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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1940_migratory_thalamus_cord_globus_substantia_hippocampus_CD14CD16
|full_id=C1940_migratory_thalamus_cord_globus_substantia_hippocampus_CD14CD16
|id=C1940
|id=C1940

Revision as of 14:34, 12 September 2012


Full id: C1940_migratory_thalamus_cord_globus_substantia_hippocampus_CD14CD16



Phase1 CAGE Peaks

Hg19::chr4:36245643..36245697,-p5@ARAP2
Hg19::chr4:36245700..36245716,-p13@ARAP2
Hg19::chr4:36246367..36246380,-p12@ARAP2
Hg19::chr4:36246391..36246453,-p2@ARAP2
Hg19::chr4:36246458..36246477,-p8@ARAP2


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
leukocyte1.29e-40140
hematopoietic lineage restricted progenitor cell7.07e-35124
nongranular leukocyte6.45e-34119
hematopoietic stem cell5.89e-32172
angioblastic mesenchymal cell5.89e-32172
hematopoietic cell1.49e-29182
hematopoietic oligopotent progenitor cell3.48e-29165
hematopoietic multipotent progenitor cell3.48e-29165
granulocyte monocyte progenitor cell3.64e-2171
myeloid leukocyte1.40e-2076
classical monocyte6.28e-2045
CD14-positive, CD16-negative classical monocyte7.03e-2042
myeloid lineage restricted progenitor cell1.45e-1970
macrophage dendritic cell progenitor1.49e-1965
monopoietic cell1.33e-1863
monocyte1.33e-1863
monoblast1.33e-1863
promonocyte1.33e-1863
myeloid cell2.21e-15112
common myeloid progenitor2.21e-15112
lymphoid lineage restricted progenitor cell7.26e-1452
lymphocyte1.22e-1353
common lymphoid progenitor1.22e-1353
mature alpha-beta T cell1.90e-0818
alpha-beta T cell1.90e-0818
immature T cell1.90e-0818
mature T cell1.90e-0818
immature alpha-beta T cell1.90e-0818
T cell4.35e-0825
pro-T cell4.35e-0825
dendritic cell2.35e-0710
Uber Anatomy
Ontology termp-valuen
adult organism4.22e-37115
neural tube7.90e-2657
neural rod7.90e-2657
future spinal cord7.90e-2657
neural keel7.90e-2657
hematopoietic system7.96e-26102
blood island7.96e-26102
hemolymphoid system6.19e-21112
regional part of forebrain8.44e-2141
forebrain8.44e-2141
future forebrain8.44e-2141
anterior neural tube9.11e-2142
regional part of brain3.05e-2059
central nervous system1.53e-1882
telencephalon5.26e-1834
gray matter6.64e-1834
brain grey matter6.64e-1834
regional part of telencephalon1.99e-1733
brain2.26e-1769
future brain2.26e-1769
neural plate2.27e-1786
presumptive neural plate2.27e-1786
bone marrow3.28e-1780
cerebral hemisphere1.23e-1632
regional part of nervous system2.40e-1594
nervous system2.40e-1594
neurectoderm2.60e-1590
bone element6.76e-1586
pre-chordal neural plate8.85e-1361
regional part of cerebral cortex2.82e-1222
immune system2.96e-12115
cerebral cortex2.96e-1225
pallium2.96e-1225
neocortex3.23e-1120
skeletal element1.60e-10101
skeletal system1.60e-10101
anterior region of body1.05e-08129
craniocervical region1.05e-08129
head2.66e-07123
nucleus of brain2.73e-079
neural nucleus2.73e-079
blood4.48e-0715
haemolymphatic fluid4.48e-0715
organism substance4.48e-0715
basal ganglion5.50e-079
nuclear complex of neuraxis5.50e-079
aggregate regional part of brain5.50e-079
collection of basal ganglia5.50e-079
cerebral subcortex5.50e-079


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
E2F1#186954.907389214879320.0003512818099256460.00353444325113916
EBF1#187935.34388010794140.01187615563868110.0432458358756048
GATA3#2625210.89460654288240.0125158291218830.0452861931007602
MAFK#7975316.26043988269790.0004748211423830540.00435801435006097
TAF1#687253.343046285745290.002394600090870310.0135527902720644



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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