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Coexpression cluster:C2717: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;3:18.2683513442277:0.000268166010572129:0.00286751202806825!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240576954331703!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227684691907828!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0281094952636416
|tf_chipseq_enrich=BATF#10538;3:18.2683513442277:0.000268166010572129:0.00286751202806825!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240576954331703!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227684691907828!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0281094952636416
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}}
}}

Revision as of 15:40, 26 November 2012


Full id: C2717_acute_B_xeroderma_b_splenic_plasma_Dendritic



Phase1 CAGE Peaks

Hg19::chr3:127454947..127454961,-p16@MGLL
Hg19::chr3:127454965..127454984,-p27@MGLL
Hg19::chr3:174988853..174988868,-p1@NAALADL2-AS2
Hg19::chr7:150130832..150130852,+p2@ENST00000486954


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:0047372acylglycerol lipase activity0.000824208171435299
GO:0004622lysophospholipase activity0.00185446838572942
GO:0004620phospholipase activity0.0145266690215472
GO:0016298lipase activity0.0145266690215472
GO:0004091carboxylesterase activity0.0154126928058401
GO:0006954inflammatory response0.019987048157306
GO:0009611response to wounding0.0249028611797951
GO:0006952defense response0.028984654028808
GO:0009605response to external stimulus0.028984654028808
GO:0006629lipid metabolic process0.0389850465088896
GO:0016788hydrolase activity, acting on ester bonds0.041965932728914
GO:0006950response to stress0.041965932728914



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
leukocyte2.27e-25136
lymphocyte of B lineage1.34e-2224
pro-B cell1.34e-2224
nongranular leukocyte1.08e-20115
dendritic cell4.32e-1910
hematopoietic stem cell8.53e-19168
angioblastic mesenchymal cell8.53e-19168
hematopoietic lineage restricted progenitor cell6.38e-18120
hematopoietic cell2.23e-17177
hematopoietic oligopotent progenitor cell4.75e-16161
hematopoietic multipotent progenitor cell4.75e-16161
conventional dendritic cell3.30e-138
plasmacytoid dendritic cell1.09e-113
lymphocyte1.17e-1153
common lymphoid progenitor1.17e-1153
precursor B cell2.34e-113
nucleate cell4.20e-1155
Langerhans cell4.34e-115
lymphoid lineage restricted progenitor cell3.22e-1052
macrophage dendritic cell progenitor6.77e-1061
monopoietic cell5.58e-0959
monocyte5.58e-0959
monoblast5.58e-0959
promonocyte5.58e-0959
granulocyte monocyte progenitor cell1.05e-0867
mature B cell2.88e-082
pre-B-II cell2.88e-082
transitional stage B cell2.88e-082
small pre-B-II cell2.88e-082
immature B cell2.88e-082
myeloid lineage restricted progenitor cell1.07e-0766
myeloid leukocyte8.37e-0772
Uber Anatomy
Ontology termp-valuen
immune system4.99e-1393
hemopoietic organ3.86e-127
immune organ3.86e-127
hematopoietic system5.02e-1298
blood island5.02e-1298
hemolymphoid system1.35e-11108
spleen1.65e-113
gastrointestinal system mesentery1.65e-113
stomach region1.65e-113
mesentery1.65e-113
gastrointestinal system serosa1.65e-113
mesentery of stomach1.65e-113
gut mesentery1.65e-113
dorsal mesentery1.65e-113
dorsal mesogastrium1.65e-113
peritoneal cavity1.65e-113
spleen primordium1.65e-113
bone marrow2.03e-0876
bone element1.54e-0782
Disease
Ontology termp-valuen
lymphoma2.31e-1210
hematologic cancer3.15e-0751
immune system cancer3.15e-0751


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
BATF#10538318.26835134422770.0002681660105721290.00286751202806825
EBF1#187936.679850134926750.005184294118278910.0240576954331703
POU2F2#545236.829593043306890.004860473775203740.0227684691907828
SPI1#668836.153242631392040.006580387113059030.0281094952636416



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.