Personal tools

Coexpression cluster:C1028

From FANTOM5_SSTAR

Revision as of 14:38, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
nephron tubule epithelium6.55e-1710
nephron epithelium5.34e-1615
renal tubule5.34e-1615
nephron tubule5.34e-1615
nephron5.34e-1615
uriniferous tubule5.34e-1615
nephrogenic mesenchyme5.34e-1615
excretory tube5.75e-1516
kidney epithelium5.75e-1516
cortex of kidney3.40e-1412
renal parenchyma3.40e-1412
kidney5.76e-1226
kidney mesenchyme5.76e-1226
upper urinary tract5.76e-1226
kidney rudiment5.76e-1226
kidney field5.76e-1226
cortex2.58e-1115
parenchyma2.58e-1115
renal cortex tubule3.82e-103
region of nephron tubule3.82e-103
proximal tubule3.82e-103
cavitated compound organ6.72e-1031
ciliary epithelium1.40e-093
ciliary body1.40e-093
lower lobe of right lung4.11e-081
right lung lobe4.11e-081
lower lobe of lung4.11e-081
lobe of lung4.11e-081
right lung4.11e-081
trunk region element1.92e-07101
atypical epithelium2.14e-074


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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1028&oldid=2557364"