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Coexpression cluster:C4433: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!2.09e-29!102;UBERON:0003061!2.09e-29!102;UBERON:0002193!2.84e-27!112;UBERON:0002371!1.78e-20!80;UBERON:0002405!1.86e-19!115;UBERON:0001474!1.06e-17!86;UBERON:0004765!1.50e-13!101;UBERON:0001434!1.50e-13!101;UBERON:0007023!6.35e-11!115;UBERON:0000178!1.09e-07!15;UBERON:0000179!1.09e-07!15;UBERON:0000463!1.09e-07!15;UBERON:0002384!7.23e-07!375
|ontology_enrichment_uberon=UBERON:0002390!2.09e-29!102;UBERON:0003061!2.09e-29!102;UBERON:0002193!2.84e-27!112;UBERON:0002371!1.78e-20!80;UBERON:0002405!1.86e-19!115;UBERON:0001474!1.06e-17!86;UBERON:0004765!1.50e-13!101;UBERON:0001434!1.50e-13!101;UBERON:0007023!6.35e-11!115;UBERON:0000178!1.09e-07!15;UBERON:0000179!1.09e-07!15;UBERON:0000463!1.09e-07!15;UBERON:0002384!7.23e-07!375
|tf_chipseq_enrich=GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438334095687577!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631183579538175
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}}
}}

Revision as of 13:33, 5 September 2012


Full id: C4433_Dendritic_CD4_lymphoma_chronic_Hepatocyte_CD19_mycosis



Phase1 CAGE Peaks

Hg19::chr4:8202300..8202347,+p@chr4:8202300..8202347
+
Hg19::chr5:142814241..142814278,-p12@NR3C1
Hg19::chr5:142814316..142814335,-p18@NR3C1


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
leukocyte2.54e-62140
nongranular leukocyte1.97e-55119
hematopoietic lineage restricted progenitor cell1.45e-52124
hematopoietic stem cell1.65e-46172
angioblastic mesenchymal cell1.65e-46172
hematopoietic cell8.18e-45182
hematopoietic oligopotent progenitor cell5.40e-41165
hematopoietic multipotent progenitor cell5.40e-41165
CD14-positive, CD16-negative classical monocyte1.06e-3142
lymphoid lineage restricted progenitor cell4.68e-2952
classical monocyte2.04e-2845
lymphocyte3.76e-2853
common lymphoid progenitor3.76e-2853
granulocyte monocyte progenitor cell1.23e-2471
myeloid leukocyte2.09e-2476
macrophage dendritic cell progenitor3.52e-2465
monopoietic cell2.61e-2363
monocyte2.61e-2363
monoblast2.61e-2363
promonocyte2.61e-2363
myeloid lineage restricted progenitor cell6.55e-2270
myeloid cell2.07e-15112
common myeloid progenitor2.07e-15112
lymphocyte of B lineage3.15e-1424
pro-B cell3.15e-1424
T cell1.56e-1325
pro-T cell1.56e-1325
mature alpha-beta T cell1.71e-1218
alpha-beta T cell1.71e-1218
immature T cell1.71e-1218
mature T cell1.71e-1218
immature alpha-beta T cell1.71e-1218
mesenchymal cell2.45e-08358
intermediate monocyte2.99e-089
CD14-positive, CD16-positive monocyte2.99e-089
B cell4.60e-0814
CD4-positive, alpha-beta T cell9.41e-086
CD8-positive, alpha-beta T cell1.02e-0711
connective tissue cell1.37e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.09e-29102
blood island2.09e-29102
hemolymphoid system2.84e-27112
bone marrow1.78e-2080
immune system1.86e-19115
bone element1.06e-1786
skeletal element1.50e-13101
skeletal system1.50e-13101
adult organism6.35e-11115
blood1.09e-0715
haemolymphatic fluid1.09e-0715
organism substance1.09e-0715
connective tissue7.23e-07375


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
GATA2#2624312.7449317335540.0004829527704283790.00438334095687577
TCF12#6938310.63446490218640.0008313523990202070.00631183579538175



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.