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Coexpression cluster:C3996

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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>


Uber Anatomy
Ontology termp-valuen
mouth1.56e-2028
stomodeum1.56e-2028
periodontium1.72e-206
dentition1.72e-206
skull1.19e-1411
subdivision of head4.61e-1448
mixed ectoderm/mesoderm/endoderm-derived structure1.61e-1318
anterior region of body5.72e-13129
craniocervical region5.72e-13129
subdivision of skeletal system3.28e-1213
skeleton3.28e-1213
sclerotome3.28e-1213
head1.16e-11123
organism subdivision5.33e-11365
gingiva9.05e-118
surface structure8.95e-1095
oral opening6.12e-0921
orifice8.68e-0935
digestive system5.98e-08155
digestive tract5.98e-08155
primitive gut5.98e-08155
breast6.98e-0810
ectoderm-derived structure2.32e-07169
throat3.44e-072
corpus striatum3.74e-074
striatum3.74e-074
ventral part of telencephalon3.74e-074
future corpus striatum3.74e-074
chest3.95e-0711
ectoderm4.76e-07173
presumptive ectoderm4.76e-07173
telencephalic nucleus5.90e-077
open tracheal system trachea6.59e-072
endoderm-derived structure8.64e-07169
endoderm8.64e-07169
presumptive endoderm8.64e-07169


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.