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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2583_CD19_Neutrophils_CD14_Peripheral_Whole_CD4_migratory
|full_id=C2583_CD19_Neutrophils_CD14_Peripheral_Whole_CD4_migratory
|id=C2583
|id=C2583

Revision as of 15:20, 12 September 2012


Full id: C2583_CD19_Neutrophils_CD14_Peripheral_Whole_CD4_migratory



Phase1 CAGE Peaks

Hg19::chr1:40845250..40845254,+p@chr1:40845250..40845254
+
Hg19::chr1:40865174..40865179,+p@chr1:40865174..40865179
+
Hg19::chr1:40882919..40882923,+p@chr1:40882919..40882923
+
Hg19::chr2:158295963..158295971,-p6@CYTIP


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
leukocyte1.28e-48140
hematopoietic stem cell2.60e-46172
angioblastic mesenchymal cell2.60e-46172
hematopoietic oligopotent progenitor cell1.48e-44165
hematopoietic multipotent progenitor cell1.48e-44165
hematopoietic cell9.97e-43182
nongranular leukocyte3.48e-42119
hematopoietic lineage restricted progenitor cell3.29e-41124
myeloid cell3.27e-23112
common myeloid progenitor3.27e-23112
myeloid leukocyte7.80e-2376
CD14-positive, CD16-negative classical monocyte6.32e-2142
macrophage dendritic cell progenitor2.75e-2065
lymphocyte4.43e-2053
common lymphoid progenitor4.43e-2053
myeloid lineage restricted progenitor cell7.53e-2070
lymphoid lineage restricted progenitor cell1.07e-1952
granulocyte monocyte progenitor cell1.98e-1971
monopoietic cell2.06e-1963
monocyte2.06e-1963
monoblast2.06e-1963
promonocyte2.06e-1963
classical monocyte2.74e-1845
T cell1.27e-0925
pro-T cell1.27e-0925
lymphocyte of B lineage1.29e-0924
pro-B cell1.29e-0924
mature alpha-beta T cell3.06e-0918
alpha-beta T cell3.06e-0918
immature T cell3.06e-0918
mature T cell3.06e-0918
immature alpha-beta T cell3.06e-0918
mesenchymal cell9.33e-09358
B cell8.88e-0814
connective tissue cell1.16e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.20e-26102
blood island1.20e-26102
hemolymphoid system1.47e-22112
adult organism9.88e-19115
bone marrow1.35e-1680
bone element4.49e-1686
skeletal element2.32e-13101
skeletal system2.32e-13101
immune system3.41e-12115
blood2.87e-1015
haemolymphatic fluid2.87e-1015
organism substance2.87e-1015
connective tissue1.32e-07375


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


No analysis results for this cluster

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.