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Coexpression cluster:C3005: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:49, 8 August 2012


Full id: C3005_Macrophage_CD14_Adipocyte_Osteoblast_Neutrophils_Eosinophils_Monocytederived



Phase1 CAGE Peaks

Hg19::chr10:20105324..20105339,+p2@PLXDC2
Hg19::chr10:20105340..20105382,+p1@PLXDC2
Hg19::chr10:20105389..20105394,+p6@PLXDC2


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>

Uber Anatomy
Ontology termp-valuen
adult organism7.83e-29115
bone marrow1.16e-2380
hematopoietic system2.90e-23102
blood island2.90e-23102
bone element9.17e-2286
hemolymphoid system4.94e-19112
skeletal element8.78e-18101
skeletal system8.78e-18101
immune system1.77e-15115
neural tube3.84e-1257
neural rod3.84e-1257
future spinal cord3.84e-1257
neural keel3.84e-1257
neurectoderm7.53e-1290
musculoskeletal system3.15e-11167
neural plate4.32e-1186
presumptive neural plate4.32e-1186
regional part of brain5.23e-1159
embryo5.57e-11612
central nervous system7.70e-1182
organ3.30e-10511
brain4.07e-1069
future brain4.07e-1069
embryonic structure4.63e-10605
developing anatomical structure4.63e-10605
anterior neural tube6.28e-1042
germ layer7.69e-10604
embryonic tissue7.69e-10604
presumptive structure7.69e-10604
epiblast (generic)7.69e-10604
regional part of nervous system1.02e-0994
nervous system1.02e-0994
regional part of forebrain1.89e-0941
forebrain1.89e-0941
future forebrain1.89e-0941
multi-cellular organism3.64e-09659
gray matter3.50e-0834
brain grey matter3.50e-0834
telencephalon4.05e-0834
regional part of telencephalon6.58e-0833
pre-chordal neural plate1.21e-0761
lateral plate mesoderm1.49e-07216
cerebral hemisphere2.80e-0732


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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