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Coexpression cluster:C3476: Difference between revisions

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|tf_chipseq_enrich=NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460311594661223!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.039002537713295!ZBTB33#10009;2:21.1098166866541:0.00292859706060324:0.0156306085656348
|tf_chipseq_enrich=NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460311594661223!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.039002537713295!ZBTB33#10009;2:21.1098166866541:0.00292859706060324:0.0156306085656348
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}}
}}

Revision as of 16:09, 26 November 2012


Full id: C3476_Neutrophils_Eosinophils_optic_spinal_Endothelial_CD14_locus



Phase1 CAGE Peaks

Hg19::chr15:31283767..31283793,-p3@MTMR10
Hg19::chr15:31283798..31283851,-p1@MTMR10
Hg19::chr20:4804051..4804099,-p3@RASSF2


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

GO IDGO nameFDR corrected p-value
GO:0046839phospholipid dephosphorylation0.0424705583529366
GO:0030258lipid modification0.0424705583529366
GO:0004437inositol or phosphatidylinositol phosphatase activity0.0424705583529366



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
myeloid leukocyte5.52e-3272
granulocyte monocyte progenitor cell4.37e-2867
defensive cell4.29e-2748
phagocyte4.29e-2748
macrophage dendritic cell progenitor5.76e-2761
myeloid lineage restricted progenitor cell6.85e-2766
monopoietic cell3.91e-2659
monocyte3.91e-2659
monoblast3.91e-2659
promonocyte3.91e-2659
classical monocyte4.12e-2542
CD14-positive, CD16-negative classical monocyte4.12e-2542
leukocyte8.10e-22136
myeloid cell4.01e-18108
common myeloid progenitor4.01e-18108
stuff accumulating cell1.85e-1787
hematopoietic lineage restricted progenitor cell1.22e-16120
nongranular leukocyte1.84e-15115
hematopoietic stem cell2.24e-13168
angioblastic mesenchymal cell2.24e-13168
hematopoietic cell1.40e-12177
hematopoietic oligopotent progenitor cell1.56e-12161
hematopoietic multipotent progenitor cell1.56e-12161
Uber Anatomy
Ontology termp-valuen
adult organism4.06e-29114
hemolymphoid system1.69e-27108
hematopoietic system8.25e-2698
blood island8.25e-2698
immune system4.26e-2293
bone marrow1.27e-2176
lateral plate mesoderm3.24e-19203
bone element1.04e-1882
skeletal element9.77e-1490
neural tube1.60e-1356
neural rod1.60e-1356
future spinal cord1.60e-1356
neural keel1.60e-1356
regional part of nervous system4.54e-1253
regional part of brain4.54e-1253
skeletal system5.82e-12100
brain2.94e-1068
future brain2.94e-1068
regional part of forebrain1.54e-0941
forebrain1.54e-0941
anterior neural tube1.54e-0941
future forebrain1.54e-0941
central nervous system2.23e-0981
brain grey matter6.53e-0934
gray matter6.53e-0934
telencephalon8.27e-0934
mesoderm5.33e-08315
mesoderm-derived structure5.33e-08315
presumptive mesoderm5.33e-08315
regional part of telencephalon6.24e-0832
cerebral hemisphere8.25e-0832
neural plate8.74e-0882
presumptive neural plate8.74e-0882


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
NR3C1#290829.982015554115360.01278474365547170.0460311594661223
TFAP2A#7020211.01242291536330.01054990655215560.039002537713295
ZBTB33#10009221.10981668665410.002928597060603240.0156306085656348



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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