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Coexpression cluster:C61

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Full id: C61_migratory_Dendritic_immature_Macrophage_xeroderma_cord_b



Phase1 CAGE Peaks


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


p.valueFDRnGenesnPathwayName
0.0007234956333209790.026939572699544189Chemokine signaling pathway (KEGG):04062
1.14932691900024e-060.000363761969863575586Apoptosis (KEGG):04210
0.001982076863616450.04825594825650833116Vascular smooth muscle contraction (KEGG):04270
0.0001651405664652950.01716101738031054128Osteoclast differentiation (KEGG):04380
0.001371450069559410.03774469104483083102Toll-like receptor signaling pathway (KEGG):04620
8.56423035042436e-050.01355289452954664108T cell receptor signaling pathway (KEGG):04660
0.0005618795586004610.025404982899578375B cell receptor signaling pathway (KEGG):04662
0.0001594808775964770.0171610173803105349Intestinal immune network for IgA production (KEGG):04672
0.0001913132292925210.01716101738031054133Toxoplasmosis (KEGG):05145
0.001531643638934320.04039710097689283106Amoebiasis (KEGG):05146
0.0006282934057305470.02651398172182914182Tuberculosis (KEGG):05152
0.0005540771065774160.0254049828995784176Influenza A (KEGG):05164
0.0008095025639053010.0269692169974766385Small cell lung cancer (KEGG):05222
0.0002439955077769270.0171610173803105211Osteopontin Signaling (Wikipathways):WP1434
0.0002328154789181280.01716101738031054140Regulation of toll-like receptor signaling pathway (Wikipathways):WP1449
0.0008660881115573470.02741168873079387MicroRNAs in cardiomyocyte hypertrophy (Wikipathways):WP1544
2.77565538333288e-050.00585663285883237481Apoptosis Modulation and Signaling (Wikipathways):WP1772
0.0007093083553436820.026939572699544188TNF-alpha/NF-kB Signaling Pathway (Wikipathways):WP231
0.001009385666843730.0304257679577181222EBV LMP1 signaling (Wikipathways):WP262
0.0004054521671066260.02138760181487454162MAPK signaling pathway (Wikipathways):WP382
0.001371450069559410.03774469104483083102Toll-like receptor signaling pathway (Wikipathways):WP75
0.0007712362400778370.02696921699747666511Signaling in Immune system (Reactome):REACT_6900
0.0004054521671066260.02138760181487454162TNF alpha/NF-kB down reg. targets (Netpath):NetPath_9
0.001911274528665470.04825594825650834246B Cell Receptor up reg. targets (Netpath):NetPath_12
0.0003430046337686950.02138760181487454155IL-1 up reg. targets (Netpath):NetPath_13
2.04164496673815e-081.29236126394525e-058217IL-4 up reg. targets (Netpath):NetPath_16



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


GO IDGO nameFDR corrected p-value
GO:0032502developmental process0.000377841516044536
GO:0048869cellular developmental process0.00628566792223742
GO:0030154cell differentiation0.00628566792223742
GO:0005886plasma membrane0.0494507038038988
GO:0043066negative regulation of apoptosis0.0494507038038988
GO:0032623interleukin-2 production0.0494507038038988
GO:0043069negative regulation of programmed cell death0.0494507038038988
GO:0044464cell part0.0494507038038988



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>



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
BATF#10538221.873677060946430.003913172685461650.0190690482501367
EBF1#1879461.432508653643970.008143700141435840.0321594093496963
MAFK#7975211.989913971658840.002408630508792760.0135799482675344
MEF2A#4205251.638394310283570.01123076063003850.0412335445911759
NFKB1#4790701.343232306620870.004932250986343850.0230488773888212
RXRA#6256261.824965194466660.00250984768875780.0140769014964919
SPI1#6688561.606440966703750.0002328489880028030.00255822800947031



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