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Coexpression cluster:C3476: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.96e-32!115;UBERON:0002193!4.27e-27!112;UBERON:0002390!4.61e-25!102;UBERON:0003061!4.61e-25!102;UBERON:0002371!7.88e-20!80;UBERON:0001049!2.22e-18!57;UBERON:0005068!2.22e-18!57;UBERON:0006241!2.22e-18!57;UBERON:0007135!2.22e-18!57;UBERON:0002405!3.29e-18!115;UBERON:0001474!3.50e-17!86;UBERON:0003081!2.08e-16!216;UBERON:0002616!3.24e-15!59;UBERON:0003080!4.11e-14!42;UBERON:0002780!9.22e-14!41;UBERON:0001890!9.22e-14!41;UBERON:0006240!9.22e-14!41;UBERON:0000955!1.23e-13!69;UBERON:0006238!1.23e-13!69;UBERON:0001017!2.61e-13!82;UBERON:0005743!3.69e-13!86;UBERON:0002020!7.24e-13!34;UBERON:0003528!7.24e-13!34;UBERON:0001893!7.94e-13!34;UBERON:0002791!2.53e-12!33;UBERON:0004765!3.26e-12!101;UBERON:0001434!3.26e-12!101;UBERON:0001869!1.23e-11!32;UBERON:0000073!1.15e-09!94;UBERON:0001016!1.15e-09!94;UBERON:0003075!4.28e-09!86;UBERON:0007284!4.28e-09!86;UBERON:0002619!6.36e-09!22;UBERON:0000956!1.75e-08!25;UBERON:0000203!1.75e-08!25;UBERON:0001950!3.27e-08!20;UBERON:0002346!2.25e-07!90;UBERON:0000178!5.35e-07!15;UBERON:0000179!5.35e-07!15;UBERON:0000463!5.35e-07!15
|ontology_enrichment_uberon=UBERON:0007023!2.96e-32!115;UBERON:0002193!4.27e-27!112;UBERON:0002390!4.61e-25!102;UBERON:0003061!4.61e-25!102;UBERON:0002371!7.88e-20!80;UBERON:0001049!2.22e-18!57;UBERON:0005068!2.22e-18!57;UBERON:0006241!2.22e-18!57;UBERON:0007135!2.22e-18!57;UBERON:0002405!3.29e-18!115;UBERON:0001474!3.50e-17!86;UBERON:0003081!2.08e-16!216;UBERON:0002616!3.24e-15!59;UBERON:0003080!4.11e-14!42;UBERON:0002780!9.22e-14!41;UBERON:0001890!9.22e-14!41;UBERON:0006240!9.22e-14!41;UBERON:0000955!1.23e-13!69;UBERON:0006238!1.23e-13!69;UBERON:0001017!2.61e-13!82;UBERON:0005743!3.69e-13!86;UBERON:0002020!7.24e-13!34;UBERON:0003528!7.24e-13!34;UBERON:0001893!7.94e-13!34;UBERON:0002791!2.53e-12!33;UBERON:0004765!3.26e-12!101;UBERON:0001434!3.26e-12!101;UBERON:0001869!1.23e-11!32;UBERON:0000073!1.15e-09!94;UBERON:0001016!1.15e-09!94;UBERON:0003075!4.28e-09!86;UBERON:0007284!4.28e-09!86;UBERON:0002619!6.36e-09!22;UBERON:0000956!1.75e-08!25;UBERON:0000203!1.75e-08!25;UBERON:0001950!3.27e-08!20;UBERON:0002346!2.25e-07!90;UBERON:0000178!5.35e-07!15;UBERON:0000179!5.35e-07!15;UBERON:0000463!5.35e-07!15
|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 13:11, 5 September 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 leukocyte7.07e-3076
granulocyte monocyte progenitor cell3.87e-2671
myeloid lineage restricted progenitor cell6.63e-2570
CD14-positive, CD16-negative classical monocyte1.44e-2442
macrophage dendritic cell progenitor3.23e-2465
leukocyte7.06e-24140
monopoietic cell2.10e-2363
monocyte2.10e-2363
monoblast2.10e-2363
promonocyte2.10e-2363
myeloid cell2.50e-23112
common myeloid progenitor2.50e-23112
classical monocyte5.87e-2145
hematopoietic stem cell1.92e-19172
angioblastic mesenchymal cell1.92e-19172
hematopoietic oligopotent progenitor cell1.77e-18165
hematopoietic multipotent progenitor cell1.77e-18165
hematopoietic cell4.88e-18182
hematopoietic lineage restricted progenitor cell8.55e-18124
nongranular leukocyte1.62e-16119
endothelial cell2.11e-0735
endothelial cell of vascular tree2.21e-0724
Uber Anatomy
Ontology termp-valuen
adult organism2.96e-32115
hemolymphoid system4.27e-27112
hematopoietic system4.61e-25102
blood island4.61e-25102
bone marrow7.88e-2080
neural tube2.22e-1857
neural rod2.22e-1857
future spinal cord2.22e-1857
neural keel2.22e-1857
immune system3.29e-18115
bone element3.50e-1786
lateral plate mesoderm2.08e-16216
regional part of brain3.24e-1559
anterior neural tube4.11e-1442
regional part of forebrain9.22e-1441
forebrain9.22e-1441
future forebrain9.22e-1441
brain1.23e-1369
future brain1.23e-1369
central nervous system2.61e-1382
gray matter7.24e-1334
brain grey matter7.24e-1334
telencephalon7.94e-1334
regional part of telencephalon2.53e-1233
skeletal element3.26e-12101
skeletal system3.26e-12101
cerebral hemisphere1.23e-1132
regional part of nervous system1.15e-0994
nervous system1.15e-0994
neural plate4.28e-0986
presumptive neural plate4.28e-0986
regional part of cerebral cortex6.36e-0922
cerebral cortex1.75e-0825
pallium1.75e-0825
neocortex3.27e-0820
neurectoderm2.25e-0790
blood5.35e-0715
haemolymphatic fluid5.35e-0715
organism substance5.35e-0715


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.