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Coexpression cluster:C2861

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Full id: C2861_Ciliary_anaplastic_paracentral_pons_parietal_postcentral_medial



Phase1 CAGE Peaks

Hg19::chr6:46293212..46293228,-p15@RCAN2
Hg19::chr6:46293378..46293415,-p1@RCAN2
Hg19::chr6:46293429..46293442,-p8@RCAN2
Hg19::chr6:46293461..46293464,-p13@RCAN2


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
oligodendrocyte6.95e-077
macroglial cell6.95e-077
astrocyte6.95e-077
oligodendrocyte precursor cell6.95e-077
Uber Anatomy
Ontology termp-valuen
neural tube1.46e-4856
neural rod1.46e-4856
future spinal cord1.46e-4856
neural keel1.46e-4856
regional part of nervous system9.97e-4653
regional part of brain9.97e-4653
neural plate1.27e-4482
presumptive neural plate1.27e-4482
central nervous system4.76e-4481
brain1.94e-4168
future brain1.94e-4168
neurectoderm2.48e-4186
nervous system5.46e-4089
regional part of forebrain8.26e-3741
forebrain8.26e-3741
anterior neural tube8.26e-3741
future forebrain8.26e-3741
pre-chordal neural plate9.61e-3761
brain grey matter1.29e-3234
gray matter1.29e-3234
telencephalon1.45e-3234
ecto-epithelium5.59e-32104
cerebral hemisphere7.64e-3132
regional part of telencephalon1.60e-3032
structure with developmental contribution from neural crest6.89e-28132
cerebral cortex3.53e-2425
pallium3.53e-2425
adult organism4.31e-24114
regional part of cerebral cortex6.97e-2222
neocortex5.88e-2020
ectoderm-derived structure7.89e-19171
ectoderm7.89e-19171
presumptive ectoderm7.89e-19171
organ system subdivision1.74e-13223
posterior neural tube1.53e-1215
chordal neural plate1.53e-1215
segmental subdivision of nervous system1.19e-1013
segmental subdivision of hindbrain6.10e-1012
hindbrain6.10e-1012
presumptive hindbrain6.10e-1012
neural nucleus8.19e-109
nucleus of brain8.19e-109
basal ganglion1.57e-099
nuclear complex of neuraxis1.57e-099
aggregate regional part of brain1.57e-099
collection of basal ganglia1.57e-099
cerebral subcortex1.57e-099
epithelium3.75e-09306
cell layer8.28e-09309
tube4.86e-08192
gyrus5.22e-086
telencephalic nucleus8.73e-087
brainstem1.59e-076
regional part of metencephalon3.24e-079
metencephalon3.24e-079
future metencephalon3.24e-079
organ part6.79e-07218
parietal lobe9.29e-075


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#372746.994663941871030.000417684217818580.00392535967108384
STAT3#6774410.51946499715428.16377768286615e-050.00123478171965367
TRIM28#10155418.59052504526258.36730015875654e-060.000230877796903666



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.