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Coexpression cluster:C2838

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Full id: C2838_occipital_medial_squamous_gastric_parietal_frontal_Melanocyte



Phase1 CAGE Peaks

Hg19::chr6:117739710..117739729,-p@chr6:117739710..117739729
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Hg19::chr7:116312570..116312577,+p11@MET
Hg19::chr7:116312581..116312589,+p12@MET
Hg19::chr7:116312598..116312603,+p15@MET


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell1.06e-11253
endo-epithelial cell4.41e-0842
endodermal cell2.59e-0758
Uber Anatomy
Ontology termp-valuen
telencephalon5.27e-1434
regional part of cerebral cortex3.76e-1322
cerebral cortex5.12e-1325
pallium5.12e-1325
regional part of forebrain6.53e-1341
forebrain6.53e-1341
anterior neural tube6.53e-1341
future forebrain6.53e-1341
cerebral hemisphere6.61e-1332
regional part of telencephalon1.06e-1232
brain grey matter2.12e-1234
gray matter2.12e-1234
neocortex1.63e-1120
pre-chordal neural plate3.28e-1061
organ system subdivision6.23e-10223
regional part of nervous system1.70e-0953
regional part of brain1.70e-0953
neural tube4.10e-0956
neural rod4.10e-0956
future spinal cord4.10e-0956
neural keel4.10e-0956
brain2.19e-0868
future brain2.19e-0868
multi-tissue structure5.35e-08342
ecto-epithelium1.40e-07104
ectoderm-derived structure1.62e-07171
ectoderm1.62e-07171
presumptive ectoderm1.62e-07171
central nervous system1.92e-0781
nervous system4.11e-0789
neural plate5.82e-0782
presumptive neural plate5.82e-0782
Disease
Ontology termp-valuen
carcinoma9.31e-12106
cell type cancer5.45e-11143


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
BHLHE40#8553333.65386016023314.35025573591721e-050.000775318018435934
FOS#235336.74846648167080.005032452776317940.0234751143644588
JUND#372735.245997956403270.01043432751748420.0387164078444784
MAX#414934.839416631755340.01315737137836840.0466459387414852
MXI1#460137.471178721569470.003741314738550960.0186430254296256
NR3C1#2908311.22976749837980.001131672068063850.0077563131064786
TCF7L2#693438.077632422353010.002978381685834620.0158711773502159
TFAP2A#7020312.38897577978370.000846941303588430.00638240153008673
TFAP2C#702238.106921457395170.002947011739866440.0157200551151699
USF1#739134.771124457905970.01370465887188020.0483351637147201
USF2#739239.74414803880220.001718341848410070.0107263106990676



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.