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Coexpression cluster:C3165: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002390!1.57e-48!98;UBERON:0003061!1.57e-48!98;UBERON:0002193!2.02e-44!108;UBERON:0002371!1.23e-38!76;UBERON:0002405!1.85e-36!93;UBERON:0001474!3.84e-34!82;UBERON:0004765!4.02e-29!90;UBERON:0007023!6.10e-26!114;UBERON:0001434!6.76e-25!100;UBERON:0003081!1.66e-14!203;UBERON:0002204!4.30e-09!167;UBERON:0000178!1.88e-08!15;UBERON:0000179!1.88e-08!15;UBERON:0000463!1.88e-08!15;UBERON:0000479!9.85e-08!773
|ontology_enrichment_uberon=UBERON:0002390!1.57e-48!98;UBERON:0003061!1.57e-48!98;UBERON:0002193!2.02e-44!108;UBERON:0002371!1.23e-38!76;UBERON:0002405!1.85e-36!93;UBERON:0001474!3.84e-34!82;UBERON:0004765!4.02e-29!90;UBERON:0007023!6.10e-26!114;UBERON:0001434!6.76e-25!100;UBERON:0003081!1.66e-14!203;UBERON:0002204!4.30e-09!167;UBERON:0000178!1.88e-08!15;UBERON:0000179!1.88e-08!15;UBERON:0000463!1.88e-08!15;UBERON:0000479!9.85e-08!773
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}}
}}

Revision as of 15:57, 26 November 2012


Full id: C3165_Dendritic_CD14_Monocytederived_Macrophage_splenic_CD14CD16_spleen



Phase1 CAGE Peaks

Hg19::chr11:58979658..58979676,-p3@MPEG1
Hg19::chr11:58980437..58980460,-p2@MPEG1
Hg19::chr12:75875067..75875110,+p4@GLIPR1


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
leukocyte5.41e-61136
nongranular leukocyte1.56e-54115
myeloid leukocyte3.70e-5272
macrophage dendritic cell progenitor7.38e-5261
monopoietic cell5.76e-5059
monocyte5.76e-5059
monoblast5.76e-5059
promonocyte5.76e-5059
defensive cell7.34e-5048
phagocyte7.34e-5048
hematopoietic stem cell4.47e-49168
angioblastic mesenchymal cell4.47e-49168
hematopoietic lineage restricted progenitor cell6.14e-48120
granulocyte monocyte progenitor cell3.85e-4567
hematopoietic cell1.24e-44177
hematopoietic oligopotent progenitor cell2.41e-44161
hematopoietic multipotent progenitor cell2.41e-44161
classical monocyte4.47e-4442
CD14-positive, CD16-negative classical monocyte4.47e-4442
myeloid lineage restricted progenitor cell2.67e-4266
myeloid cell1.66e-35108
common myeloid progenitor1.66e-35108
stuff accumulating cell1.16e-1987
lymphocyte of B lineage3.42e-1324
pro-B cell3.42e-1324
B cell8.46e-1114
intermediate monocyte8.61e-109
CD14-positive, CD16-positive monocyte8.61e-109
granulocyte6.40e-098
lymphocyte1.48e-0853
common lymphoid progenitor1.48e-0853
lymphoid lineage restricted progenitor cell4.31e-0852
nucleate cell6.08e-0855
macrophage4.86e-076
dendritic cell9.84e-0710
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.57e-4898
blood island1.57e-4898
hemolymphoid system2.02e-44108
bone marrow1.23e-3876
immune system1.85e-3693
bone element3.84e-3482
skeletal element4.02e-2990
adult organism6.10e-26114
skeletal system6.76e-25100
lateral plate mesoderm1.66e-14203
musculoskeletal system4.30e-09167
blood1.88e-0815
haemolymphatic fluid1.88e-0815
organism substance1.88e-0815
tissue9.85e-08773


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)

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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.

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