Personal tools

Coexpression cluster:C2450

From FANTOM5_SSTAR

Revision as of 14:24, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2450_Retinal_pineal_retina_Melanocyte_occipital_eye_Pericytes



Phase1 CAGE Peaks

Hg19::chr17:935036..935083,-p4@ABR
Hg19::chr3:69928371..69928385,+p@chr3:69928371..69928385
+
Hg19::chr3:69928404..69928418,+p@chr3:69928404..69928418
+
Hg19::chr3:69928426..69928436,+p@chr3:69928426..69928436
+


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
pigment cell5.25e-1214
melanocyte1.55e-0810
melanoblast1.55e-0810
Uber Anatomy
Ontology termp-valuen
adult organism1.32e-52115
neural plate3.90e-3486
presumptive neural plate3.90e-3486
neurectoderm3.44e-3390
neural tube1.70e-3257
neural rod1.70e-3257
future spinal cord1.70e-3257
neural keel1.70e-3257
pre-chordal neural plate4.94e-3161
regional part of nervous system8.12e-2994
nervous system8.12e-2994
regional part of brain8.41e-2959
anterior neural tube2.19e-2842
regional part of forebrain6.99e-2841
forebrain6.99e-2841
future forebrain6.99e-2841
brain6.00e-2669
future brain6.00e-2669
central nervous system1.30e-2582
anterior region of body4.19e-23129
craniocervical region4.19e-23129
head5.05e-23123
telencephalon1.33e-2234
gray matter6.99e-2234
brain grey matter6.99e-2234
regional part of telencephalon9.49e-2233
cerebral hemisphere2.61e-2132
ectoderm-derived structure8.59e-19169
regional part of cerebral cortex8.79e-1922
ectoderm1.12e-18173
presumptive ectoderm1.12e-18173
neocortex1.71e-1720
cerebral cortex1.22e-1625
pallium1.22e-1625
embryo2.29e-11612
organ4.62e-11511
multi-tissue structure1.52e-10347
multi-cellular organism5.80e-10659
organ part1.40e-09219
embryonic structure3.20e-09605
developing anatomical structure3.20e-09605
germ layer6.25e-09604
embryonic tissue6.25e-09604
presumptive structure6.25e-09604
epiblast (generic)6.25e-09604
organism subdivision1.01e-07365
basal ganglion1.91e-079
nuclear complex of neuraxis1.91e-079
aggregate regional part of brain1.91e-079
collection of basal ganglia1.91e-079
cerebral subcortex1.91e-079
anatomical system2.23e-07625
anatomical group2.81e-07626
temporal lobe3.07e-077
sensory system6.62e-0724
entire sense organ system6.62e-0724
epithelium7.18e-07309


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.