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Coexpression cluster:C3018

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Full id: C3018_optic_cerebellum_globus_caudate_occipital_hippocampus_medial



Phase1 CAGE Peaks

Hg19::chr10:45455081..45455101,-p2@TMEM72-AS1
Hg19::chr20:3388541..3388575,-p2@C20orf194
Hg19::chr20:3388579..3388619,-p3@C20orf194


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>


Uber Anatomy
Ontology termp-valuen
adult organism1.15e-37114
neural tube3.59e-2856
neural rod3.59e-2856
future spinal cord3.59e-2856
neural keel3.59e-2856
regional part of nervous system3.09e-2653
regional part of brain3.09e-2653
regional part of forebrain9.49e-2441
forebrain9.49e-2441
anterior neural tube9.49e-2441
future forebrain9.49e-2441
central nervous system2.98e-2281
multi-cellular organism1.40e-21656
brain9.97e-2168
future brain9.97e-2168
telencephalon7.13e-2034
brain grey matter7.31e-2034
gray matter7.31e-2034
neural plate1.37e-1982
presumptive neural plate1.37e-1982
organ1.44e-19503
nervous system5.08e-1989
anatomical system5.77e-19624
cerebral hemisphere1.13e-1832
regional part of telencephalon1.21e-1832
anatomical group1.55e-18625
neurectoderm3.19e-1886
ecto-epithelium6.56e-16104
germ layer1.06e-15560
germ layer / neural crest1.06e-15560
embryonic tissue1.06e-15560
presumptive structure1.06e-15560
germ layer / neural crest derived structure1.06e-15560
epiblast (generic)1.06e-15560
embryonic structure1.34e-15564
embryo1.69e-15592
structure with developmental contribution from neural crest2.03e-15132
developing anatomical structure2.69e-15581
regional part of cerebral cortex8.01e-1522
ectoderm-derived structure9.30e-15171
ectoderm9.30e-15171
presumptive ectoderm9.30e-15171
pre-chordal neural plate1.15e-1461
cerebral cortex2.96e-1425
pallium2.96e-1425
neocortex1.26e-1320
anatomical conduit1.79e-09240
organ system subdivision7.49e-09223
tube1.91e-08192
multi-tissue structure2.07e-07342
bone marrow2.59e-0776
neural nucleus4.00e-079
nucleus of brain4.00e-079
basal ganglion4.45e-079
nuclear complex of neuraxis4.45e-079
aggregate regional part of brain4.45e-079
collection of basal ganglia4.45e-079
cerebral subcortex4.45e-079
tissue9.01e-07773


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
ELF1#199734.258097958807540.01295179875054610.0459826940105477
IRF1#365937.63716375356390.002244692747297240.0127568953493485
MYC#460935.22228187160940.007020843755740150.0293065507995902
SIN3A#2594235.408884726815140.006318961977991520.0275287227305492



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.