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Coexpression cluster:C3601: Difference between revisions

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|ontology_enrichment_disease=DOID:1240!9.08e-09!39;DOID:2531!3.55e-07!51;DOID:0060083!3.55e-07!51;DOID:8692!3.97e-07!31
|ontology_enrichment_disease=DOID:1240!9.08e-09!39;DOID:2531!3.55e-07!51;DOID:0060083!3.55e-07!51;DOID:8692!3.97e-07!31
|ontology_enrichment_uberon=UBERON:0002390!9.52e-33!102;UBERON:0003061!9.52e-33!102;UBERON:0002193!1.34e-28!112;UBERON:0002371!3.75e-23!80;UBERON:0001474!3.56e-20!86;UBERON:0002405!1.76e-15!115;UBERON:0004765!4.71e-15!101;UBERON:0001434!4.71e-15!101;UBERON:0003081!3.48e-10!216;UBERON:0002384!9.25e-09!375;UBERON:0000178!1.35e-07!15;UBERON:0000179!1.35e-07!15;UBERON:0000463!1.35e-07!15
|ontology_enrichment_uberon=UBERON:0002390!9.52e-33!102;UBERON:0003061!9.52e-33!102;UBERON:0002193!1.34e-28!112;UBERON:0002371!3.75e-23!80;UBERON:0001474!3.56e-20!86;UBERON:0002405!1.76e-15!115;UBERON:0004765!4.71e-15!101;UBERON:0001434!4.71e-15!101;UBERON:0003081!3.48e-10!216;UBERON:0002384!9.25e-09!375;UBERON:0000178!1.35e-07!15;UBERON:0000179!1.35e-07!15;UBERON:0000463!1.35e-07!15
|tf_chipseq_enrich=EBF1#1879;3:8.906466846569:0.0014152328356098:0.00914298540877473!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320098746321308!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461521344879826!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.010898936144602
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}}
}}

Revision as of 12:37, 5 September 2012


Full id: C3601_Eosinophils_CD8_Natural_CD4_Basophils_Neutrophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr16:88767349..88767358,-p7@RNF166
Hg19::chr16:88770100..88770115,-p5@RNF166
Hg19::chr16:88770190..88770215,+p@chr16:88770190..88770215
+


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
hematopoietic stem cell7.85e-64172
angioblastic mesenchymal cell7.85e-64172
hematopoietic oligopotent progenitor cell2.26e-59165
hematopoietic multipotent progenitor cell2.26e-59165
hematopoietic cell8.46e-59182
leukocyte5.21e-58140
nongranular leukocyte1.60e-49119
hematopoietic lineage restricted progenitor cell7.75e-48124
myeloid cell3.78e-37112
common myeloid progenitor3.78e-37112
myeloid leukocyte1.19e-3576
granulocyte monocyte progenitor cell1.99e-2771
myeloid lineage restricted progenitor cell7.49e-2770
CD14-positive, CD16-negative classical monocyte1.42e-2642
monopoietic cell1.52e-2663
monocyte1.52e-2663
monoblast1.52e-2663
promonocyte1.52e-2663
macrophage dendritic cell progenitor2.04e-2665
classical monocyte8.54e-2445
T cell2.81e-2025
pro-T cell2.81e-2025
lymphoid lineage restricted progenitor cell1.15e-1952
mature alpha-beta T cell4.75e-1918
alpha-beta T cell4.75e-1918
immature T cell4.75e-1918
mature T cell4.75e-1918
immature alpha-beta T cell4.75e-1918
lymphocyte5.06e-1953
common lymphoid progenitor5.06e-1953
CD8-positive, alpha-beta T cell1.40e-1211
mesenchymal cell2.21e-10358
connective tissue cell7.05e-10365
granulocyte1.64e-098
intermediate monocyte7.15e-099
CD14-positive, CD16-positive monocyte7.15e-099
motile cell1.10e-08390
CD4-positive, alpha-beta T cell1.55e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.52e-33102
blood island9.52e-33102
hemolymphoid system1.34e-28112
bone marrow3.75e-2380
bone element3.56e-2086
immune system1.76e-15115
skeletal element4.71e-15101
skeletal system4.71e-15101
lateral plate mesoderm3.48e-10216
connective tissue9.25e-09375
blood1.35e-0715
haemolymphatic fluid1.35e-0715
organism substance1.35e-0715
Disease
Ontology termp-valuen
leukemia9.08e-0939
hematologic cancer3.55e-0751
immune system cancer3.55e-0751
myeloid leukemia3.97e-0731


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
EBF1#187938.9064668465690.00141523283560980.00914298540877473
EGR1#195834.988179094810140.008056488137383440.0320098746321308
ELF1#199734.258097958807540.01295179875054610.0461521344879826
SPI1#668838.204323508522730.001810593189410520.010898936144602



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.

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