Personal tools

Coexpression cluster:C1757

From FANTOM5_SSTAR

Revision as of 11:39, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1757_caudate_neuroectodermal_middle_hippocampus_occipital_medial_parietal



Phase1 CAGE Peaks

Hg19::chr16:24228211..24228225,+p9@PRKCB
Hg19::chr16:24228276..24228319,+p6@PRKCB
Hg19::chr16:24228354..24228378,+p8@PRKCB
Hg19::chr16:24230796..24230825,+p@chr16:24230796..24230825
+
Hg19::chr16:24230834..24230957,+p@chr16:24230834..24230957
+


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
neural tube6.06e-3356
neural rod6.06e-3356
future spinal cord6.06e-3356
neural keel6.06e-3356
telencephalon2.90e-3234
brain grey matter2.97e-3234
gray matter2.97e-3234
regional part of forebrain3.63e-3141
forebrain3.63e-3141
anterior neural tube3.63e-3141
future forebrain3.63e-3141
cerebral hemisphere4.34e-3132
regional part of telencephalon1.55e-3032
regional part of nervous system3.60e-3053
regional part of brain3.60e-3053
regional part of cerebral cortex1.82e-2622
neocortex8.35e-2420
central nervous system1.37e-2381
brain8.90e-2368
future brain8.90e-2368
cerebral cortex2.02e-2225
pallium2.02e-2225
neurectoderm2.72e-2286
nervous system3.67e-2289
adult organism4.23e-22114
neural plate5.84e-1982
presumptive neural plate5.84e-1982
pre-chordal neural plate5.10e-1761
basal ganglion2.99e-129
nuclear complex of neuraxis2.99e-129
aggregate regional part of brain2.99e-129
collection of basal ganglia2.99e-129
cerebral subcortex2.99e-129
ecto-epithelium5.11e-12104
neural nucleus2.39e-119
nucleus of brain2.39e-119
telencephalic nucleus9.58e-107
gyrus6.75e-096
limbic system5.35e-085
structure with developmental contribution from neural crest5.85e-08132
ectoderm-derived structure9.18e-08171
ectoderm9.18e-08171
presumptive ectoderm9.18e-08171
hematopoietic system1.39e-0798
blood island1.39e-0798
parietal lobe1.78e-075
occipital lobe1.83e-075
temporal lobe2.31e-076
hemolymphoid system4.93e-07108
corpus striatum8.47e-074
striatum8.47e-074
ventral part of telencephalon8.47e-074
future corpus striatum8.47e-074
Disease
Ontology termp-valuen
hematologic cancer5.24e-0851
immune system cancer5.24e-0851


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.