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Coexpression cluster:C2060: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!4.38e-58!82;UBERON:0005743!1.13e-54!86;UBERON:0000073!3.93e-52!94;UBERON:0001016!3.93e-52!94;UBERON:0001049!4.05e-52!57;UBERON:0005068!4.05e-52!57;UBERON:0006241!4.05e-52!57;UBERON:0007135!4.05e-52!57;UBERON:0002616!3.34e-47!59;UBERON:0000955!1.67e-44!69;UBERON:0006238!1.67e-44!69;UBERON:0002780!2.13e-41!41;UBERON:0001890!2.13e-41!41;UBERON:0006240!2.13e-41!41;UBERON:0003080!3.41e-40!42;UBERON:0003075!2.35e-39!86;UBERON:0007284!2.35e-39!86;UBERON:0002346!1.06e-38!90;UBERON:0002020!1.14e-38!34;UBERON:0003528!1.14e-38!34;UBERON:0001893!1.27e-38!34;UBERON:0001869!2.65e-38!32;UBERON:0002791!4.67e-37!33;UBERON:0000956!4.80e-33!25;UBERON:0000203!4.80e-33!25;UBERON:0003056!2.36e-28!61;UBERON:0002619!5.93e-28!22;UBERON:0000924!1.41e-26!173;UBERON:0006601!1.41e-26!173;UBERON:0004121!1.70e-26!169;UBERON:0000033!1.66e-24!123;UBERON:0001950!1.76e-24!20;UBERON:0000153!7.29e-24!129;UBERON:0007811!7.29e-24!129;UBERON:0007023!6.63e-23!115;UBERON:0000025!2.14e-14!194;UBERON:0004733!2.45e-13!12;UBERON:0002028!2.45e-13!12;UBERON:0007277!2.45e-13!12;UBERON:0003076!1.11e-12!15;UBERON:0003057!1.11e-12!15;UBERON:0004732!3.83e-12!13;UBERON:0001871!5.25e-12!7;UBERON:0000200!1.33e-11!6;UBERON:0004111!1.05e-10!241;UBERON:0000349!1.20e-10!5;UBERON:0000483!3.82e-09!309;UBERON:0002298!5.04e-09!8;UBERON:0000477!5.83e-09!286;UBERON:0000119!6.53e-09!312;UBERON:0002680!2.38e-08!9;UBERON:0001895!2.38e-08!9;UBERON:0010092!2.38e-08!9;UBERON:0000475!3.40e-08!365;UBERON:0002420!9.01e-08!9;UBERON:0007245!9.01e-08!9;UBERON:0010009!9.01e-08!9;UBERON:0010011!9.01e-08!9;UBERON:0000454!9.01e-08!9;UBERON:0002308!1.69e-07!9;UBERON:0000125!1.69e-07!9;UBERON:0000064!2.96e-07!219;UBERON:0001896!3.61e-07!3;UBERON:0005290!3.61e-07!3;UBERON:0010096!3.61e-07!3;UBERON:0000481!6.16e-07!347;UBERON:0000988!7.90e-07!3
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}}
}}

Revision as of 17:57, 8 August 2012


Full id: C2060_cerebellum_Neural_parietal_Neurons_brain_maxillary_occipital



Phase1 CAGE Peaks

Hg19::chr10:47023421..47023433,-p@chr10:47023421..47023433
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Hg19::chr5:20471939..20471943,-p@chr5:20471939..20471943
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Hg19::chr7:137039191..137039196,-p1@ENST00000438969
Hg19::chrX:10644728..10644748,-p@chrX:10644728..10644748
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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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
neuronal stem cell1.70e-128
neuron8.44e-096
neuroblast8.44e-096
electrically signaling cell8.44e-096
neural cell6.61e-0725
astrocyte of the cerebral cortex8.22e-073
Uber Anatomy
Ontology termp-valuen
central nervous system4.38e-5882
regional part of nervous system3.93e-5294
nervous system3.93e-5294
neural tube4.05e-5257
neural rod4.05e-5257
future spinal cord4.05e-5257
neural keel4.05e-5257
regional part of brain3.34e-4759
brain1.67e-4469
future brain1.67e-4469
regional part of forebrain2.13e-4141
forebrain2.13e-4141
future forebrain2.13e-4141
anterior neural tube3.41e-4042
neural plate2.35e-3986
presumptive neural plate2.35e-3986
neurectoderm1.06e-3890
gray matter1.14e-3834
brain grey matter1.14e-3834
telencephalon1.27e-3834
cerebral hemisphere2.65e-3832
regional part of telencephalon4.67e-3733
cerebral cortex4.80e-3325
pallium4.80e-3325
pre-chordal neural plate2.36e-2861
regional part of cerebral cortex5.93e-2822
ectoderm1.41e-26173
presumptive ectoderm1.41e-26173
ectoderm-derived structure1.70e-26169
head1.66e-24123
neocortex1.76e-2420
anterior region of body7.29e-24129
craniocervical region7.29e-24129
adult organism6.63e-23115
tube2.14e-14194
segmental subdivision of hindbrain2.45e-1312
hindbrain2.45e-1312
presumptive hindbrain2.45e-1312
posterior neural tube1.11e-1215
chordal neural plate1.11e-1215
segmental subdivision of nervous system3.83e-1213
temporal lobe5.25e-127
gyrus1.33e-116
anatomical conduit1.05e-10241
limbic system1.20e-105
epithelium3.82e-09309
brainstem5.04e-098
anatomical cluster5.83e-09286
cell layer6.53e-09312
regional part of metencephalon2.38e-089
metencephalon2.38e-089
future metencephalon2.38e-089
organism subdivision3.40e-08365
basal ganglion9.01e-089
nuclear complex of neuraxis9.01e-089
aggregate regional part of brain9.01e-089
collection of basal ganglia9.01e-089
cerebral subcortex9.01e-089
nucleus of brain1.69e-079
neural nucleus1.69e-079
organ part2.96e-07219
medulla oblongata3.61e-073
myelencephalon3.61e-073
future myelencephalon3.61e-073
multi-tissue structure6.16e-07347
pons7.90e-073


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.