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Coexpression cluster:C4076: Difference between revisions

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|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.00898698755560956!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.010920336227122
|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.00898698755560956!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.010920336227122
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}}
}}

Revision as of 16:31, 26 November 2012


Full id: C4076_CD14_Synoviocyte_mesenchymal_Adipocyte_Myoblast_Preadipocyte_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr21:39668478..39668496,+p11@KCNJ15
Hg19::chr21:39668499..39668519,+p14@KCNJ15
Hg19::chr21:39668520..39668534,+p9@KCNJ15


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
classical monocyte1.64e-3342
CD14-positive, CD16-negative classical monocyte1.64e-3342
defensive cell3.88e-2948
phagocyte3.88e-2948
macrophage dendritic cell progenitor4.74e-2561
monopoietic cell3.34e-2359
monocyte3.34e-2359
monoblast3.34e-2359
promonocyte3.34e-2359
granulocyte monocyte progenitor cell1.44e-2167
myeloid leukocyte2.41e-2172
connective tissue cell1.05e-20361
mesenchymal cell8.35e-20354
multi fate stem cell2.20e-19427
myeloid lineage restricted progenitor cell2.32e-1966
stuff accumulating cell1.15e-1887
somatic stem cell1.36e-18433
stem cell3.36e-18441
motile cell1.37e-16386
myeloid cell2.20e-11108
common myeloid progenitor2.20e-11108
cell of skeletal muscle1.55e-099
mesenchymal stem cell of adipose2.91e-088
somatic cell3.01e-08588
leukocyte6.37e-08136
nongranular leukocyte1.02e-07115
hematopoietic lineage restricted progenitor cell3.42e-07120
preadipocyte4.96e-0712
stromal cell8.19e-0728
Uber Anatomy
Ontology termp-valuen
bone marrow2.34e-2176
skeletal system1.95e-20100
hematopoietic system2.09e-2098
blood island2.09e-2098
connective tissue5.89e-20371
bone element7.29e-2082
skeletal element7.88e-2090
musculoskeletal system2.62e-18167
immune system1.94e-1793
hemolymphoid system5.25e-17108
mesoderm2.60e-15315
mesoderm-derived structure2.60e-15315
presumptive mesoderm2.60e-15315
lateral plate mesoderm3.05e-07203
adipose tissue6.51e-0714


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
FOS#235338.99795530889440.001372499272417130.00898698755560956
SPI1#668838.204323508522730.001810593189410520.010920336227122



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.