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Coexpression cluster:C1812: Difference between revisions

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|tf_chipseq_enrich=MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256820993751589
|tf_chipseq_enrich=MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256820993751589
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}}
}}

Revision as of 15:07, 26 November 2012


Full id: C1812_Mast_granulocyte_acute_Eosinophils_chronic_Basophils_CD133



Phase1 CAGE Peaks

Hg19::chr19:18391340..18391345,-p8@BC169275
Hg19::chr20:1448319..1448351,-p3@NSFL1C
Hg19::chr6:36665587..36665612,+p1@uc010jwl.1
Hg19::chr6:36665624..36665632,+p2@uc010jwl.1
Hg19::chr8:145516154..145516162,-p@chr8:145516154..145516162
-


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>disease_data<br>


Cell Type
Ontology termp-valuen
myeloid cell1.12e-56108
common myeloid progenitor1.12e-56108
hematopoietic stem cell8.80e-40168
angioblastic mesenchymal cell8.80e-40168
myeloid leukocyte8.25e-3772
hematopoietic cell1.21e-36177
hematopoietic oligopotent progenitor cell1.22e-36161
hematopoietic multipotent progenitor cell1.22e-36161
myeloid lineage restricted progenitor cell5.41e-3066
granulocyte monocyte progenitor cell5.08e-2867
classical monocyte3.65e-2642
CD14-positive, CD16-negative classical monocyte3.65e-2642
defensive cell9.09e-2248
phagocyte9.09e-2248
monopoietic cell1.20e-2159
monocyte1.20e-2159
monoblast1.20e-2159
promonocyte1.20e-2159
macrophage dendritic cell progenitor1.26e-2061
leukocyte5.50e-20136
hematopoietic lineage restricted progenitor cell6.17e-15120
granulocyte1.01e-118
nongranular leukocyte3.14e-11115
intermediate monocyte5.52e-119
CD14-positive, CD16-positive monocyte5.52e-119
histamine secreting cell7.91e-105
biogenic amine secreting cell7.91e-105
granulocytopoietic cell7.91e-105
mast cell7.91e-105
mast cell progenitor7.91e-105
basophil mast progenitor cell7.91e-105
stuff accumulating cell2.22e-0887
mesenchymal cell2.86e-08354
blood cell4.11e-0811
connective tissue cell9.02e-08361
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.71e-3798
blood island4.71e-3798
hemolymphoid system4.17e-32108
bone marrow6.17e-2576
immune system6.48e-2393
bone element3.04e-2282
skeletal element3.16e-1990
skeletal system3.68e-16100
lateral plate mesoderm3.77e-13203
blood3.47e-1115
haemolymphatic fluid3.47e-1115
organism substance3.47e-1115
connective tissue1.69e-07371
adult organism1.70e-07114
Disease
Ontology termp-valuen
myeloid leukemia5.25e-2331
leukemia7.32e-1739
hematologic cancer2.35e-1151
immune system cancer2.35e-1151


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
MYC#460944.177825497287520.005691969036823440.0256820993751589



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.