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Coexpression cluster:C1092: Difference between revisions

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|tf_chipseq_enrich=FOS#2353;4:4.4989776544472:0.00737448991622712:0.0304818281695826!POLR2A#5430;8:2.14745317655807:0.00221072578897191:0.0127266007427206!SPI1#6688;4:4.10216175426136:0.0102780066240076:0.0381920135844564
|tf_chipseq_enrich=FOS#2353;4:4.4989776544472:0.00737448991622712:0.0304818281695826!POLR2A#5430;8:2.14745317655807:0.00221072578897191:0.0127266007427206!SPI1#6688;4:4.10216175426136:0.0102780066240076:0.0381920135844564
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}}
}}

Revision as of 14:40, 26 November 2012


Full id: C1092_Hepatic_CD8_CD4_Endothelial_Renal_lymph_spleen



Phase1 CAGE Peaks

Hg19::chr7:150147807..150147847,+p1@GIMAP8
Hg19::chr7:150147877..150147898,+p3@GIMAP8
Hg19::chr7:150147899..150147910,+p7@GIMAP8
Hg19::chr7:150147930..150147943,+p4@GIMAP8
Hg19::chr7:150329353..150329364,-p7@GIMAP6
Hg19::chr7:150329389..150329412,-p3@GIMAP6
Hg19::chr7:150329421..150329482,-p1@GIMAP6
Hg19::chr7:150329530..150329552,-p2@GIMAP6


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:0005525GTP binding0.00118477953347309
GO:0032561guanyl ribonucleotide binding0.00118477953347309
GO:0019001guanyl nucleotide binding0.00118477953347309
GO:0032553ribonucleotide binding0.0133979824776932
GO:0032555purine ribonucleotide binding0.0133979824776932
GO:0017076purine nucleotide binding0.0133979824776932
GO:0000166nucleotide binding0.0157508168628174



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>


Cell Type
Ontology termp-valuen
endothelial cell2.19e-2536
endothelial cell of vascular tree9.13e-2224
meso-epithelial cell2.50e-1745
blood vessel endothelial cell4.07e-1718
embryonic blood vessel endothelial progenitor cell4.07e-1718
defensive cell6.33e-1548
phagocyte6.33e-1548
nongranular leukocyte1.33e-13115
classical monocyte1.65e-1342
CD14-positive, CD16-negative classical monocyte1.65e-1342
monopoietic cell1.09e-1259
monocyte1.09e-1259
monoblast1.09e-1259
promonocyte1.09e-1259
mature alpha-beta T cell5.34e-1218
alpha-beta T cell5.34e-1218
immature T cell5.34e-1218
mature T cell5.34e-1218
immature alpha-beta T cell5.34e-1218
myeloid leukocyte5.93e-1272
macrophage dendritic cell progenitor7.83e-1261
myeloid lineage restricted progenitor cell1.17e-1166
hematopoietic lineage restricted progenitor cell1.19e-11120
leukocyte2.00e-11136
granulocyte monocyte progenitor cell2.81e-1167
lining cell1.80e-1058
barrier cell1.80e-1058
endothelial cell of artery2.02e-099
CD8-positive, alpha-beta T cell5.00e-0911
T cell2.74e-0825
pro-T cell2.74e-0825
hematopoietic stem cell8.25e-08168
angioblastic mesenchymal cell8.25e-08168
vein endothelial cell2.37e-076
hematopoietic oligopotent progenitor cell2.43e-07161
hematopoietic multipotent progenitor cell2.43e-07161
aortic endothelial cell5.36e-076
Uber Anatomy
Ontology termp-valuen
adult organism8.24e-47114
hemolymphoid system1.21e-19108
blood vessel endothelium4.07e-1718
endothelium4.07e-1718
cardiovascular system endothelium4.07e-1718
lateral plate mesoderm5.89e-17203
hematopoietic system8.67e-1698
blood island8.67e-1698
immune system1.63e-1493
simple squamous epithelium1.51e-1222
squamous epithelium3.84e-1025
endothelial tube2.02e-099
arterial system endothelium2.02e-099
endothelium of artery2.02e-099
bone marrow7.86e-0976
circulatory system2.14e-08112
neural tube4.52e-0856
neural rod4.52e-0856
future spinal cord4.52e-0856
neural keel4.52e-0856
cardiovascular system2.68e-07109
bone element2.79e-0782
regional part of nervous system3.42e-0753
regional part of brain3.42e-0753
anatomical conduit7.63e-07240
blood8.56e-0715
haemolymphatic fluid8.56e-0715
organism substance8.56e-0715


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
FOS#235344.49897765444720.007374489916227120.0304818281695826
POLR2A#543082.147453176558070.002210725788971910.0127266007427206
SPI1#668844.102161754261360.01027800662400760.0381920135844564



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.