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Coexpression cluster:C1891: Difference between revisions

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|tf_chipseq_enrich=MAFF#23764;2:22.5261425959781:0.00304181845127288:0.0160487232751952!MAFK#7975;2:10.840293255132:0.0126368327733788:0.0456907799210285
|tf_chipseq_enrich=MAFF#23764;2:22.5261425959781:0.00304181845127288:0.0160487232751952!MAFK#7975;2:10.840293255132:0.0126368327733788:0.0456907799210285
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}}
}}

Revision as of 15:10, 26 November 2012


Full id: C1891_Mesothelial_Placental_mesenchymal_Osteoblast_basal_leiomyoma_Olfactory



Phase1 CAGE Peaks

Hg19::chr2:217498105..217498129,+p3@IGFBP2
Hg19::chr2:217498134..217498154,+p2@IGFBP2
Hg19::chr2:217498164..217498242,+p1@IGFBP2
Hg19::chr2:217526606..217526625,+p@chr2:217526606..217526625
+
Hg19::chr2:217526641..217526672,+p@chr2:217526641..217526672
+


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
ectodermal cell2.82e-1072
embryonic cell1.07e-09250
epithelial cell3.49e-08253
neurectodermal cell5.91e-0859
epithelial cell of nephron1.87e-0715
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure1.21e-13171
ectoderm1.21e-13171
presumptive ectoderm1.21e-13171
anatomical cluster1.07e-11373
head9.87e-1056
organism subdivision1.06e-09264
subdivision of head2.98e-0949
anterior region of body5.65e-0962
craniocervical region5.65e-0962
organ part1.15e-08218
multi-cellular organism1.51e-08656
ectodermal placode2.67e-0831
multi-tissue structure5.10e-08342
anterior segment of eyeball7.74e-0814
cell layer9.04e-08309
excretory tube1.24e-0716
kidney epithelium1.24e-0716
embryo1.72e-07592
nephron epithelium1.87e-0715
renal tubule1.87e-0715
nephron tubule1.87e-0715
nephron1.87e-0715
uriniferous tubule1.87e-0715
nephrogenic mesenchyme1.87e-0715
renal system1.89e-0748
urinary system structure2.03e-0747
epithelium3.42e-07306
sense organ4.82e-0724
sensory system4.82e-0724
entire sense organ system4.82e-0724
vasculature of organ4.99e-0711
eye5.29e-0721
visual system5.29e-0721
anatomical system6.91e-07624
face7.26e-0722


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
MAFF#23764222.52614259597810.003041818451272880.0160487232751952
MAFK#7975210.8402932551320.01263683277337880.0456907799210285



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.