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Coexpression cluster:C2998: Difference between revisions

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}}
}}

Revision as of 15:51, 26 November 2012


Full id: C2998_gastrointestinal_pineal_medial_retinoblastoma_cerebral_frontal_brain



Phase1 CAGE Peaks

Hg19::chr10:16562999..16563114,-p3@C1QL3
Hg19::chr10:16563302..16563311,-p7@C1QL3
Hg19::chr10:16563446..16563457,-p6@C1QL3


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
brain2.86e-4468
future brain2.86e-4468
neural tube1.84e-4356
neural rod1.84e-4356
future spinal cord1.84e-4356
neural keel1.84e-4356
regional part of nervous system2.12e-4253
regional part of brain2.12e-4253
central nervous system2.74e-4281
nervous system2.64e-4089
regional part of cerebral cortex7.02e-3622
brain grey matter1.92e-3334
gray matter1.92e-3334
neural plate3.53e-3382
presumptive neural plate3.53e-3382
cerebral hemisphere9.18e-3232
cerebral cortex2.26e-3125
pallium2.26e-3125
neurectoderm2.31e-3186
regional part of forebrain2.90e-3141
forebrain2.90e-3141
anterior neural tube2.90e-3141
future forebrain2.90e-3141
telencephalon9.83e-3034
neocortex7.80e-2920
adult organism9.38e-29114
regional part of telencephalon9.43e-2832
ecto-epithelium6.63e-25104
pre-chordal neural plate8.43e-2561
structure with developmental contribution from neural crest4.55e-20132
ectoderm-derived structure2.11e-19171
ectoderm2.11e-19171
presumptive ectoderm2.11e-19171
organ system subdivision1.41e-15223
limbic system7.77e-155
parietal lobe1.24e-145
pons2.99e-133
posterior neural tube4.85e-1315
chordal neural plate4.85e-1315
gyrus2.02e-126
segmental subdivision of hindbrain3.28e-1212
hindbrain3.28e-1212
presumptive hindbrain3.28e-1212
regional part of metencephalon1.18e-119
metencephalon1.18e-119
future metencephalon1.18e-119
brainstem1.95e-116
segmental subdivision of nervous system3.15e-1113
pineal body8.28e-112
regional part of epithalamus8.28e-112
secretory circumventricular organ8.28e-112
circumventricular organ8.28e-112
epithalamus8.28e-112
tube9.67e-11192
Ammon's horn2.93e-102
lobe parts of cerebral cortex2.93e-102
hippocampal formation2.93e-102
limbic lobe2.93e-102
locus ceruleus1.70e-092
brainstem nucleus1.70e-092
hindbrain nucleus1.70e-092
anatomical conduit3.38e-08240
organ part7.22e-08218
anatomical cluster8.97e-08373
frontal cortex2.64e-073


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)

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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.

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