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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1627_Whole_Neutrophils_CD14CD16_CD14_blood_CD8_Eosinophils
|full_id=C1627_Whole_Neutrophils_CD14CD16_CD14_blood_CD8_Eosinophils
|id=C1627
|id=C1627

Revision as of 14:13, 12 September 2012


Full id: C1627_Whole_Neutrophils_CD14CD16_CD14_blood_CD8_Eosinophils



Phase1 CAGE Peaks

Hg19::chr11:2323089..2323154,-p1@C11orf21
Hg19::chr11:2323349..2323407,+p1@TSPAN32
Hg19::chr12:51717875..51717920,-p1@BIN2
Hg19::chr21:46340976..46341000,+p1@ENST00000441379
p1@uc002zgh.2
Hg19::chr9:21031615..21031651,-p1@PTPLAD2


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 cell3.01e-54172
angioblastic mesenchymal cell3.01e-54172
hematopoietic oligopotent progenitor cell1.98e-51165
hematopoietic multipotent progenitor cell1.98e-51165
hematopoietic cell3.46e-48182
leukocyte4.87e-45140
hematopoietic lineage restricted progenitor cell4.79e-38124
nongranular leukocyte3.96e-37119
myeloid cell7.06e-35112
common myeloid progenitor7.06e-35112
myeloid leukocyte5.59e-2776
connective tissue cell1.19e-24365
mesenchymal cell5.97e-24358
granulocyte monocyte progenitor cell2.79e-2371
myeloid lineage restricted progenitor cell6.76e-2370
CD14-positive, CD16-negative classical monocyte1.93e-2142
macrophage dendritic cell progenitor3.48e-2165
monopoietic cell9.85e-2163
monocyte9.85e-2163
monoblast9.85e-2163
promonocyte9.85e-2163
classical monocyte2.16e-1745
motile cell7.98e-15390
lymphocyte3.16e-1453
common lymphoid progenitor3.16e-1453
lymphoid lineage restricted progenitor cell4.54e-1452
multi fate stem cell4.70e-13430
somatic stem cell1.52e-12436
stem cell2.74e-12444
mature alpha-beta T cell1.35e-1118
alpha-beta T cell1.35e-1118
immature T cell1.35e-1118
mature T cell1.35e-1118
immature alpha-beta T cell1.35e-1118
T cell1.92e-0925
pro-T cell1.92e-0925
CD8-positive, alpha-beta T cell2.34e-0811
intermediate monocyte3.27e-079
CD14-positive, CD16-positive monocyte3.27e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.01e-29102
blood island2.01e-29102
hemolymphoid system2.20e-26112
connective tissue1.86e-22375
bone marrow1.92e-2280
bone element7.69e-1986
skeletal element3.57e-18101
skeletal system3.57e-18101
immune system3.01e-15115
adult organism8.47e-08115
musculoskeletal system2.33e-07167
Disease
Ontology termp-valuen
myeloid leukemia1.35e-0731
leukemia4.26e-0739


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
EBF1#187935.34388010794140.01187615563868110.0432277495817175
ELF1#199754.258097958807540.0007142416939776840.0057252811633537
TAL1#6886211.94744667097610.0104757781809920.0387999077042564



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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