Personal tools

Coexpression cluster:C3671

From FANTOM5_SSTAR

Revision as of 14:39, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3671_Neural_Chondrocyte_hepatocellular_caudate_signet_hippocampus_papillotubular



Phase1 CAGE Peaks

Hg19::chr17:70117153..70117174,+p1@SOX9
Hg19::chr17:70120097..70120118,+p@chr17:70120097..70120118
+
Hg19::chr17:70120252..70120370,-p@chr17:70120252..70120370
-


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
organism subdivision6.26e-36365
ectoderm-derived structure1.40e-34169
ectoderm1.06e-33173
presumptive ectoderm1.06e-33173
head3.14e-33123
multi-tissue structure2.25e-32347
anterior region of body1.74e-31129
craniocervical region1.74e-31129
neural plate1.56e-2986
presumptive neural plate1.56e-2986
central nervous system2.63e-2982
regional part of nervous system7.55e-2994
nervous system7.55e-2994
neural tube1.42e-2857
neural rod1.42e-2857
future spinal cord1.42e-2857
neural keel1.42e-2857
neurectoderm4.52e-2890
brain2.58e-2669
future brain2.58e-2669
regional part of brain1.43e-2459
pre-chordal neural plate8.70e-2361
cell layer1.79e-22312
epithelium4.52e-22309
anterior neural tube4.50e-2142
regional part of forebrain7.59e-2141
forebrain7.59e-2141
future forebrain7.59e-2141
organ7.99e-20511
anatomical conduit1.13e-19241
gray matter1.37e-1934
brain grey matter1.37e-1934
telencephalon1.37e-1934
regional part of telencephalon3.65e-1933
multi-cellular organism4.11e-19659
embryo4.97e-19612
anatomical cluster1.55e-18286
cerebral hemisphere1.60e-1832
embryonic structure6.66e-18605
developing anatomical structure6.66e-18605
adult organism9.52e-18115
germ layer9.55e-18604
embryonic tissue9.55e-18604
presumptive structure9.55e-18604
epiblast (generic)9.55e-18604
organ part2.23e-17219
tube4.52e-17194
anatomical system9.36e-17625
anatomical group1.95e-16626
cerebral cortex7.46e-1525
pallium7.46e-1525
regional part of cerebral cortex2.17e-1322
neocortex4.27e-1220
endoderm-derived structure6.70e-10169
endoderm6.70e-10169
presumptive endoderm6.70e-10169
primordium7.20e-10168
digestive system7.72e-09155
digestive tract7.72e-09155
primitive gut7.72e-09155
posterior neural tube1.26e-0815
chordal neural plate1.26e-0815
compound organ4.56e-0869
trunk region element1.38e-07107
immaterial anatomical entity3.57e-07126
mesenchyme4.28e-07238
entire embryonic mesenchyme4.28e-07238
subdivision of head5.29e-0748
segmental subdivision of hindbrain5.96e-0712
hindbrain5.96e-0712
presumptive hindbrain5.96e-0712


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.