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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2817_Natural_CD8_CD4_CD34_Basophils_thymus_CD14
|full_id=C2817_Natural_CD8_CD4_CD34_Basophils_thymus_CD14
|id=C2817
|id=C2817

Revision as of 15:36, 12 September 2012


Full id: C2817_Natural_CD8_CD4_CD34_Basophils_thymus_CD14



Phase1 CAGE Peaks

Hg19::chr5:162932997..162933017,+p@chr5:162932997..162933017
+
Hg19::chr5:43019699..43019711,-p@chr5:43019699..43019711
-
Hg19::chr5:43019717..43019732,-p@chr5:43019717..43019732
-
Hg19::chr5:43041092..43041124,+p@chr5:43041092..43041124
+


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 cell3.92e-67172
angioblastic mesenchymal cell3.92e-67172
hematopoietic cell1.68e-63182
hematopoietic oligopotent progenitor cell1.59e-62165
hematopoietic multipotent progenitor cell1.59e-62165
leukocyte6.85e-57140
hematopoietic lineage restricted progenitor cell3.01e-52124
nongranular leukocyte9.40e-50119
myeloid cell1.99e-33112
common myeloid progenitor1.99e-33112
lymphocyte3.15e-2653
common lymphoid progenitor3.15e-2653
lymphoid lineage restricted progenitor cell3.39e-2652
myeloid leukocyte1.20e-2476
myeloid lineage restricted progenitor cell3.39e-2470
granulocyte monocyte progenitor cell5.48e-2471
macrophage dendritic cell progenitor2.25e-2165
monopoietic cell8.06e-2163
monocyte8.06e-2163
monoblast8.06e-2163
promonocyte8.06e-2163
classical monocyte2.50e-1945
CD14-positive, CD16-negative classical monocyte2.13e-1842
T cell2.87e-1425
pro-T cell2.87e-1425
mesenchymal cell2.07e-13358
mature alpha-beta T cell2.80e-1318
alpha-beta T cell2.80e-1318
immature T cell2.80e-1318
mature T cell2.80e-1318
immature alpha-beta T cell2.80e-1318
connective tissue cell1.76e-12365
lymphocyte of B lineage5.30e-1124
pro-B cell5.30e-1124
motile cell4.37e-10390
B cell3.63e-0914
CD8-positive, alpha-beta T cell3.93e-0911
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.06e-31102
blood island5.06e-31102
hemolymphoid system3.23e-28112
bone marrow6.60e-2180
bone element4.05e-2086
immune system5.25e-16115
skeletal element1.17e-13101
skeletal system1.17e-13101
connective tissue5.63e-12375
blood8.43e-0815
haemolymphatic fluid8.43e-0815
organism substance8.43e-0815
Disease
Ontology termp-valuen
hematologic cancer5.62e-1351
immune system cancer5.62e-1351
leukemia3.44e-1039
myeloid leukemia2.09e-0831


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
GTF2F1#296239.554745657568240.001820362319304780.0109024441028714
SMARCB1#6598418.25271578115749.00423392720929e-060.000242057448423117
SMARCC2#6601370.61653082017324.74678670742709e-060.000147281538008609
SUZ12#23512225.05789045553150.002325256716520610.013186766193348
TAF1#687243.343046285745290.008005664898701650.032309437991943
TBP#690843.706770687096390.005296377814784350.0244885958295671



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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