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Coexpression cluster:C3308: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3308_hippocampus_medial_cerebellum_middle_occipital_parietal_olfactory
|full_id=C3308_hippocampus_medial_cerebellum_middle_occipital_parietal_olfactory
|id=C3308
|id=C3308

Revision as of 16:12, 12 September 2012


Full id: C3308_hippocampus_medial_cerebellum_middle_occipital_parietal_olfactory



Phase1 CAGE Peaks

Hg19::chr12:58005170..58005192,+p2@ARHGEF25
Hg19::chr12:58005204..58005235,+p1@ARHGEF25
Hg19::chr12:58005243..58005248,+p3@ARHGEF25


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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell5.02e-13180
Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.41e-3294
nervous system2.41e-3294
central nervous system7.59e-3182
brain4.40e-2769
future brain4.40e-2769
neural tube2.24e-2657
neural rod2.24e-2657
future spinal cord2.24e-2657
neural keel2.24e-2657
neurectoderm9.40e-2690
ectoderm5.40e-25173
presumptive ectoderm5.40e-25173
regional part of brain2.61e-2459
neural plate3.69e-2486
presumptive neural plate3.69e-2486
ectoderm-derived structure1.65e-23169
organism subdivision3.85e-21365
anterior neural tube2.31e-2042
adult organism4.30e-20115
regional part of forebrain5.09e-2041
forebrain5.09e-2041
future forebrain5.09e-2041
head7.32e-20123
gray matter1.09e-1834
brain grey matter1.09e-1834
telencephalon2.54e-1834
cerebral hemisphere2.66e-1832
anterior region of body3.92e-18129
craniocervical region3.92e-18129
regional part of telencephalon9.88e-1833
pre-chordal neural plate1.22e-1761
regional part of cerebral cortex7.84e-1622
cerebral cortex1.97e-1525
pallium1.97e-1525
multi-tissue structure4.01e-15347
neocortex1.78e-1420
tube2.80e-13194
epithelium1.85e-12309
cell layer2.12e-12312
anatomical conduit2.46e-12241
anatomical cluster4.12e-10286
multi-cellular organism7.08e-10659
organ part6.30e-09219
embryo7.31e-09612
embryonic structure4.28e-08605
developing anatomical structure4.28e-08605
germ layer7.97e-08604
embryonic tissue7.97e-08604
presumptive structure7.97e-08604
epiblast (generic)7.97e-08604
posterior neural tube3.33e-0715
chordal neural plate3.33e-0715
anatomical system8.33e-07625


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
CCNT2#90536.336201576962630.003930750035764890.0189478262247415
E2F6#187635.017155731697390.00791769806886330.0320995484885685
HNF4A#3172215.42152690863580.005444210486686610.0246707987598847
ZNF263#1012738.221841637010680.001799043925565870.010906103351647



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.