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|full_id=C666_tenocyte_Synoviocyte_Fibroblast_Chondrocyte_Nucleus_normal_mesenchymal
|full_id=C666_tenocyte_Synoviocyte_Fibroblast_Chondrocyte_Nucleus_normal_mesenchymal
|id=C666
|id=C666
|ontology_enrichment_celltype=CL:0000055!2.20e-13!180;CL:0000057!9.13e-13!75;CL:0000136!3.31e-08!15;CL:0002620!4.93e-08!23
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!5.36e-25!659;UBERON:0007023!1.16e-23!115;UBERON:0000475!2.77e-22!365;UBERON:0000467!1.02e-18!625;UBERON:0000480!2.52e-18!626;UBERON:0000062!9.75e-16!511;UBERON:0000481!9.91e-15!347;UBERON:0001049!2.60e-14!57;UBERON:0005068!2.60e-14!57;UBERON:0006241!2.60e-14!57;UBERON:0007135!2.60e-14!57;UBERON:0000477!2.98e-14!286;UBERON:0001017!5.71e-14!82;UBERON:0002616!2.56e-13!59;UBERON:0005743!3.02e-13!86;UBERON:0000922!3.98e-13!612;UBERON:0000033!4.90e-12!123;UBERON:0000153!5.33e-12!129;UBERON:0007811!5.33e-12!129;UBERON:0000955!6.19e-12!69;UBERON:0006238!6.19e-12!69;UBERON:0002050!6.88e-12!605;UBERON:0005423!6.88e-12!605;UBERON:0003075!7.13e-12!86;UBERON:0007284!7.13e-12!86;UBERON:0004111!1.17e-11!241;UBERON:0000923!1.52e-11!604;UBERON:0005291!1.52e-11!604;UBERON:0006598!1.52e-11!604;UBERON:0002532!1.52e-11!604;UBERON:0003080!1.80e-11!42;UBERON:0000483!3.73e-11!309;UBERON:0000119!3.97e-11!312;UBERON:0002780!4.40e-11!41;UBERON:0001890!4.40e-11!41;UBERON:0006240!4.40e-11!41;UBERON:0001893!1.64e-10!34;UBERON:0002020!1.65e-10!34;UBERON:0003528!1.65e-10!34;UBERON:0002791!2.94e-10!33;UBERON:0000073!4.83e-10!94;UBERON:0001016!4.83e-10!94;UBERON:0002346!7.32e-10!90;UBERON:0001869!7.36e-10!32;UBERON:0004121!1.36e-09!169;UBERON:0000025!3.53e-09!194;UBERON:0003056!1.45e-08!61;UBERON:0003102!1.57e-08!95;UBERON:0000924!2.38e-08!173;UBERON:0006601!2.38e-08!173;UBERON:0000956!6.85e-08!25;UBERON:0000203!6.85e-08!25;UBERON:0000914!7.08e-08!83;UBERON:0002329!7.08e-08!83;UBERON:0003077!7.08e-08!83;UBERON:0003059!7.08e-08!83;UBERON:0007282!7.08e-08!83;UBERON:0009618!7.08e-08!83;UBERON:0007285!7.08e-08!83;UBERON:0000479!8.30e-08!787;UBERON:0002619!1.97e-07!22;UBERON:0005256!6.43e-07!143;UBERON:0000064!8.50e-07!219
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Revision as of 14:56, 21 May 2012


Full id: C666_tenocyte_Synoviocyte_Fibroblast_Chondrocyte_Nucleus_normal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr1:56962127..56962135,-p@chr1:56962127..56962135
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Hg19::chr1:56962213..56962224,-p@chr1:56962213..56962224
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Hg19::chr1:56977768..56977801,-p@chr1:56977768..56977801
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Hg19::chr1:56977818..56977827,-p@chr1:56977818..56977827
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Hg19::chr1:56990054..56990076,-p@chr1:56990054..56990076
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Hg19::chr1:56990149..56990181,-p@chr1:56990149..56990181
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Hg19::chr1:56990206..56990220,-p@chr1:56990206..56990220
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Hg19::chr1:57044697..57044720,-p9@PPAP2B
Hg19::chr1:57044945..57044953,-p13@PPAP2B
Hg19::chr1:57044980..57045112,-p1@PPAP2B
Hg19::chr1:57045115..57045143,-p6@PPAP2B
Hg19::chr1:57045207..57045226,-p2@PPAP2B
Hg19::chr1:57045228..57045242,-p3@PPAP2B


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 cell2.20e-13180
fibroblast9.13e-1375
fat cell3.31e-0815
skin fibroblast4.93e-0823
Uber Anatomy
Ontology termp-valuen
multi-cellular organism5.36e-25659
adult organism1.16e-23115
organism subdivision2.77e-22365
anatomical system1.02e-18625
anatomical group2.52e-18626
organ9.75e-16511
multi-tissue structure9.91e-15347
neural tube2.60e-1457
neural rod2.60e-1457
future spinal cord2.60e-1457
neural keel2.60e-1457
anatomical cluster2.98e-14286
central nervous system5.71e-1482
regional part of brain2.56e-1359
embryo3.98e-13612
head4.90e-12123
anterior region of body5.33e-12129
craniocervical region5.33e-12129
brain6.19e-1269
future brain6.19e-1269
embryonic structure6.88e-12605
developing anatomical structure6.88e-12605
neural plate7.13e-1286
presumptive neural plate7.13e-1286
anatomical conduit1.17e-11241
germ layer1.52e-11604
embryonic tissue1.52e-11604
presumptive structure1.52e-11604
epiblast (generic)1.52e-11604
anterior neural tube1.80e-1142
epithelium3.73e-11309
cell layer3.97e-11312
regional part of forebrain4.40e-1141
forebrain4.40e-1141
future forebrain4.40e-1141
telencephalon1.64e-1034
gray matter1.65e-1034
brain grey matter1.65e-1034
regional part of telencephalon2.94e-1033
regional part of nervous system4.83e-1094
nervous system4.83e-1094
neurectoderm7.32e-1090
cerebral hemisphere7.36e-1032
ectoderm-derived structure1.36e-09169
tube3.53e-09194
pre-chordal neural plate1.45e-0861
surface structure1.57e-0895
ectoderm2.38e-08173
presumptive ectoderm2.38e-08173
cerebral cortex6.85e-0825
pallium6.85e-0825
somite7.08e-0883
paraxial mesoderm7.08e-0883
presomitic mesoderm7.08e-0883
presumptive segmental plate7.08e-0883
trunk paraxial mesoderm7.08e-0883
presumptive paraxial mesoderm7.08e-0883
tissue8.30e-08787
regional part of cerebral cortex1.97e-0722
trunk mesenchyme6.43e-07143
organ part8.50e-07219


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.