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Coexpression cluster:C1191

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Full id: C1191_Melanocyte_retina_spinal_locus_medulla_teratocarcinoma_sacrococcigeal



Phase1 CAGE Peaks

Hg19::chr13:78492927..78492943,-p2@EDNRB
Hg19::chr13:78492955..78492973,-p1@EDNRB
Hg19::chr13:78493559..78493593,-p4@EDNRB
Hg19::chr13:78493594..78493623,-p5@EDNRB
Hg19::chr13:78493657..78493668,-p8@EDNRB
Hg19::chr13:78493676..78493690,-p7@EDNRB
Hg19::chr13:78493703..78493726,-p3@EDNRB


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
melanocyte5.74e-0810
melanoblast5.74e-0810
fat cell8.32e-0815
stuff accumulating cell1.72e-0739
Uber Anatomy
Ontology termp-valuen
adult organism9.02e-42115
neural tube1.39e-2857
neural rod1.39e-2857
future spinal cord1.39e-2857
neural keel1.39e-2857
central nervous system4.29e-2582
regional part of brain3.02e-2359
regional part of nervous system2.21e-2294
nervous system2.21e-2294
anterior neural tube1.67e-2142
neural plate3.10e-2186
presumptive neural plate3.10e-2186
regional part of forebrain8.37e-2141
forebrain8.37e-2141
future forebrain8.37e-2141
neurectoderm8.01e-1990
brain1.03e-1869
future brain1.03e-1869
gray matter3.37e-1834
brain grey matter3.37e-1834
telencephalon8.08e-1834
regional part of telencephalon2.47e-1733
anatomical conduit8.24e-17241
multi-cellular organism9.83e-17659
cerebral hemisphere1.18e-1632
anatomical cluster1.59e-15286
tube3.85e-15194
pre-chordal neural plate1.41e-1461
embryo7.35e-14612
anatomical system1.19e-13625
anatomical group1.87e-13626
ectoderm-derived structure3.19e-13169
anterior region of body8.87e-13129
craniocervical region8.87e-13129
head1.33e-12123
cerebral cortex2.81e-1225
pallium2.81e-1225
epithelium3.22e-12309
ectoderm4.83e-12173
presumptive ectoderm4.83e-12173
cell layer5.57e-12312
regional part of cerebral cortex1.40e-1122
embryonic structure1.68e-11605
developing anatomical structure1.68e-11605
germ layer3.22e-11604
embryonic tissue3.22e-11604
presumptive structure3.22e-11604
epiblast (generic)3.22e-11604
neocortex2.40e-1020
organism subdivision3.01e-09365
posterior neural tube3.29e-0815
chordal neural plate3.29e-0815
multi-tissue structure5.49e-08347
organ7.91e-08511
nucleus of brain1.31e-079
neural nucleus1.31e-079
basal ganglion2.00e-079
nuclear complex of neuraxis2.00e-079
aggregate regional part of brain2.00e-079
collection of basal ganglia2.00e-079
cerebral subcortex2.00e-079
brainstem3.02e-078


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
TRIM28#10155513.27894646090188.62103642667186e-060.00023410619432272



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.