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Coexpression cluster:C931

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Full id: C931_neuroectodermal_peripheral_maxillary_gastrointestinal_Hepatocyte_small_liver



Phase1 CAGE Peaks

Hg19::chr1:214160884..214160892,-p@chr1:214160884..214160892
-
Hg19::chr1:214161272..214161322,+p1@PROX1
Hg19::chr1:214161328..214161348,+p2@PROX1
Hg19::chr1:214161358..214161377,+p3@PROX1
Hg19::chr1:214161428..214161437,+p6@PROX1
Hg19::chr1:214170889..214170891,+p@chr1:214170889..214170891
+
Hg19::chr1:214171294..214171305,+p@chr1:214171294..214171305
+
Hg19::chr1:214175769..214175774,+p@chr1:214175769..214175774
+
Hg19::chr1:214214418..214214425,+p@chr1:214214418..214214425
+


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
endothelial cell of vascular tree1.81e-0724
Uber Anatomy
Ontology termp-valuen
adult organism9.88e-35115
central nervous system1.75e-2882
neural tube1.55e-2657
neural rod1.55e-2657
future spinal cord1.55e-2657
neural keel1.55e-2657
regional part of nervous system5.26e-2694
nervous system5.26e-2694
neurectoderm4.47e-2490
brain7.18e-2469
future brain7.18e-2469
neural plate8.69e-2386
presumptive neural plate8.69e-2386
regional part of brain9.97e-2359
anterior neural tube3.59e-2042
regional part of forebrain8.16e-2041
forebrain8.16e-2041
future forebrain8.16e-2041
ectoderm1.24e-18173
presumptive ectoderm1.24e-18173
anatomical conduit6.15e-18241
ectoderm-derived structure1.67e-17169
epithelium3.41e-17309
tube1.13e-16194
pre-chordal neural plate1.33e-1661
gray matter1.47e-1634
brain grey matter1.47e-1634
telencephalon1.80e-1634
cell layer2.54e-16312
anterior region of body3.53e-16129
craniocervical region3.53e-16129
regional part of telencephalon4.45e-1633
head1.28e-15123
cerebral hemisphere2.48e-1532
anatomical cluster4.20e-15286
multi-cellular organism6.19e-14659
cerebral cortex2.57e-1225
pallium2.57e-1225
regional part of cerebral cortex5.85e-1222
anatomical group2.04e-11626
anatomical system2.78e-11625
embryo3.13e-11612
neocortex6.95e-1120
embryonic structure9.88e-10605
developing anatomical structure9.88e-10605
multi-tissue structure1.02e-09347
germ layer1.69e-09604
embryonic tissue1.69e-09604
presumptive structure1.69e-09604
epiblast (generic)1.69e-09604
organism subdivision8.38e-09365
posterior neural tube1.55e-0715
chordal neural plate1.55e-0715
organ2.07e-07511
organ part7.62e-07219


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
CTBP2#1488427.87422237303477.62341479845092e-060.000217417208666143
FOXA1#316978.61888202729981.48686672954246e-065.7322581899847e-05
FOXA2#3170719.15702736318416.07362166732378e-094.816423487575e-07



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.