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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1950_testicular_H9_teratocarcinoma_Neural_iPS_small_HES3GFP
|full_id=C1950_testicular_H9_teratocarcinoma_Neural_iPS_small_HES3GFP
|id=C1950
|id=C1950

Revision as of 14:35, 12 September 2012


Full id: C1950_testicular_H9_teratocarcinoma_Neural_iPS_small_HES3GFP



Phase1 CAGE Peaks

Hg19::chr5:115782001..115782019,-p@chr5:115782001..115782019
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Hg19::chr5:115782080..115782113,-p@chr5:115782080..115782113
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Hg19::chr5:115782117..115782137,-p@chr5:115782117..115782137
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Hg19::chr5:115782150..115782161,-p@chr5:115782150..115782161
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Hg19::chr5:115910116..115910141,-p4@SEMA6A


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
melanocyte3.23e-0810
melanoblast3.23e-0810
pigment cell4.94e-0714
neuronal stem cell7.88e-078
Uber Anatomy
Ontology termp-valuen
adult organism9.70e-36115
central nervous system7.60e-3482
regional part of nervous system3.34e-3294
nervous system3.34e-3294
neural tube7.84e-3257
neural rod7.84e-3257
future spinal cord7.84e-3257
neural keel7.84e-3257
neurectoderm2.04e-2790
regional part of brain1.54e-2659
neural plate1.55e-2686
presumptive neural plate1.55e-2686
brain9.52e-2669
future brain9.52e-2669
anterior neural tube8.35e-2442
regional part of forebrain2.38e-2341
forebrain2.38e-2341
future forebrain2.38e-2341
ectoderm5.41e-22173
presumptive ectoderm5.41e-22173
ectoderm-derived structure4.51e-21169
gray matter5.40e-2134
brain grey matter5.40e-2134
telencephalon1.00e-2034
regional part of telencephalon3.07e-2033
anterior region of body1.84e-19129
craniocervical region1.84e-19129
cerebral hemisphere2.84e-1932
pre-chordal neural plate2.88e-1961
head3.55e-19123
cerebral cortex2.43e-1525
pallium2.43e-1525
regional part of cerebral cortex4.43e-1422
tube9.06e-14194
anatomical conduit1.52e-13241
neocortex7.66e-1320
anatomical cluster4.30e-12286
multi-tissue structure6.22e-12347
cell layer1.37e-11312
epithelium2.23e-11309
organ part9.39e-11219
organ3.85e-10511
embryo6.11e-10612
organism subdivision7.78e-10365
posterior neural tube4.29e-0915
chordal neural plate4.29e-0915
multi-cellular organism4.54e-09659
anatomical system8.24e-08625
segmental subdivision of nervous system9.98e-0813
anatomical group1.13e-07626
embryonic structure1.15e-07605
developing anatomical structure1.15e-07605
germ layer1.81e-07604
embryonic tissue1.81e-07604
presumptive structure1.81e-07604
epiblast (generic)1.81e-07604
nucleus of brain3.90e-079
neural nucleus3.90e-079
segmental subdivision of hindbrain4.13e-0712
hindbrain4.13e-0712
presumptive hindbrain4.13e-0712
basal ganglion8.18e-079
nuclear complex of neuraxis8.18e-079
aggregate regional part of brain8.18e-079
collection of basal ganglia8.18e-079
cerebral subcortex8.18e-079


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.

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