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Coexpression cluster:C4433: Difference between revisions

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|tf_chipseq_enrich=GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438334095687577!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631183579538175
|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 16:44, 26 November 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
leukocyte1.01e-67136
nongranular leukocyte4.20e-67115
hematopoietic lineage restricted progenitor cell8.84e-59120
hematopoietic stem cell5.60e-49168
angioblastic mesenchymal cell5.60e-49168
hematopoietic cell1.21e-47177
hematopoietic oligopotent progenitor cell3.13e-43161
hematopoietic multipotent progenitor cell3.13e-43161
classical monocyte1.86e-3942
CD14-positive, CD16-negative classical monocyte1.86e-3942
defensive cell2.19e-3648
phagocyte2.19e-3648
lymphoid lineage restricted progenitor cell2.29e-3452
lymphocyte1.94e-3353
common lymphoid progenitor1.94e-3353
nucleate cell1.09e-3155
monopoietic cell3.84e-2859
monocyte3.84e-2859
monoblast3.84e-2859
promonocyte3.84e-2859
macrophage dendritic cell progenitor9.03e-2761
myeloid leukocyte3.70e-2672
myeloid lineage restricted progenitor cell6.17e-2566
granulocyte monocyte progenitor cell2.33e-2467
lymphocyte of B lineage1.90e-1824
pro-B cell1.90e-1824
stuff accumulating cell7.11e-1587
myeloid cell3.01e-14108
common myeloid progenitor3.01e-14108
T cell6.43e-1425
pro-T cell6.43e-1425
mature alpha-beta T cell1.11e-1218
alpha-beta T cell1.11e-1218
immature T cell1.11e-1218
mature T cell1.11e-1218
immature alpha-beta T cell1.11e-1218
intermediate monocyte1.25e-109
CD14-positive, CD16-positive monocyte1.25e-109
mesenchymal cell1.93e-10354
CD4-positive, alpha-beta T cell6.98e-106
connective tissue cell9.14e-10361
B cell2.98e-0914
motile cell1.82e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.08e-2698
blood island1.08e-2698
hemolymphoid system9.28e-24108
immune system3.12e-2093
bone marrow7.20e-2076
bone element1.89e-1782
skeletal element9.28e-1590
skeletal system4.73e-12100
connective tissue3.08e-09371


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.