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Coexpression cluster:C1069: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002390!5.96e-57!98;UBERON:0003061!5.96e-57!98;UBERON:0002193!5.18e-54!108;UBERON:0002405!2.18e-45!93;UBERON:0002371!2.89e-44!76;UBERON:0001474!5.31e-39!82;UBERON:0004765!3.98e-33!90;UBERON:0001434!5.36e-28!100;UBERON:0003081!8.60e-16!203;UBERON:0002384!1.16e-12!371;UBERON:0007023!9.20e-10!114;UBERON:0000178!7.96e-09!15;UBERON:0000179!7.96e-09!15;UBERON:0000463!7.96e-09!15;UBERON:0002204!1.51e-08!167
|ontology_enrichment_uberon=UBERON:0002390!5.96e-57!98;UBERON:0003061!5.96e-57!98;UBERON:0002193!5.18e-54!108;UBERON:0002405!2.18e-45!93;UBERON:0002371!2.89e-44!76;UBERON:0001474!5.31e-39!82;UBERON:0004765!3.98e-33!90;UBERON:0001434!5.36e-28!100;UBERON:0003081!8.60e-16!203;UBERON:0002384!1.16e-12!371;UBERON:0007023!9.20e-10!114;UBERON:0000178!7.96e-09!15;UBERON:0000179!7.96e-09!15;UBERON:0000463!7.96e-09!15;UBERON:0002204!1.51e-08!167
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}}
}}

Revision as of 14:40, 26 November 2012


Full id: C1069_Neutrophils_Monocytederived_CD14_Mast_CD19_blood_lung



Phase1 CAGE Peaks

Hg19::chr1:31210536..31210552,-p@chr1:31210536..31210552
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Hg19::chr1:31211816..31211826,-p@chr1:31211816..31211826
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Hg19::chr1:31212682..31212694,-p@chr1:31212682..31212694
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Hg19::chr1:31212698..31212714,-p@chr1:31212698..31212714
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Hg19::chr1:31212715..31212725,-p@chr1:31212715..31212725
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Hg19::chr1:31212731..31212751,-p@chr1:31212731..31212751
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Hg19::chr1:31212755..31212784,-p@chr1:31212755..31212784
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Hg19::chr1:31214519..31214570,-p@chr1:31214519..31214570
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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
hematopoietic stem cell1.77e-83168
angioblastic mesenchymal cell1.77e-83168
hematopoietic oligopotent progenitor cell3.03e-81161
hematopoietic multipotent progenitor cell3.03e-81161
leukocyte6.56e-80136
hematopoietic cell1.04e-78177
hematopoietic lineage restricted progenitor cell2.76e-70120
nongranular leukocyte3.32e-70115
myeloid leukocyte3.48e-5872
myeloid cell4.52e-57108
common myeloid progenitor4.52e-57108
granulocyte monocyte progenitor cell4.91e-5167
myeloid lineage restricted progenitor cell2.25e-5066
monopoietic cell1.41e-4759
monocyte1.41e-4759
monoblast1.41e-4759
promonocyte1.41e-4759
macrophage dendritic cell progenitor5.12e-4761
defensive cell2.41e-4448
phagocyte2.41e-4448
classical monocyte1.34e-3842
CD14-positive, CD16-negative classical monocyte1.34e-3842
lymphocyte5.91e-2053
common lymphoid progenitor5.91e-2053
lymphoid lineage restricted progenitor cell1.58e-1952
nucleate cell1.16e-1855
stuff accumulating cell2.47e-1587
mesenchymal cell1.19e-14354
connective tissue cell1.39e-13361
lymphocyte of B lineage1.46e-1324
pro-B cell1.46e-1324
motile cell1.31e-10386
B cell6.38e-0914
intermediate monocyte8.42e-089
CD14-positive, CD16-positive monocyte8.42e-089
mature alpha-beta T cell3.73e-0718
alpha-beta T cell3.73e-0718
immature T cell3.73e-0718
mature T cell3.73e-0718
immature alpha-beta T cell3.73e-0718
macrophage5.01e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.96e-5798
blood island5.96e-5798
hemolymphoid system5.18e-54108
immune system2.18e-4593
bone marrow2.89e-4476
bone element5.31e-3982
skeletal element3.98e-3390
skeletal system5.36e-28100
lateral plate mesoderm8.60e-16203
connective tissue1.16e-12371
adult organism9.20e-10114
blood7.96e-0915
haemolymphatic fluid7.96e-0915
organism substance7.96e-0915
musculoskeletal system1.51e-08167
Disease
Ontology termp-valuen
hematologic cancer6.51e-0951
immune system cancer6.51e-0951
leukemia1.83e-0739
myeloid leukemia3.35e-0731


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


No analysis results for this cluster

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.