system1.56e-2994
nervous system1.56e-2994
pre-chordal neural plate2.10e-2561
regional part of cerebral cortex5.46e-2522
neocortex1.32e-2420
cerebral cortex1.07e-2325
pallium1.07e-2325
head8.88e-19123
ectoderm1.04e-18173
presumptive ectoderm1.04e-18173
anterior region of body2.79e-18129
craniocervical region2.79e-18129
ectoderm-derived structure2.13e-17169
basal ganglion7.04e-139
nuclear complex of neuraxis7.04e-139
aggregate regional part of brain7.04e-139
collection of basal ganglia7.04e-139
cerebral subcortex7.04e-139
nucleus of brain8.14e-139
neural nucleus8.14e-139
tube2.68e-12194
gyrus2.91e-116
brainstem4.29e-118
posterior neural tube5.11e-1115
chordal neural plate5.11e-1115
temporal lobe6.05e-117
telencephalic nucleus1.30e-097
anatomical conduit1.79e-09241
organ part7.21e-09219
corpus striatum1.20e-084
striatum1.20e-084
ventral part of telencephalon1.20e-084
future corpus striatum1.20e-084
cell layer1.22e-07312
organ1.89e-07511
epithelium1.96e-07309
segmental subdivision of hindbrain4.11e-0712
hindbrain4.11e-0712
presumptive hindbrain4.11e-0712
caudate-putamen5.93e-073
dorsal striatum5.93e-073
acellular anatomical structure7.19e-073
egg chorion7.19e-073
chorion7.80e-077
anatomical cluster8.10e-07286
limbic system8.43e-075


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


No analysis results for this cluster

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.