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Coexpression cluster:C3996: Difference between revisions

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|tf_chipseq_enrich=SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109146633251859!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000222809252591194
|tf_chipseq_enrich=SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109146633251859!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000222809252591194
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}}
}}

Revision as of 16:29, 26 November 2012


Full id: C3996_Fibroblast_normal_Preadipocyte_tenocyte_cholangiocellular_medulloblastoma_liposarcoma



Phase1 CAGE Peaks

Hg19::chr1:75599672..75599682,-p@chr1:75599672..75599682
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Hg19::chr1:75599683..75599699,-p@chr1:75599683..75599699
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Hg19::chr1:75600067..75600094,+p2@LHX8


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
fibroblast of periodontium1.06e-356
fibroblast of gingiva2.60e-305
fibroblast9.56e-1976
preadipocyte of the breast1.34e-083
Uber Anatomy
Ontology termp-valuen
mouth1.82e-3729
stomodeum1.82e-3729
periodontium1.06e-356
dentition1.06e-356
skull1.56e-307
cranial skeletal system4.11e-2611
subdivision of head3.92e-2449
anterior region of body5.12e-2162
craniocervical region5.12e-2162
head1.03e-2056
axial skeletal system2.50e-2014
gingiva7.01e-198
subdivision of skeletal system1.13e-1716
oral opening3.70e-1622
surface structure1.58e-1399
orifice9.33e-1236
mouth mucosa1.59e-1113
digestive system2.00e-10145
digestive tract2.00e-10145
primitive gut2.00e-10145
mucosa3.40e-1020
endoderm-derived structure4.40e-09160
endoderm4.40e-09160
presumptive endoderm4.40e-09160
ectoderm-derived structure3.92e-08171
ectoderm3.92e-08171
presumptive ectoderm3.92e-08171
organism subdivision1.12e-07264
primary palate mesenchyme1.55e-071
pneumatized bone1.55e-071
subdivision of skeleton1.55e-071
intramembranous bone1.55e-071
head bone1.55e-071
dermal bone1.55e-071
irregular bone1.55e-071
mesenchyme derived from head neural crest1.55e-071
facial mesenchyme1.55e-071
head or neck bone1.55e-071
embryonic nasal process1.55e-071
cranial neural crest1.55e-071
roof of mouth1.55e-071
mesenchyme of upper jaw1.55e-071
mesenchyme from rhombencephalic neural crest1.55e-071
membrane bone1.55e-071
pharyngeal arch mesenchymal region1.55e-071
1st arch mesenchyme1.55e-071
1st arch maxillary mesenchyme1.55e-071
1st arch mesenchyme from neural crest1.55e-071
pharyngeal arch mesenchyme from neural crest1.55e-071
maxillary process mesenchyme1.55e-071
maxilla1.55e-071
dermatocranium1.55e-071
skeleton of upper jaw1.55e-071
upper jaw region1.55e-071
frontonasal prominence1.55e-071
premaxilla1.55e-071
primary palate1.55e-071
pharyngeal arch 11.55e-071
dermal skeleton1.55e-071
entire pharyngeal arch associated mesenchyme1.55e-071
maxillary prominence1.55e-071
1st arch maxillary component1.55e-071
skeleton1.55e-071
medial nasal prominence1.55e-071
maxillary process mesenchyme from neural crest1.55e-071
rhombencephalon neural crest1.55e-071
1st arch maxillary mesenchyme from neural crest1.55e-071
intralobular bile duct3.20e-071
acinus3.20e-071
intrahepatic bile duct3.20e-071
portal lobule3.20e-071
hepatic acinus3.20e-071


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
SPI1#668838.204323508522730.001810593189410520.0109146633251859
SUZ12#23512350.11578091106297.93834897779404e-060.000222809252591194



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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