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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 19:01, 8 August 2012


Full id: C3247_Eosinophils_CD14_cerebellum_Neutrophils_brain_occipital_temporal



Phase1 CAGE Peaks

Hg19::chr12:121734496..121734564,-p1@CAMKK2
Hg19::chr16:11762271..11762344,+p1@SNN
Hg19::chr2:16847115..16847139,-p2@FAM49A


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
CD14-positive, CD16-negative classical monocyte1.28e-2442
myeloid leukocyte1.38e-2376
classical monocyte5.05e-2045
granulocyte monocyte progenitor cell1.01e-1971
macrophage dendritic cell progenitor3.00e-1965
monopoietic cell9.79e-1963
monocyte9.79e-1963
monoblast9.79e-1963
promonocyte9.79e-1963
leukocyte8.87e-18140
myeloid lineage restricted progenitor cell4.29e-1770
myeloid cell6.89e-15112
common myeloid progenitor6.89e-15112
nongranular leukocyte1.88e-12119
hematopoietic stem cell5.47e-12172
angioblastic mesenchymal cell5.47e-12172
hematopoietic lineage restricted progenitor cell3.03e-11124
hematopoietic cell3.55e-11182
hematopoietic oligopotent progenitor cell3.80e-11165
hematopoietic multipotent progenitor cell3.80e-11165
endothelial cell6.19e-1035
endothelial cell of vascular tree2.61e-0824
meso-epithelial cell1.95e-0744
Uber Anatomy
Ontology termp-valuen
adult organism1.11e-29115
central nervous system2.79e-2382
neural tube3.59e-2357
neural rod3.59e-2357
future spinal cord3.59e-2357
neural keel3.59e-2357
hemolymphoid system4.05e-22112
regional part of brain9.26e-2259
regional part of nervous system1.03e-2094
nervous system1.03e-2094
hematopoietic system4.89e-20102
blood island4.89e-20102
brain1.95e-1969
future brain1.95e-1969
neurectoderm5.21e-1990
neural plate8.62e-1986
presumptive neural plate8.62e-1986
anterior neural tube2.57e-1842
regional part of forebrain4.70e-1841
forebrain4.70e-1841
future forebrain4.70e-1841
telencephalon1.08e-1734
gray matter2.73e-1734
brain grey matter2.73e-1734
bone marrow3.59e-1780
cerebral hemisphere3.89e-1732
regional part of telencephalon4.58e-1733
pre-chordal neural plate4.05e-1561
bone element5.70e-1586
cerebral cortex1.12e-1325
pallium1.12e-1325
regional part of cerebral cortex1.21e-1322
immune system2.05e-13115
skeletal element5.80e-13101
skeletal system5.80e-13101
neocortex9.32e-1320
head2.39e-12123
anterior region of body3.08e-12129
craniocervical region3.08e-12129
ectoderm5.61e-10173
presumptive ectoderm5.61e-10173
ectoderm-derived structure1.20e-09169
lateral plate mesoderm1.44e-09216
embryo4.75e-07612


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


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.