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Coexpression cluster:C4260: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4260_pineal_globus_thalamus_occipital_corpus_middle_extraskeletal
|full_id=C4260_pineal_globus_thalamus_occipital_corpus_middle_extraskeletal
|id=C4260
|id=C4260

Revision as of 17:19, 12 September 2012


Full id: C4260_pineal_globus_thalamus_occipital_corpus_middle_extraskeletal



Phase1 CAGE Peaks

Hg19::chr3:106959530..106959548,+p1@LOC344595
Hg19::chr3:106959552..106959576,+p1@ENST00000473550
Hg19::chr3:106959578..106959602,+p2@ENST00000473550


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 cell2.81e-10180
fibroblast6.14e-0875
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure2.28e-36169
ectoderm7.54e-36173
presumptive ectoderm7.54e-36173
central nervous system1.16e-3482
regional part of nervous system1.57e-3494
nervous system1.57e-3494
head2.77e-34123
brain3.71e-3369
future brain3.71e-3369
anterior region of body7.18e-33129
craniocervical region7.18e-33129
neural tube3.63e-3157
neural rod3.63e-3157
future spinal cord3.63e-3157
neural keel3.63e-3157
regional part of brain5.43e-3159
neural plate4.23e-2986
presumptive neural plate4.23e-2986
neurectoderm4.03e-2890
anterior neural tube1.35e-2542
regional part of forebrain1.64e-2541
forebrain1.64e-2541
future forebrain1.64e-2541
organism subdivision4.37e-25365
pre-chordal neural plate8.96e-2461
adult organism1.30e-22115
telencephalon1.79e-2134
gray matter2.05e-2134
brain grey matter2.05e-2134
regional part of telencephalon7.36e-2133
cerebral hemisphere4.14e-2032
multi-tissue structure1.03e-17347
cerebral cortex9.57e-1625
pallium9.57e-1625
epithelium1.22e-15309
cell layer1.64e-15312
regional part of cerebral cortex5.73e-1522
multi-cellular organism7.45e-15659
anatomical cluster8.33e-15286
neocortex8.21e-1420
embryonic structure8.61e-12605
developing anatomical structure8.61e-12605
anatomical conduit9.39e-12241
organ part1.38e-11219
germ layer1.56e-11604
embryonic tissue1.56e-11604
presumptive structure1.56e-11604
epiblast (generic)1.56e-11604
anatomical system1.76e-11625
embryo2.47e-11612
anatomical group2.70e-11626
tube6.84e-09194
organ7.54e-09511
nucleus of brain3.85e-079
neural nucleus3.85e-079
basal ganglion4.20e-079
nuclear complex of neuraxis4.20e-079
aggregate regional part of brain4.20e-079
collection of basal ganglia4.20e-079
cerebral subcortex4.20e-079
posterior neural tube6.56e-0715
chordal neural plate6.56e-0715


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
E2F1#186934.907389214879320.008460985347239390.0326458123496503
E2F6#187635.017155731697390.00791769806886330.0323304714631901
EGR1#195834.988179094810140.008056488137383440.0321579042453732
MXI1#460139.96157162875930.001011470541259020.00721564015427261
MYC#460935.22228187160940.007020843755740150.0295319948852449
NRF1#4899312.21027944771090.0005492172401020010.00472290649147904



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.