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Coexpression cluster:C3601: Difference between revisions

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|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
|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 16:13, 26 November 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 cell1.46e-62168
angioblastic mesenchymal cell1.46e-62168
hematopoietic oligopotent progenitor cell2.04e-59161
hematopoietic multipotent progenitor cell2.04e-59161
leukocyte2.99e-58136
hematopoietic cell8.29e-58177
nongranular leukocyte1.43e-51115
hematopoietic lineage restricted progenitor cell8.44e-48120
myeloid leukocyte5.76e-4072
myeloid cell1.61e-39108
common myeloid progenitor1.61e-39108
classical monocyte5.65e-3242
CD14-positive, CD16-negative classical monocyte5.65e-3242
defensive cell6.08e-3248
phagocyte6.08e-3248
monopoietic cell1.39e-3059
monocyte1.39e-3059
monoblast1.39e-3059
promonocyte1.39e-3059
myeloid lineage restricted progenitor cell1.43e-3066
granulocyte monocyte progenitor cell6.73e-3067
macrophage dendritic cell progenitor3.87e-2961
mature alpha-beta T cell1.52e-2318
alpha-beta T cell1.52e-2318
immature T cell1.52e-2318
mature T cell1.52e-2318
immature alpha-beta T cell1.52e-2318
T cell1.20e-2025
pro-T cell1.20e-2025
lymphoid lineage restricted progenitor cell1.83e-1752
CD8-positive, alpha-beta T cell4.22e-1711
lymphocyte5.96e-1753
common lymphoid progenitor5.96e-1753
nucleate cell5.52e-1655
mesenchymal cell2.60e-14354
connective tissue cell1.61e-13361
stuff accumulating cell3.53e-1387
motile cell1.02e-11386
intermediate monocyte2.75e-119
CD14-positive, CD16-positive monocyte2.75e-119
granulocyte8.15e-108
CD4-positive, alpha-beta T cell8.16e-106
multi fate stem cell6.07e-08427
somatic stem cell1.65e-07433
stem cell2.22e-07441
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.00e-3498
blood island6.00e-3498
hemolymphoid system2.94e-30108
bone marrow1.15e-2476
immune system7.21e-2393
bone element7.76e-2282
skeletal element1.12e-1890
skeletal system1.77e-15100
connective tissue1.89e-12371
lateral plate mesoderm3.07e-10203
blood9.72e-0915
haemolymphatic fluid9.72e-0915
organism substance9.72e-0915
Disease
Ontology termp-valuen
myeloid leukemia3.01e-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.