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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1806_acute_mesothelioma_small_neuroblastoma_Astrocyte_hepatoma_gastrointestinal
|full_id=C1806_acute_mesothelioma_small_neuroblastoma_Astrocyte_hepatoma_gastrointestinal
|id=C1806
|id=C1806

Revision as of 14:25, 12 September 2012


Full id: C1806_acute_mesothelioma_small_neuroblastoma_Astrocyte_hepatoma_gastrointestinal



Phase1 CAGE Peaks

Hg19::chr18:907515..907538,+p@chr18:907515..907538
+
Hg19::chr18:907556..907570,+p@chr18:907556..907570
+
Hg19::chr18:907582..907595,+p@chr18:907582..907595
+
Hg19::chr18:907687..907707,+p@chr18:907687..907707
+
Hg19::chr18:907781..907800,+p@chr18:907781..907800
+


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
regional part of nervous system7.40e-4694
nervous system7.40e-4694
neural tube1.22e-4557
neural rod1.22e-4557
future spinal cord1.22e-4557
neural keel1.22e-4557
central nervous system5.74e-4482
regional part of brain3.44e-3959
neural plate1.24e-3886
presumptive neural plate1.24e-3886
neurectoderm4.34e-3690
brain1.68e-3569
future brain1.68e-3569
regional part of forebrain2.98e-3341
forebrain2.98e-3341
future forebrain2.98e-3341
anterior neural tube3.42e-3242
telencephalon3.92e-3034
gray matter4.84e-3034
brain grey matter4.84e-3034
regional part of telencephalon6.48e-2933
cerebral hemisphere1.95e-2832
pre-chordal neural plate5.77e-2661
neocortex7.86e-2620
cerebral cortex8.47e-2625
pallium8.47e-2625
regional part of cerebral cortex2.73e-2522
adult organism9.25e-23115
ectoderm-derived structure1.95e-22169
ectoderm1.93e-21173
presumptive ectoderm1.93e-21173
head8.29e-20123
anterior region of body6.22e-19129
craniocervical region6.22e-19129
posterior neural tube2.81e-1415
chordal neural plate2.81e-1415
tube2.87e-12194
segmental subdivision of hindbrain3.90e-1112
hindbrain3.90e-1112
presumptive hindbrain3.90e-1112
temporal lobe1.59e-107
segmental subdivision of nervous system4.53e-1013
regional part of metencephalon4.69e-109
metencephalon4.69e-109
future metencephalon4.69e-109
gyrus2.40e-086
anatomical conduit5.66e-08241
occipital lobe1.42e-075
epithelium2.06e-07309
parietal lobe2.10e-075
cell layer3.60e-07312
organ part3.92e-07219
anatomical cluster8.03e-07286


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


No analysis results for this cluster

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.