Personal tools

Coexpression cluster:C3585

From FANTOM5_SSTAR

Revision as of 16:31, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3585_Prostate_Sebocyte_oral_Small_Keratinocyte_Tracheal_Bronchial



Phase1 CAGE Peaks

Hg19::chr16:68712449..68712467,+p@chr16:68712449..68712467
+
Hg19::chr17:7491787..7491799,-p@chr17:7491787..7491799
-
Hg19::chr17:7492504..7492520,-p3@SOX15


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 tube1.56e-2057
neural rod1.56e-2057
future spinal cord1.56e-2057
neural keel1.56e-2057
ectoderm8.02e-20173
presumptive ectoderm8.02e-20173
ectoderm-derived structure1.15e-19169
central nervous system1.36e-1882
organ part7.97e-18219
anterior region of body3.39e-17129
craniocervical region3.39e-17129
anterior neural tube8.32e-1742
head2.24e-16123
regional part of forebrain2.47e-1641
forebrain2.47e-1641
future forebrain2.47e-1641
regional part of brain4.71e-1659
gray matter2.45e-1534
brain grey matter2.45e-1534
telencephalon4.50e-1534
adult organism4.95e-15115
regional part of telencephalon8.44e-1533
regional part of nervous system1.43e-1494
nervous system1.43e-1494
cerebral hemisphere2.21e-1432
brain7.73e-1469
future brain7.73e-1469
neurectoderm1.89e-1390
neural plate2.05e-1386
presumptive neural plate2.05e-1386
regional part of cerebral cortex8.64e-1322
cerebral cortex2.66e-1225
pallium2.66e-1225
organ3.62e-12511
pre-chordal neural plate4.92e-1261
neocortex9.19e-1220
embryo9.80e-12612
respiratory system1.07e-1172
multi-cellular organism2.48e-10659
organism subdivision7.41e-10365
respiratory tract1.48e-0953
embryonic structure3.20e-09605
developing anatomical structure3.20e-09605
orifice3.77e-0935
anatomical system6.65e-09625
germ layer6.68e-09604
embryonic tissue6.68e-09604
presumptive structure6.68e-09604
epiblast (generic)6.68e-09604
anatomical group8.52e-09626
endoderm-derived structure2.26e-08169
endoderm2.26e-08169
presumptive endoderm2.26e-08169
segment of respiratory tract8.17e-0846
multi-tissue structure1.27e-07347
anatomical conduit1.64e-07241
epithelium4.51e-07309
respiratory primordium6.97e-0738
endoderm of foregut6.97e-0738
anatomical cluster7.31e-07286
cell layer9.64e-07312
Disease
Ontology termp-valuen
squamous cell carcinoma4.38e-0914


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.