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Coexpression cluster:C4052: Difference between revisions

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|tf_chipseq_enrich=EBF1#1879;3:8.906466846569:0.0014152328356098:0.00915998401823577!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463038000105529!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269938640224413!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.01091907507269!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630038554540827
|tf_chipseq_enrich=EBF1#1879;3:8.906466846569:0.0014152328356098:0.00915998401823577!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463038000105529!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269938640224413!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.01091907507269!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630038554540827
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}}
}}

Revision as of 16:31, 26 November 2012


Full id: C4052_Eosinophils_CD19_Natural_CD8_Whole_CD4_Basophils



Phase1 CAGE Peaks

Hg19::chr20:56195449..56195459,-p4@ZBP1
Hg19::chr20:56195474..56195506,-p1@ZBP1
Hg19::chr20:56195509..56195520,-p3@ZBP1


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><br>


Cell Type
Ontology termp-valuen
leukocyte2.19e-64136
nongranular leukocyte3.94e-60115
hematopoietic lineage restricted progenitor cell9.86e-53120
hematopoietic stem cell4.58e-46168
angioblastic mesenchymal cell4.58e-46168
hematopoietic oligopotent progenitor cell6.61e-44161
hematopoietic multipotent progenitor cell6.61e-44161
hematopoietic cell3.91e-42177
lymphocyte2.38e-4053
common lymphoid progenitor2.38e-4053
lymphoid lineage restricted progenitor cell1.08e-3952
nucleate cell2.88e-3855
classical monocyte2.44e-2442
CD14-positive, CD16-negative classical monocyte2.44e-2442
myeloid leukocyte1.15e-2372
mature alpha-beta T cell1.01e-2118
alpha-beta T cell1.01e-2118
immature T cell1.01e-2118
mature T cell1.01e-2118
immature alpha-beta T cell1.01e-2118
defensive cell6.97e-2048
phagocyte6.97e-2048
T cell6.03e-1925
pro-T cell6.03e-1925
monopoietic cell6.21e-1859
monocyte6.21e-1859
monoblast6.21e-1859
promonocyte6.21e-1859
lymphocyte of B lineage9.90e-1824
pro-B cell9.90e-1824
macrophage dendritic cell progenitor5.67e-1761
myeloid lineage restricted progenitor cell8.24e-1766
granulocyte monocyte progenitor cell2.20e-1667
CD8-positive, alpha-beta T cell3.87e-1411
B cell8.08e-1414
myeloid cell8.20e-12108
common myeloid progenitor8.20e-12108
intermediate monocyte3.44e-099
CD14-positive, CD16-positive monocyte3.44e-099
granulocyte1.41e-088
mesenchymal cell3.62e-08354
CD4-positive, alpha-beta T cell3.93e-086
connective tissue cell1.43e-07361
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.83e-2798
blood island1.83e-2798
hemolymphoid system1.93e-25108
immune system4.82e-1793
bone marrow3.28e-1476
bone element2.50e-1282
blood3.11e-1115
haemolymphatic fluid3.11e-1115
organism substance3.11e-1115
skeletal element3.00e-1090
skeletal system3.51e-08100
hemopoietic organ2.43e-077
immune organ2.43e-077
connective tissue8.97e-07371


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#187938.9064668465690.00141523283560980.00915998401823577
ELF1#199734.258097958807540.01295179875054610.0463038000105529
NFKB1#479035.488063424193840.006049381815655430.0269938640224413
SPI1#668838.204323508522730.001810593189410520.01091907507269
TCF12#6938310.63446490218640.0008313523990202070.00630038554540827



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.