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Coexpression cluster:C4511

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Full id: C4511_occipital_ductus_parietal_temporal_aorta_spinal_pituitary



Phase1 CAGE Peaks

Hg19::chr5:63461487..63461525,+p3@RNF180
Hg19::chr5:63461526..63461560,+p2@RNF180
Hg19::chr5:63461642..63461722,+p1@RNF180


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 organism8.23e-43115
central nervous system1.07e-3282
neural tube2.17e-3157
neural rod2.17e-3157
future spinal cord2.17e-3157
neural keel2.17e-3157
regional part of nervous system2.94e-3194
nervous system2.94e-3194
regional part of brain2.87e-2959
neural plate3.37e-2986
presumptive neural plate3.37e-2986
brain1.80e-2769
future brain1.80e-2769
neurectoderm5.76e-2790
ectoderm-derived structure8.56e-25169
anterior neural tube1.21e-2442
head2.77e-24123
regional part of forebrain2.81e-2441
forebrain2.81e-2441
future forebrain2.81e-2441
ectoderm1.42e-23173
presumptive ectoderm1.42e-23173
anterior region of body2.89e-23129
craniocervical region2.89e-23129
pre-chordal neural plate4.41e-2261
anatomical conduit6.04e-22241
epithelium7.06e-21309
cell layer9.17e-21312
tube1.08e-20194
gray matter2.58e-2034
brain grey matter2.58e-2034
anatomical cluster3.43e-20286
telencephalon5.42e-2034
regional part of telencephalon1.87e-1933
cerebral hemisphere4.69e-1932
organism subdivision2.96e-18365
multi-tissue structure8.06e-17347
cerebral cortex6.66e-1525
pallium6.66e-1525
regional part of cerebral cortex7.36e-1422
multi-cellular organism2.37e-13659
neocortex9.26e-1320
anatomical system2.65e-11625
embryo3.88e-11612
anatomical group4.64e-11626
embryonic structure5.77e-10605
developing anatomical structure5.77e-10605
germ layer1.08e-09604
embryonic tissue1.08e-09604
presumptive structure1.08e-09604
epiblast (generic)1.08e-09604
organ part3.67e-09219
organ5.35e-09511
posterior neural tube6.69e-0815
chordal neural plate6.69e-0815
nucleus of brain6.81e-079
neural nucleus6.81e-079
segmental subdivision of nervous system9.37e-0713


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#186934.907389214879320.008460985347239390.0327207601525711



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.