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Coexpression cluster:C4018: Difference between revisions

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|full_id=C4018_occipital_Osteoblast_brain_Dendritic_Monocytederived_submaxillary_Adipocyte
|full_id=C4018_occipital_Osteoblast_brain_Dendritic_Monocytederived_submaxillary_Adipocyte
|id=C4018
|id=C4018
|ontology_enrichment_celltype=CL:0002009!1.16e-18!65;CL:0002057!6.09e-18!42;CL:0002194!6.11e-18!63;CL:0000576!6.11e-18!63;CL:0000040!6.11e-18!63;CL:0000559!6.11e-18!63;CL:0000557!3.49e-16!71;CL:0000860!2.97e-15!45;CL:0000839!1.19e-14!70;CL:0000766!1.33e-13!76
|ontology_enrichment_celltype=CL:0002009!7.46e-21!61;CL:0002194!3.39e-20!59;CL:0000576!3.39e-20!59;CL:0000040!3.39e-20!59;CL:0000559!3.39e-20!59;CL:0000473!5.16e-20!48;CL:0000234!5.16e-20!48;CL:0000557!5.87e-18!67;CL:0000860!1.40e-17!42;CL:0002057!1.40e-17!42;CL:0000325!6.49e-17!87;CL:0000839!2.20e-16!66;CL:0000766!9.16e-15!72
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.81e-28!115;UBERON:0000468!1.55e-26!659;UBERON:0000467!1.21e-24!625;UBERON:0000480!2.15e-24!626;UBERON:0002050!5.22e-23!605;UBERON:0005423!5.22e-23!605;UBERON:0000923!8.32e-23!604;UBERON:0005291!8.32e-23!604;UBERON:0006598!8.32e-23!604;UBERON:0002532!8.32e-23!604;UBERON:0000922!3.18e-22!612;UBERON:0000062!3.56e-20!511;UBERON:0002371!6.06e-15!80;UBERON:0000926!9.24e-14!448;UBERON:0004120!9.24e-14!448;UBERON:0006603!9.24e-14!448;UBERON:0002204!2.37e-13!167;UBERON:0002405!2.58e-13!115;UBERON:0001474!5.47e-13!86;UBERON:0003081!8.83e-13!216;UBERON:0001049!3.16e-12!57;UBERON:0005068!3.16e-12!57;UBERON:0006241!3.16e-12!57;UBERON:0007135!3.16e-12!57;UBERON:0004765!1.17e-11!101;UBERON:0001434!1.17e-11!101;UBERON:0002390!1.32e-10!102;UBERON:0003061!1.32e-10!102;UBERON:0002193!1.78e-10!112;UBERON:0002616!2.95e-10!59;UBERON:0004111!6.20e-10!241;UBERON:0003080!4.91e-09!42;UBERON:0000025!6.97e-09!194;UBERON:0002780!1.55e-08!41;UBERON:0001890!1.55e-08!41;UBERON:0006240!1.55e-08!41;UBERON:0003075!3.54e-08!86;UBERON:0007284!3.54e-08!86;UBERON:0000477!3.85e-08!286;UBERON:0001017!5.87e-08!82;UBERON:0005743!7.71e-08!86;UBERON:0000479!1.02e-07!787;UBERON:0002020!1.18e-07!34;UBERON:0003528!1.18e-07!34;UBERON:0000955!1.21e-07!69;UBERON:0006238!1.21e-07!69;UBERON:0001893!2.66e-07!34;UBERON:0002791!3.17e-07!33;UBERON:0002346!3.89e-07!90;UBERON:0001869!4.98e-07!32
|ontology_enrichment_uberon=UBERON:0007023!6.17e-27!114;UBERON:0000468!1.76e-26!656;UBERON:0000923!6.87e-26!560;UBERON:0010316!6.87e-26!560;UBERON:0005291!6.87e-26!560;UBERON:0006598!6.87e-26!560;UBERON:0010317!6.87e-26!560;UBERON:0002532!6.87e-26!560;UBERON:0002050!7.27e-26!564;UBERON:0000467!3.92e-25!624;UBERON:0000480!6.98e-25!625;UBERON:0005423!9.58e-24!581;UBERON:0000922!1.06e-22!592;UBERON:0000062!1.27e-19!503;UBERON:0000926!1.02e-18!315;UBERON:0004120!1.02e-18!315;UBERON:0006603!1.02e-18!315;UBERON:0002371!2.08e-16!76;UBERON:0002204!5.30e-15!167;UBERON:0001474!2.29e-14!82;UBERON:0004765!2.72e-14!90;UBERON:0003081!4.03e-14!203;UBERON:0001434!8.94e-14!100;UBERON:0002405!1.52e-13!93;UBERON:0002390!7.66e-12!98;UBERON:0003061!7.66e-12!98;UBERON:0002193!9.04e-12!108;UBERON:0001049!4.52e-11!56;UBERON:0005068!4.52e-11!56;UBERON:0006241!4.52e-11!56;UBERON:0007135!4.52e-11!56;UBERON:0000073!8.00e-10!53;UBERON:0002616!8.00e-10!53;UBERON:0004111!2.04e-09!240;UBERON:0000479!2.87e-09!773;UBERON:0002780!6.16e-08!41;UBERON:0001890!6.16e-08!41;UBERON:0003080!6.16e-08!41;UBERON:0006240!6.16e-08!41;UBERON:0000025!8.21e-08!192;UBERON:0003075!1.08e-07!82;UBERON:0007284!1.08e-07!82;UBERON:0010314!1.90e-07!132;UBERON:0001017!3.10e-07!81;UBERON:0000481!3.60e-07!342;UBERON:0003528!3.60e-07!34;UBERON:0002020!3.60e-07!34;UBERON:0001893!7.49e-07!34;UBERON:0000955!7.84e-07!68;UBERON:0006238!7.84e-07!68;UBERON:0002791!9.30e-07!32
|tf_chipseq_enrich=NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.046051798393937
|tf_chipseq_enrich=NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.046051798393937
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}}
}}

Revision as of 15:36, 19 October 2012


Full id: C4018_occipital_Osteoblast_brain_Dendritic_Monocytederived_submaxillary_Adipocyte



Phase1 CAGE Peaks

Hg19::chr20:23614485..23614564,-p@chr20:23614485..23614564
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Hg19::chr20:23615923..23615953,-p@chr20:23615923..23615953
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Hg19::chr20:23615955..23616000,-p@chr20:23615955..23616000
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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>


Uber Anatomy
Ontology termp-valuen
adult organism6.17e-27114
multi-cellular organism1.76e-26656
germ layer6.87e-26560
germ layer / neural crest6.87e-26560
embryonic tissue6.87e-26560
presumptive structure6.87e-26560
germ layer / neural crest derived structure6.87e-26560
epiblast (generic)6.87e-26560
embryonic structure7.27e-26564
anatomical system3.92e-25624
anatomical group6.98e-25625
developing anatomical structure9.58e-24581
embryo1.06e-22592
organ1.27e-19503
mesoderm1.02e-18315
mesoderm-derived structure1.02e-18315
presumptive mesoderm1.02e-18315
bone marrow2.08e-1676
musculoskeletal system5.30e-15167
bone element2.29e-1482
skeletal element2.72e-1490
lateral plate mesoderm4.03e-14203
skeletal system8.94e-14100
immune system1.52e-1393
hematopoietic system7.66e-1298
blood island7.66e-1298
hemolymphoid system9.04e-12108
neural tube4.52e-1156
neural rod4.52e-1156
future spinal cord4.52e-1156
neural keel4.52e-1156
regional part of nervous system8.00e-1053
regional part of brain8.00e-1053
anatomical conduit2.04e-09240
tissue2.87e-09773
regional part of forebrain6.16e-0841
forebrain6.16e-0841
anterior neural tube6.16e-0841
future forebrain6.16e-0841
tube8.21e-08192
neural plate1.08e-0782
presumptive neural plate1.08e-0782
structure with developmental contribution from neural crest1.90e-07132
central nervous system3.10e-0781
multi-tissue structure3.60e-07342
brain grey matter3.60e-0734
gray matter3.60e-0734
telencephalon7.49e-0734
brain7.84e-0768
future brain7.84e-0768
regional part of telencephalon9.30e-0732


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
NR3C1#290829.982015554115360.01278474365547170.046051798393937



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.