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Coexpression cluster:C1668

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Full id: C1668_spinal_thalamus_substantia_pineal_lymphangiectasia_globus_renal



Phase1 CAGE Peaks

Hg19::chr12:26276068..26276086,-p1@AK311258
Hg19::chr12:26277798..26277809,-p5@BHLHE41
Hg19::chr12:26277817..26277863,-p2@BHLHE41
Hg19::chr12:26277929..26277955,-p3@BHLHE41
Hg19::chr12:26277956..26277980,-p1@BHLHE41


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
adult organism1.30e-38115
neural tube2.31e-2757
neural rod2.31e-2757
future spinal cord2.31e-2757
neural keel2.31e-2757
neural plate3.04e-2786
presumptive neural plate3.04e-2786
neurectoderm4.64e-2690
regional part of brain2.10e-2359
central nervous system6.58e-2382
regional part of nervous system9.42e-2394
nervous system9.42e-2394
brain3.28e-2269
future brain3.28e-2269
anterior neural tube1.85e-1942
regional part of forebrain2.88e-1941
forebrain2.88e-1941
future forebrain2.88e-1941
pre-chordal neural plate3.29e-1961
head5.27e-16123
anterior region of body7.94e-16129
craniocervical region7.94e-16129
gray matter1.78e-1534
brain grey matter1.78e-1534
telencephalon1.83e-1534
ectoderm-derived structure2.37e-15169
ectoderm5.21e-15173
presumptive ectoderm5.21e-15173
regional part of telencephalon6.81e-1533
cerebral hemisphere3.76e-1432
organism subdivision7.51e-14365
tube8.39e-12194
anatomical conduit1.01e-11241
multi-cellular organism1.32e-11659
regional part of cerebral cortex5.45e-1122
organ7.45e-11511
cerebral cortex3.77e-1025
pallium3.77e-1025
epithelium8.00e-10309
neocortex8.91e-1020
anatomical group9.05e-10626
cell layer1.01e-09312
multi-tissue structure1.07e-09347
anatomical system2.00e-09625
anatomical cluster2.08e-09286
embryo2.72e-09612
posterior neural tube4.34e-0915
chordal neural plate4.34e-0915
embryonic structure2.97e-08605
developing anatomical structure2.97e-08605
germ layer3.99e-08604
embryonic tissue3.99e-08604
presumptive structure3.99e-08604
epiblast (generic)3.99e-08604
segmental subdivision of nervous system7.09e-0813
segmental subdivision of hindbrain2.95e-0712
hindbrain2.95e-0712
presumptive hindbrain2.95e-0712
nucleus of brain4.14e-079
neural nucleus4.14e-079
basal ganglion5.09e-079
nuclear complex of neuraxis5.09e-079
aggregate regional part of brain5.09e-079
collection of basal ganglia5.09e-079
cerebral subcortex5.09e-079


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
JUND#372745.595731153496820.001849593301755460.0109308326642168
MAX#414956.452555509007128.93743970843928e-050.00130602667652118
SUZ12#23512550.11578091106293.15480790456198e-092.61288646109872e-07
TRIM28#10155414.872420036214.00368496902357e-050.000734482442437822
USF1#739156.361499277207969.59569864925045e-050.0013675834760222



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.