Personal tools

Coexpression cluster:C440

From FANTOM5_SSTAR

Revision as of 20:00, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C440_biphenotypic_acute_immature_splenic_B_myelodysplastic_Eosinophils



Phase1 CAGE Peaks

Hg19::chr10:7454538..7454551,-p@chr10:7454538..7454551
-
Hg19::chr12:120031498..120031508,+p4@TMEM233
Hg19::chr12:66801329..66801341,-p7@GRIP1
Hg19::chr15:28970769..28970773,+p@chr15:28970769..28970773
+
Hg19::chr15:52392705..52392752,-p1@ENST00000558607
Hg19::chr16:2256848..2256864,+p@chr16:2256848..2256864
+
Hg19::chr16:68389531..68389545,+p@chr16:68389531..68389545
+
Hg19::chr19:828296..828310,+p@chr19:828296..828310
+
Hg19::chr19:834404..834417,+p@chr19:834404..834417
+
Hg19::chr19:834523..834536,+p@chr19:834523..834536
+
Hg19::chr1:246257630..246257635,-p@chr1:246257630..246257635
-
Hg19::chr3:18244864..18244870,+p@chr3:18244864..18244870
+
Hg19::chr3:18467290..18467311,-p8@SATB1
Hg19::chr5:134788068..134788078,-p6@TIFAB
Hg19::chr5:134788131..134788156,-p5@TIFAB
Hg19::chr5:49732522..49732546,-p@chr5:49732522..49732546
-
Hg19::chr5:49949931..49949969,-p@chr5:49949931..49949969
-
Hg19::chr6:135501708..135501716,+p@chr6:135501708..135501716
+
Hg19::chr6:135501768..135501779,+p@chr6:135501768..135501779
+
Hg19::chr8:124031213..124031224,-p@chr8:124031213..124031224
-
Hg19::chr8:27456169..27456180,-p@chr8:27456169..27456180
-
Hg19::chr8:38008551..38008585,-p2@STAR


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:0016571histone methylation0.018557891113116
GO:0017127cholesterol transporter activity0.018557891113116
GO:0005720nuclear heterochromatin0.018557891113116
GO:0006700C21-steroid hormone biosynthetic process0.018557891113116
GO:0015248sterol transporter activity0.018557891113116
GO:0008207C21-steroid hormone metabolic process0.018557891113116
GO:0015485cholesterol binding0.018557891113116
GO:0030159receptor signaling complex scaffold activity0.018557891113116
GO:0000792heterochromatin0.018557891113116
GO:0032947protein complex scaffold0.018557891113116
GO:0006479protein amino acid methylation0.018557891113116
GO:0008213protein amino acid alkylation0.018557891113116
GO:0050681androgen receptor binding0.018557891113116
GO:0000790nuclear chromatin0.018557891113116
GO:0032934sterol binding0.0203305991360511
GO:0035258steroid hormone receptor binding0.0211758367765745
GO:0030521androgen receptor signaling pathway0.0225848989214989
GO:0042446hormone biosynthetic process0.0257293510819914
GO:0043414biopolymer methylation0.0257293510819914
GO:0016570histone modification0.0257293510819914
GO:0016569covalent chromatin modification0.0257293510819914
GO:0030518steroid hormone receptor signaling pathway0.0257293510819914
GO:0030522intracellular receptor-mediated signaling pathway0.0257293510819914
GO:0035257nuclear hormone receptor binding0.0257293510819914
GO:0051427hormone receptor binding0.0257293510819914
GO:0044454nuclear chromosome part0.0290715053333163
GO:0032259methylation0.030079515237829
GO:0005496steroid binding0.0334467056568891
GO:0042445hormone metabolic process0.0334467056568891
GO:0006694steroid biosynthetic process0.0334467056568891
GO:0005319lipid transporter activity0.0348691894377747
GO:0000228nuclear chromosome0.0348691894377747
GO:0003690double-stranded DNA binding0.0368766342591346
GO:0006869lipid transport0.0447044467987155
GO:0045211postsynaptic membrane0.0476656236037313
GO:0006730one-carbon compound metabolic process0.0476656236037313
GO:0043566structure-specific DNA binding0.0476656236037313
GO:0044456synapse part0.0476656236037313



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
hematopoietic stem cell7.35e-40172
angioblastic mesenchymal cell7.35e-40172
hematopoietic cell6.60e-38182
hematopoietic oligopotent progenitor cell2.54e-36165
hematopoietic multipotent progenitor cell2.54e-36165
myeloid cell1.46e-28112
common myeloid progenitor1.46e-28112
leukocyte3.99e-23140
nongranular leukocyte1.53e-18119
hematopoietic lineage restricted progenitor cell1.81e-18124
myeloid leukocyte5.79e-1376
granulocyte monocyte progenitor cell8.28e-1271
macrophage dendritic cell progenitor1.09e-1165
myeloid lineage restricted progenitor cell7.00e-1170
monopoietic cell8.42e-1163
monocyte8.42e-1163
monoblast8.42e-1163
promonocyte8.42e-1163
CD14-positive, CD16-negative classical monocyte4.93e-0942
classical monocyte2.37e-0845
lymphocyte1.57e-0753
common lymphoid progenitor1.57e-0753
lymphoid lineage restricted progenitor cell2.60e-0752
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.79e-15102
blood island5.79e-15102
hemolymphoid system2.45e-14112
adult organism4.63e-14115
regional part of forebrain9.59e-1241
forebrain9.59e-1241
future forebrain9.59e-1241
anterior neural tube6.44e-1142
bone marrow4.29e-1080
cerebral hemisphere4.38e-1032
telencephalon4.41e-1034
gray matter4.56e-1034
brain grey matter4.56e-1034
neural tube5.62e-1057
neural rod5.62e-1057
future spinal cord5.62e-1057
neural keel5.62e-1057
regional part of cerebral cortex1.11e-0922
regional part of telencephalon1.40e-0933
bone element2.93e-0986
neocortex5.33e-0920
regional part of brain7.29e-0959
immune system2.67e-08115
brain1.69e-0769
future brain1.69e-0769
cerebral cortex4.10e-0725
pallium4.10e-0725
central nervous system4.24e-0782
regional part of nervous system7.19e-0794
nervous system7.19e-0794
Disease
Ontology termp-valuen
hematologic cancer2.37e-2151
immune system cancer2.37e-2151
leukemia2.50e-2039
myeloid leukemia3.65e-1931


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:C440&oldid=1993396"