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|full_id=C2880_normal_sacrococcigeal_left_heart_stomach_Mesenchymal_smooth
|full_id=C2880_normal_sacrococcigeal_left_heart_stomach_Mesenchymal_smooth
|id=C2880
|id=C2880
|ontology_enrichment_celltype=CL:0000057!4.60e-09!75
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.90e-28!115;UBERON:0001049!3.99e-25!57;UBERON:0005068!3.99e-25!57;UBERON:0006241!3.99e-25!57;UBERON:0007135!3.99e-25!57;UBERON:0002616!1.93e-23!59;UBERON:0000955!6.42e-22!69;UBERON:0006238!6.42e-22!69;UBERON:0005743!9.09e-22!86;UBERON:0000073!1.62e-21!94;UBERON:0001016!1.62e-21!94;UBERON:0002346!1.64e-21!90;UBERON:0001017!2.01e-21!82;UBERON:0003075!2.95e-21!86;UBERON:0007284!2.95e-21!86;UBERON:0002020!8.27e-19!34;UBERON:0003528!8.27e-19!34;UBERON:0001893!2.06e-18!34;UBERON:0002780!5.30e-18!41;UBERON:0001890!5.30e-18!41;UBERON:0006240!5.30e-18!41;UBERON:0002791!9.34e-18!33;UBERON:0001869!9.60e-18!32;UBERON:0003080!3.10e-17!42;UBERON:0000475!4.08e-17!365;UBERON:0000153!2.12e-16!129;UBERON:0007811!2.12e-16!129;UBERON:0000033!3.77e-16!123;UBERON:0002619!4.66e-16!22;UBERON:0001950!4.01e-15!20;UBERON:0000062!8.55e-15!511;UBERON:0000468!3.83e-14!659;UBERON:0000924!4.76e-14!173;UBERON:0006601!4.76e-14!173;UBERON:0000956!5.84e-14!25;UBERON:0000203!5.84e-14!25;UBERON:0000481!8.39e-14!347;UBERON:0004121!1.22e-13!169;UBERON:0003056!1.54e-13!61;UBERON:0000477!1.10e-12!286;UBERON:0004111!5.37e-12!241;UBERON:0000064!1.07e-11!219;UBERON:0000025!2.21e-11!194;UBERON:0000467!2.78e-10!625;UBERON:0000480!3.70e-10!626;UBERON:0003076!3.37e-09!15;UBERON:0003057!3.37e-09!15;UBERON:0000483!1.31e-07!309;UBERON:0000922!1.66e-07!612;UBERON:0000119!1.82e-07!312;UBERON:0004733!2.49e-07!12;UBERON:0002028!2.49e-07!12;UBERON:0007277!2.49e-07!12;UBERON:0002050!2.80e-07!605;UBERON:0005423!2.80e-07!605;UBERON:0000923!5.14e-07!604;UBERON:0005291!5.14e-07!604;UBERON:0006598!5.14e-07!604;UBERON:0002532!5.14e-07!604
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Revision as of 14:29, 21 May 2012


Full id: C2880_normal_sacrococcigeal_left_heart_stomach_Mesenchymal_smooth



Phase1 CAGE Peaks

Hg19::chr7:136553370..136553421,+p1@CHRM2
Hg19::chr7:136553426..136553441,+p5@CHRM2
Hg19::chr7:136553519..136553541,+p4@CHRM2
Hg19::chr7:136553824..136553846,+p2@CHRM2


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
fibroblast4.60e-0975
Uber Anatomy
Ontology termp-valuen
adult organism1.90e-28115
neural tube3.99e-2557
neural rod3.99e-2557
future spinal cord3.99e-2557
neural keel3.99e-2557
regional part of brain1.93e-2359
brain6.42e-2269
future brain6.42e-2269
regional part of nervous system1.62e-2194
nervous system1.62e-2194
neurectoderm1.64e-2190
central nervous system2.01e-2182
neural plate2.95e-2186
presumptive neural plate2.95e-2186
gray matter8.27e-1934
brain grey matter8.27e-1934
telencephalon2.06e-1834
regional part of forebrain5.30e-1841
forebrain5.30e-1841
future forebrain5.30e-1841
regional part of telencephalon9.34e-1833
cerebral hemisphere9.60e-1832
anterior neural tube3.10e-1742
organism subdivision4.08e-17365
anterior region of body2.12e-16129
craniocervical region2.12e-16129
head3.77e-16123
regional part of cerebral cortex4.66e-1622
neocortex4.01e-1520
organ8.55e-15511
multi-cellular organism3.83e-14659
ectoderm4.76e-14173
presumptive ectoderm4.76e-14173
cerebral cortex5.84e-1425
pallium5.84e-1425
multi-tissue structure8.39e-14347
ectoderm-derived structure1.22e-13169
pre-chordal neural plate1.54e-1361
anatomical cluster1.10e-12286
anatomical conduit5.37e-12241
organ part1.07e-11219
tube2.21e-11194
anatomical system2.78e-10625
anatomical group3.70e-10626
posterior neural tube3.37e-0915
chordal neural plate3.37e-0915
epithelium1.31e-07309
embryo1.66e-07612
cell layer1.82e-07312
segmental subdivision of hindbrain2.49e-0712
hindbrain2.49e-0712
presumptive hindbrain2.49e-0712
embryonic structure2.80e-07605
developing anatomical structure2.80e-07605
germ layer5.14e-07604
embryonic tissue5.14e-07604
presumptive structure5.14e-07604
epiblast (generic)5.14e-07604


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.