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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1851_salivary_submaxillary_parotid_small_pons_thyroid_throat
|full_id=C1851_salivary_submaxillary_parotid_small_pons_thyroid_throat
|id=C1851
|id=C1851

Revision as of 14:28, 12 September 2012


Full id: C1851_salivary_submaxillary_parotid_small_pons_thyroid_throat



Phase1 CAGE Peaks

Hg19::chr1:217250308..217250349,-p9@ESRRG
Hg19::chr1:217251561..217251581,-p8@ESRRG
Hg19::chr1:217251585..217251611,-p11@ESRRG
Hg19::chr1:217251619..217251658,-p6@ESRRG
Hg19::chr1:217251670..217251682,-p19@ESRRG


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism3.07e-81115
neural tube9.62e-5257
neural rod9.62e-5257
future spinal cord9.62e-5257
neural keel9.62e-5257
regional part of brain9.07e-4559
central nervous system9.55e-4582
brain6.67e-4269
future brain6.67e-4269
neural plate1.71e-4186
presumptive neural plate1.71e-4186
regional part of nervous system3.19e-4094
nervous system3.19e-4094
neurectoderm4.67e-4090
anterior neural tube6.73e-3742
regional part of forebrain4.17e-3641
forebrain4.17e-3641
future forebrain4.17e-3641
gray matter6.53e-3434
brain grey matter6.53e-3434
telencephalon1.03e-3334
regional part of telencephalon1.96e-3233
anterior region of body3.13e-32129
craniocervical region3.13e-32129
cerebral hemisphere3.55e-3232
head9.71e-30123
pre-chordal neural plate1.88e-2861
cerebral cortex4.00e-2725
pallium4.00e-2725
ectoderm-derived structure8.09e-26169
ectoderm1.80e-25173
presumptive ectoderm1.80e-25173
regional part of cerebral cortex4.01e-2522
neocortex3.74e-2320
anatomical cluster1.37e-15286
posterior neural tube1.61e-1515
chordal neural plate1.61e-1515
anatomical conduit1.51e-14241
multi-tissue structure3.80e-14347
tube3.97e-14194
segmental subdivision of nervous system2.55e-1313
organ2.80e-13511
segmental subdivision of hindbrain1.69e-1212
hindbrain1.69e-1212
presumptive hindbrain1.69e-1212
organ part3.24e-12219
organism subdivision6.42e-12365
epithelium7.74e-12309
cell layer1.73e-11312
brainstem4.58e-108
temporal lobe3.69e-097
regional part of metencephalon4.17e-099
metencephalon4.17e-099
future metencephalon4.17e-099
multi-cellular organism5.91e-09659
embryo1.03e-08612
anatomical system1.23e-08625
gyrus1.38e-086
anatomical group1.46e-08626
nucleus of brain2.91e-089
neural nucleus2.91e-089
embryonic structure3.22e-08605
developing anatomical structure3.22e-08605
basal ganglion5.97e-089
nuclear complex of neuraxis5.97e-089
aggregate regional part of brain5.97e-089
collection of basal ganglia5.97e-089
cerebral subcortex5.97e-089
germ layer7.14e-08604
embryonic tissue7.14e-08604
presumptive structure7.14e-08604
epiblast (generic)7.14e-08604
parietal lobe4.90e-075
occipital lobe8.04e-075


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
FOXA1#316948.865135799508360.0003075468591372710.00316826656356653



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.