Personal tools

Coexpression cluster:C1153

From FANTOM5_SSTAR

Revision as of 12:15, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1153_Monocytederived_CD14_Dendritic_Macrophage_acute_spleen_lymph



Phase1 CAGE Peaks

Hg19::chr11:72983377..72983428,+p1@P2RY6
Hg19::chr11:72983450..72983455,+p11@P2RY6
Hg19::chr1:159796094..159796108,-p@chr1:159796094..159796108
-
Hg19::chr1:159796534..159796545,+p6@SLAMF8
Hg19::chr1:159796561..159796581,+p4@SLAMF8
Hg19::chr1:159796620..159796645,+p3@SLAMF8
Hg19::chr1:159796650..159796690,+p1@SLAMF8


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:0045029UDP-activated nucleotide receptor activity0.00326730049767864
GO:0015065uridine nucleotide receptor activity0.00326730049767864
GO:0030321transepithelial chloride transport0.005808106742807
GO:0045028purinergic nucleotide receptor activity, G-protein coupled0.0136832824560085
GO:0001608nucleotide receptor activity, G-protein coupled0.0136832824560085
GO:0001614purinergic nucleotide receptor activity0.0136832824560085
GO:0016502nucleotide receptor activity0.0136832824560085
GO:0006821chloride transport0.0212713128400425
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0212713128400425
GO:0048015phosphoinositide-mediated signaling0.02804667290501
GO:0015698inorganic anion transport0.0484567284829324
GO:0019932second-messenger-mediated signaling0.0484567284829324



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
adult organism1.42e-36115
hematopoietic system5.80e-25102
blood island5.80e-25102
bone marrow4.62e-2480
hemolymphoid system3.86e-23112
bone element1.29e-2186
immune system2.53e-18115
skeletal element1.63e-15101
skeletal system1.63e-15101
organ3.66e-13511
neural tube1.06e-1157
neural rod1.06e-1157
future spinal cord1.06e-1157
neural keel1.06e-1157
regional part of brain1.92e-0859
tissue2.79e-08787
anterior neural tube3.11e-0842
regional part of forebrain7.37e-0841
forebrain7.37e-0841
future forebrain7.37e-0841
brain1.25e-0769
future brain1.25e-0769
anatomical group1.60e-07626
anatomical system2.54e-07625
central nervous system2.61e-0782
gray matter6.88e-0734
brain grey matter6.88e-0734
embryo8.56e-07612
embryonic structure9.57e-07605
developing anatomical structure9.57e-07605


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
MAFF#23764216.090101854270.006238346814265030.0275300728021223
MAX#414976.452555509007122.14589603858566e-067.76560070595454e-05
MYC#460975.22228187160949.4355989882785e-060.000250876915157031
NFKB1#479053.92004530299560.003036581424484610.0161179877714855
SMARCC1#6599212.47524551989470.01020047316571840.0379877056395117



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:C1153&oldid=2131079"