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Coexpression cluster:C1678

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Full id: C1678_medulla_spinal_locus_pons_corpus_globus_thalamus



Phase1 CAGE Peaks

Hg19::chr12:54765345..54765358,-p@chr12:54765345..54765358
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Hg19::chr14:62010202..62010207,-p@chr14:62010202..62010207
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Hg19::chr15:93616900..93616918,-p6@RGMA
Hg19::chr2:69741788..69741801,-p@chr2:69741788..69741801
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Hg19::chr2:69741832..69741847,-p@chr2:69741832..69741847
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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 organism2.80e-40115
neural tube1.71e-2857
neural rod1.71e-2857
future spinal cord1.71e-2857
neural keel1.71e-2857
central nervous system7.83e-2782
regional part of brain3.14e-2359
brain1.05e-2269
future brain1.05e-2269
regional part of forebrain4.69e-2241
forebrain4.69e-2241
future forebrain4.69e-2241
regional part of nervous system8.85e-2294
nervous system8.85e-2294
anterior neural tube3.26e-2142
gray matter1.34e-1934
brain grey matter1.34e-1934
telencephalon1.61e-1934
regional part of telencephalon1.31e-1833
cerebral hemisphere1.30e-1732
neural plate2.74e-1786
presumptive neural plate2.74e-1786
neurectoderm1.02e-1590
regional part of cerebral cortex4.21e-1422
neocortex2.38e-1220
pre-chordal neural plate3.03e-1261
cerebral cortex1.31e-1125
pallium1.31e-1125
head5.14e-11123
anterior region of body9.85e-11129
craniocervical region9.85e-11129
nucleus of brain2.38e-109
neural nucleus2.38e-109
posterior neural tube2.09e-0815
chordal neural plate2.09e-0815
telencephalic nucleus3.09e-087
ectoderm-derived structure4.29e-08169
basal ganglion6.52e-089
nuclear complex of neuraxis6.52e-089
aggregate regional part of brain6.52e-089
collection of basal ganglia6.52e-089
cerebral subcortex6.52e-089
brainstem1.34e-078
ectoderm1.68e-07173
presumptive ectoderm1.68e-07173
gyrus2.93e-076


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.