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Coexpression cluster:C3256

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Full id: C3256_large_Synoviocyte_heart_smooth_gastrointestinal_Sertoli_gall



Phase1 CAGE Peaks

Hg19::chr12:131438426..131438439,+p3@GPR133
Hg19::chr12:131438443..131438461,+p1@GPR133
Hg19::chr12:131438496..131438513,+p2@GPR133


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
classical monocyte1.75e-1142
CD14-positive, CD16-negative classical monocyte1.75e-1142
defensive cell2.23e-0948
phagocyte2.23e-0948
macrophage dendritic cell progenitor3.40e-0761
Uber Anatomy
Ontology termp-valuen
adult organism3.05e-37114
organ6.16e-16503
neural tube4.92e-1256
neural rod4.92e-1256
future spinal cord4.92e-1256
neural keel4.92e-1256
multi-cellular organism3.10e-11656
regional part of nervous system6.90e-1153
regional part of brain6.90e-1153
regional part of forebrain2.06e-1041
forebrain2.06e-1041
anterior neural tube2.06e-1041
future forebrain2.06e-1041
anatomical system4.23e-09624
anatomical group5.80e-09625
telencephalon4.44e-0834
brain grey matter5.08e-0834
gray matter5.08e-0834
neural plate6.03e-0882
presumptive neural plate6.03e-0882
regional part of telencephalon1.39e-0732
cerebral hemisphere1.60e-0732
organ system subdivision2.13e-07223
tissue5.95e-07773
regional part of cerebral cortex6.42e-0722
brain7.22e-0768
future brain7.22e-0768
neurectoderm7.32e-0786


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
E2F6#187635.017155731697390.00791769806886330.0320808685837218
JUND#372736.994663941871030.002921845042734990.01562891546316
MEF2A#4205318.74323090964410.0001518243905622470.00194915642605169
MEF2C#4208341.31135449262411.41744912101957e-050.000340158475988426
SPI1#668838.204323508522730.001810593189410520.0108857602964046
ZNF143#7702313.50087655222790.0004062804962997170.00387998616981036



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.