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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3262_splenic_myeloma_Gingival_Mallassezderived_Corneal_B_Macrophage
|full_id=C3262_splenic_myeloma_Gingival_Mallassezderived_Corneal_B_Macrophage
|id=C3262
|id=C3262

Revision as of 16:09, 12 September 2012


Full id: C3262_splenic_myeloma_Gingival_Mallassezderived_Corneal_B_Macrophage



Phase1 CAGE Peaks

Hg19::chr12:15114658..15114684,-p4@ARHGDIB
Hg19::chr12:15114685..15114697,-p8@ARHGDIB
Hg19::chr12:15114705..15114712,-p9@ARHGDIB


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 cell3.05e-37172
angioblastic mesenchymal cell3.05e-37172
hematopoietic cell1.48e-36182
hematopoietic oligopotent progenitor cell1.91e-34165
hematopoietic multipotent progenitor cell1.91e-34165
leukocyte2.63e-29140
hematopoietic lineage restricted progenitor cell2.95e-27124
nongranular leukocyte1.81e-26119
lymphocyte1.09e-1853
common lymphoid progenitor1.09e-1853
lymphoid lineage restricted progenitor cell3.59e-1852
myeloid cell4.69e-16112
common myeloid progenitor4.69e-16112
lymphocyte of B lineage1.99e-1124
pro-B cell1.99e-1124
myeloid lineage restricted progenitor cell1.22e-0970
granulocyte monocyte progenitor cell1.23e-0971
macrophage dendritic cell progenitor2.77e-0965
monopoietic cell1.59e-0863
monocyte1.59e-0863
monoblast1.59e-0863
promonocyte1.59e-0863
myeloid leukocyte1.93e-0876
T cell1.27e-0725
pro-T cell1.27e-0725
blood vessel endothelial cell2.50e-0718
embryonic blood vessel endothelial progenitor cell2.50e-0718
dendritic cell5.39e-0710
endothelial cell of artery8.73e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.36e-14102
blood island3.36e-14102
lateral plate mesoderm6.27e-14216
hemolymphoid system1.21e-13112
bone marrow1.45e-0780
endothelium2.50e-0718
blood vessel endothelium2.50e-0718
cardiovascular system endothelium2.50e-0718
blood4.81e-0715
haemolymphatic fluid4.81e-0715
organism substance4.81e-0715
endothelial tube8.73e-079
arterial system endothelium8.73e-079
endothelium of artery8.73e-079
Disease
Ontology termp-valuen
hematologic cancer8.47e-1351
immune system cancer8.47e-1351
leukemia4.39e-1039
myeloid leukemia5.79e-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
BCLAF1#9774321.65264761012189.8473954032885e-050.00138942465350452
E2F6#187635.017155731697390.00791769806886330.0320846028252052
EGR1#195834.988179094810140.008056488137383440.0319418253959528
GATA1#2623313.56030814380040.0004009615963782630.00387095841783596
GATA2#2624312.7449317335540.0004829527704283790.00436135792397488
GATA3#2625327.2365163572064.94721007899563e-050.000849665636310187
MAX#414936.452555509007120.003721913834265510.0185960368816369
MYC#460935.22228187160940.007020843755740150.0293464300410528
NFKB1#479035.488063424193840.006049381815655430.0268813082349163
PBX3#5090321.91451268674419.49854535978121e-050.00136247572974892
SPI1#668838.204323508522730.001810593189410520.010887013766414



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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