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Coexpression cluster:C4578: Difference between revisions

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|tf_chipseq_enrich=NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381555317674159!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329418978754824
|tf_chipseq_enrich=NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381555317674159!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329418978754824
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}}
}}

Revision as of 16:49, 26 November 2012


Full id: C4578_CD14_CD19_CD4_CD14CD16_CD8_Natural_Peripheral



Phase1 CAGE Peaks

Hg19::chr6:158248908..158248912,+p@chr6:158248908..158248912
+
Hg19::chr6:158255218..158255219,+p@chr6:158255218..158255219
+
Hg19::chr6:158255392..158255396,+p@chr6:158255392..158255396
+


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 monocyte3.17e-2642
CD14-positive, CD16-negative classical monocyte3.17e-2642
defensive cell1.68e-2548
phagocyte1.68e-2548
myeloid lineage restricted progenitor cell1.55e-2166
macrophage dendritic cell progenitor1.60e-2161
monopoietic cell1.61e-2159
monocyte1.61e-2159
monoblast1.61e-2159
promonocyte1.61e-2159
leukocyte3.19e-20136
granulocyte monocyte progenitor cell3.89e-2067
nongranular leukocyte1.02e-19115
myeloid leukocyte1.67e-1972
hematopoietic lineage restricted progenitor cell4.60e-19120
hematopoietic stem cell2.83e-14168
angioblastic mesenchymal cell2.83e-14168
hematopoietic cell1.50e-13177
hematopoietic oligopotent progenitor cell1.38e-12161
hematopoietic multipotent progenitor cell1.38e-12161
stuff accumulating cell2.98e-1287
myeloid cell6.26e-12108
common myeloid progenitor6.26e-12108
intermediate monocyte7.13e-099
CD14-positive, CD16-positive monocyte7.13e-099
CD4-positive, alpha-beta T cell6.16e-076
Uber Anatomy
Ontology termp-valuen
bone marrow1.40e-1676
hematopoietic system1.49e-1598
blood island1.49e-1598
bone element1.03e-1482
immune system3.45e-1493
hemolymphoid system1.54e-13108
skeletal element8.19e-1290
skeletal system3.68e-11100


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)

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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
NFYB#4801211.17319550235760.01025467135054530.0381555317674159
TRIM28#10155212.39368336350830.008368344129438470.0329418978754824



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.