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Coexpression cluster:C2604: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2604_Mast_occipital_parietal_temporal_duodenum_Neural_hepatoblastoma
|full_id=C2604_Mast_occipital_parietal_temporal_duodenum_Neural_hepatoblastoma
|id=C2604
|id=C2604

Revision as of 15:22, 12 September 2012


Full id: C2604_Mast_occipital_parietal_temporal_duodenum_Neural_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr1:93913606..93913625,+p3@FNBP1L
Hg19::chr1:93913627..93913659,+p2@FNBP1L
Hg19::chr1:93913665..93913705,+p1@FNBP1L
Hg19::chr1:93913713..93913724,+p4@FNBP1L


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell1.04e-08254
Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.13e-2094
nervous system4.13e-2094
central nervous system7.97e-2082
ectoderm9.76e-18173
presumptive ectoderm9.76e-18173
adult organism1.52e-17115
ectoderm-derived structure1.09e-16169
multi-cellular organism2.59e-15659
neurectoderm1.62e-1490
brain2.56e-1469
future brain2.56e-1469
neural tube8.88e-1457
neural rod8.88e-1457
future spinal cord8.88e-1457
neural keel8.88e-1457
neural plate1.87e-1386
presumptive neural plate1.87e-1386
regional part of brain2.35e-1259
head1.35e-11123
embryo1.63e-11612
anterior region of body6.13e-11129
craniocervical region6.13e-11129
anterior neural tube6.99e-1142
regional part of forebrain2.11e-1041
forebrain2.11e-1041
future forebrain2.11e-1041
multi-tissue structure6.08e-10347
anatomical system7.26e-10625
anatomical conduit8.22e-10241
anatomical group9.25e-10626
pre-chordal neural plate2.46e-0961
embryonic structure2.51e-09605
developing anatomical structure2.51e-09605
gray matter3.81e-0934
brain grey matter3.81e-0934
germ layer5.20e-09604
embryonic tissue5.20e-09604
presumptive structure5.20e-09604
epiblast (generic)5.20e-09604
anatomical cluster1.20e-08286
regional part of telencephalon1.69e-0833
tube1.83e-08194
telencephalon2.21e-0834
cerebral hemisphere2.44e-0832
organism subdivision2.93e-08365
organ5.33e-08511
epithelium9.18e-08309
cell layer1.36e-07312
organ part4.89e-07219
Disease
Ontology termp-valuen
cell type cancer9.14e-17143
carcinoma1.20e-12106
germ cell and embryonal cancer2.76e-1122
germ cell cancer2.76e-1122


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
E2F6#187645.017155731697390.00157802193473060.00997560879131584
EGR1#195844.988179094810140.001615011500076050.0101498487216538
HEY1#2346244.040111043105710.00375304636917980.0186241760786263
RAD21#5885410.35503389545638.6948481184721e-050.00129503885146193
REST#597849.650028716128020.0001152825614219170.00157180097027984
TAF1#687243.343046285745290.008005664898701650.0322545959553855
TAF7#6879411.43306940492395.85061525419808e-050.000970200709007928
TBP#690843.706770687096390.005296377814784350.0244517904074911
ZNF263#1012748.221841637010680.0002187871180958320.00249153939884534



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.