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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4501_Natural_CD14_CD4_CD8_Peripheral_CD34_Basophils
|full_id=C4501_Natural_CD14_CD4_CD8_Peripheral_CD34_Basophils
|id=C4501
|id=C4501

Revision as of 17:35, 12 September 2012


Full id: C4501_Natural_CD14_CD4_CD8_Peripheral_CD34_Basophils



Phase1 CAGE Peaks

Hg19::chr5:42950094..42950117,+p@chr5:42950094..42950117
+
Hg19::chr5:42994673..42994693,-p@chr5:42994673..42994693
-
Hg19::chr8:29387130..29387137,+p@chr8:29387130..29387137
+


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 cell2.69e-59182
hematopoietic stem cell5.38e-59172
angioblastic mesenchymal cell5.38e-59172
leukocyte1.69e-56140
hematopoietic oligopotent progenitor cell1.89e-54165
hematopoietic multipotent progenitor cell1.89e-54165
hematopoietic lineage restricted progenitor cell8.59e-51124
nongranular leukocyte3.30e-47119
myeloid cell1.24e-32112
common myeloid progenitor1.24e-32112
myeloid leukocyte4.45e-3076
myeloid lineage restricted progenitor cell4.73e-2970
granulocyte monocyte progenitor cell2.50e-2871
CD14-positive, CD16-negative classical monocyte3.47e-2842
macrophage dendritic cell progenitor6.38e-2665
classical monocyte8.40e-2545
monopoietic cell8.83e-2563
monocyte8.83e-2563
monoblast8.83e-2563
promonocyte8.83e-2563
mesenchymal cell3.41e-21358
connective tissue cell1.10e-20365
lymphocyte4.49e-1953
common lymphoid progenitor4.49e-1953
lymphoid lineage restricted progenitor cell4.70e-1952
motile cell2.01e-16390
multi fate stem cell7.11e-16430
stem cell7.15e-15444
somatic stem cell1.01e-14436
T cell9.31e-1325
pro-T cell9.31e-1325
mature alpha-beta T cell1.03e-1118
alpha-beta T cell1.03e-1118
immature T cell1.03e-1118
mature T cell1.03e-1118
immature alpha-beta T cell1.03e-1118
CD8-positive, alpha-beta T cell8.19e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.30e-36102
blood island5.30e-36102
hemolymphoid system1.03e-32112
bone marrow3.15e-2880
bone element9.20e-2786
connective tissue3.55e-20375
skeletal element4.17e-20101
skeletal system4.17e-20101
immune system2.71e-19115
lateral plate mesoderm2.91e-11216
musculoskeletal system9.16e-10167


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#199734.258097958807540.01295179875054610.0464452997427648
SMARCB1#6598212.16847718743830.008675002221921740.0330105864991359



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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