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Coexpression cluster:C4244: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 19:51, 8 August 2012


Full id: C4244_parotid_pancreas_salivary_heart_submaxillary_left_umbilical



Phase1 CAGE Peaks

Hg19::chr2:71453519..71453532,-p@chr2:71453519..71453532
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Hg19::chr2:71453533..71453553,-p@chr2:71453533..71453553
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Hg19::chr2:71453567..71453584,-p@chr2:71453567..71453584
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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 organism6.83e-71115
neural tube2.50e-2757
neural rod2.50e-2757
future spinal cord2.50e-2757
neural keel2.50e-2757
central nervous system1.79e-2582
regional part of nervous system4.49e-2494
nervous system4.49e-2494
regional part of brain1.99e-2159
neural plate2.83e-2186
presumptive neural plate2.83e-2186
brain6.62e-2169
future brain6.62e-2169
regional part of forebrain1.60e-2041
forebrain1.60e-2041
future forebrain1.60e-2041
anterior neural tube8.42e-2042
neurectoderm1.23e-1990
telencephalon7.62e-1634
gray matter1.49e-1534
brain grey matter1.49e-1534
regional part of telencephalon7.47e-1533
ectoderm-derived structure2.38e-14169
anterior region of body2.82e-14129
craniocervical region2.82e-14129
cerebral hemisphere4.56e-1432
ectoderm1.37e-13173
presumptive ectoderm1.37e-13173
head2.52e-13123
pre-chordal neural plate1.14e-1261
anatomical conduit5.99e-12241
regional part of cerebral cortex1.13e-1122
neocortex1.23e-1120
anatomical cluster3.66e-10286
tube6.62e-10194
cerebral cortex9.53e-1025
pallium9.53e-1025
posterior neural tube1.10e-0815
chordal neural plate1.10e-0815
multi-tissue structure2.70e-08347
organ part6.12e-08219
organ8.60e-08511
nucleus of brain8.90e-089
neural nucleus8.90e-089
segmental subdivision of nervous system4.11e-0713
gyrus4.86e-076
organism subdivision4.90e-07365
epithelium7.38e-07309


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.