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Coexpression cluster:C1028

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Full id: C1028_Alveolar_Renal_iPS_teratocarcinoma_H9_HES3GFP_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr14:104033742..104033743,+p1@ENST00000364314
Hg19::chr16:3064836..3064855,+p@chr16:3064836..3064855
+
Hg19::chr16:3068178..3068191,-p1@CLDN6
Hg19::chr16:3068393..3068407,+p@chr16:3068393..3068407
+
Hg19::chr19:18557270..18557282,-p2@ELL
Hg19::chr22:47030082..47030087,+p@chr22:47030082..47030087
+
Hg19::chr2:234322838..234322854,+p@chr2:234322838..234322854
+
Hg19::chr4:25679305..25679316,+p@chr4:25679305..25679316
+


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


GO IDGO nameFDR corrected p-value
GO:0008159positive transcription elongation factor activity0.0152784505458963
GO:0006368RNA elongation from RNA polymerase II promoter0.0152784505458963
GO:0003711transcription elongation regulator activity0.0152784505458963
GO:0006354RNA elongation0.0152784505458963
GO:0016338calcium-independent cell-cell adhesion0.0152784505458963
GO:0016607nuclear speck0.0374541676159651
GO:0005923tight junction0.0374541676159651
GO:0043296apical junction complex0.0374541676159651
GO:0016327apicolateral plasma membrane0.0374541676159651
GO:0016604nuclear body0.0374541676159651



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>


Uber Anatomy
Ontology termp-valuen
nephron epithelium2.17e-0916
nephron2.17e-0916
uriniferous tubule2.17e-0916
metanephric mesenchyme2.17e-0916
nephrogenic mesenchyme2.17e-0916
excretory tube3.23e-0917
mesonephric epithelium3.23e-0917
mesonephric tubule3.23e-0917
nephric duct3.23e-0917
kidney epithelium3.23e-0917
renal duct3.23e-0917
mesonephric duct3.23e-0917
pronephric duct3.23e-0917
mesonephros3.70e-0918
pronephros3.70e-0918
nephrogenic cord3.70e-0918
pronephric mesoderm3.70e-0918
rostral part of nephrogenic cord3.70e-0918
presumptive pronephric mesoderm3.70e-0918
urogenital ridge4.83e-0820
renal tubule9.79e-0812
nephron tubule9.79e-0812
nephron tubule epithelium9.79e-0812
cortex of kidney1.74e-0713
renal parenchyma1.74e-0713
duct3.83e-0726
tube6.64e-07194


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


No analysis results for this cluster

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.