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Coexpression cluster:C2106: Difference between revisions

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|full_id=C2106_pineal_locus_hippocampus_occipital_colon_middle_parietal
|full_id=C2106_pineal_locus_hippocampus_occipital_colon_middle_parietal
|id=C2106
|id=C2106
|ontology_enrichment_celltype=CL:0000738!6.90e-12!140;CL:0002087!8.96e-12!119;CL:0002057!1.50e-09!42;CL:0002031!1.73e-09!124;CL:0000037!5.08e-09!172;CL:0000566!5.08e-09!172;CL:0000860!1.62e-08!45;CL:0002032!2.35e-08!165;CL:0000837!2.35e-08!165;CL:0000988!1.49e-07!182;CL:0000766!4.87e-07!76
|ontology_enrichment_celltype=CL:0002087!5.95e-08!115;CL:0000738!7.95e-07!136
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.92e-42!115;UBERON:0001049!1.09e-28!57;UBERON:0005068!1.09e-28!57;UBERON:0006241!1.09e-28!57;UBERON:0007135!1.09e-28!57;UBERON:0002780!3.70e-24!41;UBERON:0001890!3.70e-24!41;UBERON:0006240!3.70e-24!41;UBERON:0002616!2.28e-23!59;UBERON:0003080!4.19e-23!42;UBERON:0001017!2.30e-22!82;UBERON:0000955!4.20e-21!69;UBERON:0006238!4.20e-21!69;UBERON:0005743!7.93e-21!86;UBERON:0002020!8.99e-20!34;UBERON:0003528!8.99e-20!34;UBERON:0001893!3.45e-19!34;UBERON:0002791!9.59e-19!33;UBERON:0001869!5.32e-18!32;UBERON:0000073!9.67e-18!94;UBERON:0001016!9.67e-18!94;UBERON:0003075!8.63e-17!86;UBERON:0007284!8.63e-17!86;UBERON:0002619!3.13e-16!22;UBERON:0002346!5.76e-16!90;UBERON:0001950!1.18e-14!20;UBERON:0000956!9.35e-14!25;UBERON:0000203!9.35e-14!25;UBERON:0003056!6.33e-12!61;UBERON:0000153!2.14e-11!129;UBERON:0007811!2.14e-11!129;UBERON:0000033!9.97e-11!123;UBERON:0004121!1.11e-07!169;UBERON:0002308!1.32e-07!9;UBERON:0000125!1.32e-07!9;UBERON:0002420!1.64e-07!9;UBERON:0007245!1.64e-07!9;UBERON:0010009!1.64e-07!9;UBERON:0010011!1.64e-07!9;UBERON:0000454!1.64e-07!9;UBERON:0000924!1.84e-07!173;UBERON:0006601!1.84e-07!173;UBERON:0003076!7.43e-07!15;UBERON:0003057!7.43e-07!15
|ontology_enrichment_uberon=UBERON:0007023!4.98e-44!114;UBERON:0001049!6.25e-42!56;UBERON:0005068!6.25e-42!56;UBERON:0006241!6.25e-42!56;UBERON:0007135!6.25e-42!56;UBERON:0000073!3.97e-39!53;UBERON:0002616!3.97e-39!53;UBERON:0002780!2.24e-33!41;UBERON:0001890!2.24e-33!41;UBERON:0003080!2.24e-33!41;UBERON:0006240!2.24e-33!41;UBERON:0001017!1.13e-29!81;UBERON:0000955!1.55e-28!68;UBERON:0006238!1.55e-28!68;UBERON:0003528!3.85e-27!34;UBERON:0002020!3.85e-27!34;UBERON:0001893!1.83e-26!34;UBERON:0001016!6.06e-26!89;UBERON:0003075!1.12e-25!82;UBERON:0007284!1.12e-25!82;UBERON:0002791!5.28e-25!32;UBERON:0001869!8.47e-25!32;UBERON:0002346!2.04e-24!86;UBERON:0002619!2.50e-22!22;UBERON:0001950!3.84e-20!20;UBERON:0003056!7.89e-20!61;UBERON:0000956!1.13e-18!25;UBERON:0000203!1.13e-18!25;UBERON:0010371!6.68e-17!104;UBERON:0011216!1.71e-15!223;UBERON:0010314!4.66e-13!132;UBERON:0000125!4.72e-10!9;UBERON:0002308!4.72e-10!9;UBERON:0002420!6.22e-10!9;UBERON:0007245!6.22e-10!9;UBERON:0010009!6.22e-10!9;UBERON:0010011!6.22e-10!9;UBERON:0000454!6.22e-10!9;UBERON:0003076!1.18e-09!15;UBERON:0003057!1.18e-09!15;UBERON:0004121!1.98e-08!171;UBERON:0000924!1.98e-08!171;UBERON:0006601!1.98e-08!171;UBERON:0001894!2.17e-08!7;UBERON:0006222!2.17e-08!7;UBERON:0004732!4.55e-08!13;UBERON:0009663!6.51e-08!7;UBERON:0000025!7.42e-08!192;UBERON:0001871!7.62e-08!6;UBERON:0002298!2.04e-07!6;UBERON:0004733!3.72e-07!12;UBERON:0002028!3.72e-07!12;UBERON:0007277!3.72e-07!12;UBERON:0000200!4.76e-07!6;UBERON:0004111!8.26e-07!240
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}}
}}

Revision as of 12:04, 19 October 2012


Full id: C2106_pineal_locus_hippocampus_occipital_colon_middle_parietal



Phase1 CAGE Peaks

Hg19::chr11:121501269..121501285,+p16@SORL1
Hg19::chr11:121501288..121501326,+p11@SORL1
Hg19::chr11:121502000..121502045,+p14@SORL1
Hg19::chr1:26093561..26093572,+p@chr1:26093561..26093572
+


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
nongranular leukocyte5.95e-08115
leukocyte7.95e-07136
Uber Anatomy
Ontology termp-valuen
adult organism4.98e-44114
neural tube6.25e-4256
neural rod6.25e-4256
future spinal cord6.25e-4256
neural keel6.25e-4256
regional part of nervous system3.97e-3953
regional part of brain3.97e-3953
regional part of forebrain2.24e-3341
forebrain2.24e-3341
anterior neural tube2.24e-3341
future forebrain2.24e-3341
central nervous system1.13e-2981
brain1.55e-2868
future brain1.55e-2868
brain grey matter3.85e-2734
gray matter3.85e-2734
telencephalon1.83e-2634
nervous system6.06e-2689
neural plate1.12e-2582
presumptive neural plate1.12e-2582
regional part of telencephalon5.28e-2532
cerebral hemisphere8.47e-2532
neurectoderm2.04e-2486
regional part of cerebral cortex2.50e-2222
neocortex3.84e-2020
pre-chordal neural plate7.89e-2061
cerebral cortex1.13e-1825
pallium1.13e-1825
ecto-epithelium6.68e-17104
organ system subdivision1.71e-15223
structure with developmental contribution from neural crest4.66e-13132
neural nucleus4.72e-109
nucleus of brain4.72e-109
basal ganglion6.22e-109
nuclear complex of neuraxis6.22e-109
aggregate regional part of brain6.22e-109
collection of basal ganglia6.22e-109
cerebral subcortex6.22e-109
posterior neural tube1.18e-0915
chordal neural plate1.18e-0915
ectoderm-derived structure1.98e-08171
ectoderm1.98e-08171
presumptive ectoderm1.98e-08171
diencephalon2.17e-087
future diencephalon2.17e-087
segmental subdivision of nervous system4.55e-0813
telencephalic nucleus6.51e-087
tube7.42e-08192
temporal lobe7.62e-086
brainstem2.04e-076
segmental subdivision of hindbrain3.72e-0712
hindbrain3.72e-0712
presumptive hindbrain3.72e-0712
gyrus4.76e-076
anatomical conduit8.26e-07240


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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