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Coexpression cluster:C4095: Difference between revisions

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|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463244147160371!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109215976729147
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463244147160371!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109215976729147
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}}
}}

Revision as of 16:32, 26 November 2012


Full id: C4095_CD14CD16_B_Eosinophils_CD14_Basophils_Neutrophils_CD19



Phase1 CAGE Peaks

Hg19::chr22:35806354..35806377,+p4@MCM5
Hg19::chrX:12994220..12994275,+p4@TMSB4X
Hg19::chrX:12994281..12994313,+p2@TMSB4X


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
hematopoietic stem cell2.62e-59168
angioblastic mesenchymal cell2.62e-59168
leukocyte6.83e-59136
hematopoietic oligopotent progenitor cell3.25e-56161
hematopoietic multipotent progenitor cell3.25e-56161
hematopoietic cell2.03e-55177
hematopoietic lineage restricted progenitor cell9.71e-49120
nongranular leukocyte3.28e-48115
myeloid leukocyte2.58e-3972
myeloid cell3.74e-39108
common myeloid progenitor3.74e-39108
granulocyte monocyte progenitor cell4.65e-3567
macrophage dendritic cell progenitor3.44e-3361
myeloid lineage restricted progenitor cell3.50e-3366
monopoietic cell3.91e-3259
monocyte3.91e-3259
monoblast3.91e-3259
promonocyte3.91e-3259
defensive cell7.18e-3048
phagocyte7.18e-3048
classical monocyte3.10e-2742
CD14-positive, CD16-negative classical monocyte3.10e-2742
mesenchymal cell4.37e-23354
connective tissue cell5.24e-22361
multi fate stem cell1.08e-18427
stem cell1.98e-17441
somatic stem cell1.22e-16433
motile cell5.74e-16386
lymphocyte1.23e-1453
common lymphoid progenitor1.23e-1453
nucleate cell2.39e-1455
lymphoid lineage restricted progenitor cell2.71e-1452
stuff accumulating cell2.57e-1187
lymphocyte of B lineage6.23e-1124
pro-B cell6.23e-1124
B cell9.53e-0814
intermediate monocyte2.43e-079
CD14-positive, CD16-positive monocyte2.43e-079
Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.46e-41108
hematopoietic system1.52e-4098
blood island1.52e-4098
immune system3.78e-3593
bone marrow7.14e-3376
bone element8.61e-2782
skeletal element3.14e-2390
connective tissue1.68e-20371
skeletal system2.82e-19100
lateral plate mesoderm6.75e-18203
musculoskeletal system3.24e-09167


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
ELF1#199734.258097958807540.01295179875054610.0463244147160371
SPI1#668838.204323508522730.001810593189410520.0109215976729147



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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