Personal tools

Coexpression cluster:C732

From FANTOM5_SSTAR

Revision as of 09:26, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C732_small_merkel_nonsmall_argyrophil_neuroblastoma_acute_carcinoid



Phase1 CAGE Peaks

Hg19::chr11:12341235..12341246,+p@chr11:12341235..12341246
+
Hg19::chr11:64834357..64834371,-p@chr11:64834357..64834371
-
Hg19::chr1:10928103..10928127,-p@chr1:10928103..10928127
-
Hg19::chr2:219849644..219849655,-p7@FEV
Hg19::chr2:219849692..219849702,-p11@FEV
Hg19::chr2:219849723..219849743,-p@chr2:219849723..219849743
-
Hg19::chr2:219849784..219849798,-p5@FEV
Hg19::chr2:219849805..219849819,-p3@FEV
Hg19::chr2:219850049..219850060,-p8@FEV
Hg19::chr2:219850277..219850288,-p9@FEV
Hg19::chr2:219866929..219866945,+p1@ENST00000441450


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
embryonic stem cell1.22e-075
Uber Anatomy
Ontology termp-valuen
adult organism1.21e-09115
neural tube1.58e-0957
neural rod1.58e-0957
future spinal cord1.58e-0957
neural keel1.58e-0957
regional part of forebrain5.20e-0941
forebrain5.20e-0941
future forebrain5.20e-0941
regional part of brain5.43e-0959
regional part of nervous system6.94e-0994
nervous system6.94e-0994
anterior neural tube1.11e-0842
brain3.32e-0869
future brain3.32e-0869
central nervous system5.30e-0882
neurectoderm1.24e-0790
nucleus of brain1.99e-079
neural nucleus1.99e-079
gray matter5.17e-0734
brain grey matter5.17e-0734
telencephalon9.98e-0734
Disease
Ontology termp-valuen
neuroectodermal tumor1.06e-1210
cancer1.10e-09235
cell type cancer1.15e-09143
disease of cellular proliferation3.70e-09239
germ cell and embryonal cancer2.21e-0822
germ cell cancer2.21e-0822
neuroendocrine tumor1.82e-076


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
CTBP2#1488634.20927291236087.05259877447434e-095.48857200750615e-07
EGR1#195873.174295787606450.001993572090999620.0115947360701626
SUZ12#23512836.44784066259123.90115474127522e-125.15085587893859e-10



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.