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Coexpression cluster:C3499

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Full id: C3499_Prostate_substantia_Smooth_placenta_globus_thalamus_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr15:51669444..51669479,+p3@GLDN
Hg19::chr15:51669496..51669509,+p5@GLDN
Hg19::chr15:51669513..51669571,+p2@GLDN


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
fibroblast of gingiva1.56e-075
Uber Anatomy
Ontology termp-valuen
neural tube4.86e-3857
neural rod4.86e-3857
future spinal cord4.86e-3857
neural keel4.86e-3857
regional part of brain5.02e-3259
brain4.59e-3069
future brain4.59e-3069
central nervous system6.91e-2982
neural plate1.36e-2886
presumptive neural plate1.36e-2886
regional part of forebrain4.70e-2741
forebrain4.70e-2741
future forebrain4.70e-2741
gray matter6.67e-2734
brain grey matter6.67e-2734
telencephalon9.11e-2734
neurectoderm1.26e-2690
anterior neural tube3.54e-2642
regional part of telencephalon1.61e-2533
adult organism3.54e-25115
head2.06e-24123
regional part of nervous system2.75e-2494
nervous system2.75e-2494
cerebral hemisphere6.28e-2432
anterior region of body1.82e-22129
craniocervical region1.82e-22129
pre-chordal neural plate4.29e-1961
ectoderm-derived structure1.28e-18169
regional part of cerebral cortex3.77e-1822
ectoderm9.12e-18173
presumptive ectoderm9.12e-18173
neocortex6.94e-1620
cerebral cortex2.19e-1525
pallium2.19e-1525
nucleus of brain2.45e-149
neural nucleus2.45e-149
organism subdivision1.02e-13365
posterior neural tube6.35e-1315
chordal neural plate6.35e-1315
segmental subdivision of nervous system1.19e-1213
telencephalic nucleus2.43e-117
segmental subdivision of hindbrain2.55e-1112
hindbrain2.55e-1112
presumptive hindbrain2.55e-1112
basal ganglion7.45e-119
nuclear complex of neuraxis7.45e-119
aggregate regional part of brain7.45e-119
collection of basal ganglia7.45e-119
cerebral subcortex7.45e-119
brainstem3.78e-108
organ part8.96e-10219
gyrus2.14e-096
organ1.42e-08511
anatomical conduit1.76e-07241
regional part of metencephalon1.92e-079
metencephalon1.92e-079
future metencephalon1.92e-079
epithelium4.11e-07309
tube6.39e-07194
anatomical cluster6.82e-07286
cell layer6.99e-07312


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
CTCF#1066435.360256373075030.0064925092527670.0278984231166317



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.