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Coexpression cluster:C3594: Difference between revisions

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|full_id=C3594_gall_Melanocyte_normal_smooth_Fibroblast_bladder_umbilical
|full_id=C3594_gall_Melanocyte_normal_smooth_Fibroblast_bladder_umbilical
|id=C3594
|id=C3594
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0000148!4.80e-07!10;CL:0000541!4.80e-07!10
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!7.12e-41!115;UBERON:0001049!3.29e-17!57;UBERON:0005068!3.29e-17!57;UBERON:0006241!3.29e-17!57;UBERON:0007135!3.29e-17!57;UBERON:0003075!2.75e-16!86;UBERON:0007284!2.75e-16!86;UBERON:0002616!3.19e-16!59;UBERON:0002346!2.32e-15!90;UBERON:0000955!4.09e-14!69;UBERON:0006238!4.09e-14!69;UBERON:0000033!4.80e-14!123;UBERON:0000153!2.15e-13!129;UBERON:0007811!2.15e-13!129;UBERON:0005743!7.75e-13!86;UBERON:0001017!1.48e-12!82;UBERON:0000064!3.73e-12!219;UBERON:0002780!5.28e-12!41;UBERON:0001890!5.28e-12!41;UBERON:0006240!5.28e-12!41;UBERON:0001893!8.06e-12!34;UBERON:0002020!1.71e-11!34;UBERON:0003528!1.71e-11!34;UBERON:0003080!1.74e-11!42;UBERON:0002791!3.18e-11!33;UBERON:0004121!7.07e-11!169;UBERON:0001869!8.03e-11!32;UBERON:0003056!8.07e-11!61;UBERON:0000924!1.69e-10!173;UBERON:0006601!1.69e-10!173;UBERON:0000481!3.14e-10!347;UBERON:0000062!3.23e-10!511;UBERON:0000073!3.59e-10!94;UBERON:0001016!3.59e-10!94;UBERON:0001950!3.99e-09!20;UBERON:0002619!5.84e-09!22;UBERON:0000475!1.50e-08!365;UBERON:0001737!3.28e-08!9;UBERON:0000477!2.11e-07!286;UBERON:0000956!2.89e-07!25;UBERON:0000203!2.89e-07!25;UBERON:0003076!3.13e-07!15;UBERON:0003057!3.13e-07!15;UBERON:0004733!4.01e-07!12;UBERON:0002028!4.01e-07!12;UBERON:0007277!4.01e-07!12
|ontology_enrichment_uberon=UBERON:0007023!1.33e-33!114;UBERON:0011216!1.15e-14!223;UBERON:0001049!1.65e-13!56;UBERON:0005068!1.65e-13!56;UBERON:0006241!1.65e-13!56;UBERON:0007135!1.65e-13!56;UBERON:0000073!8.46e-13!53;UBERON:0002616!8.46e-13!53;UBERON:0003075!3.98e-12!82;UBERON:0007284!3.98e-12!82;UBERON:0000955!8.63e-12!68;UBERON:0006238!8.63e-12!68;UBERON:0001017!2.72e-11!81;UBERON:0002346!4.83e-11!86;UBERON:0010371!4.57e-10!104;UBERON:0001737!4.72e-10!9;UBERON:0010314!1.23e-09!132;UBERON:0000064!1.77e-09!218;UBERON:0000481!3.09e-09!342;UBERON:0001016!3.94e-09!89;UBERON:0001893!1.63e-08!34;UBERON:0003528!2.51e-08!34;UBERON:0002020!2.51e-08!34;UBERON:0000062!3.16e-08!503;UBERON:0002780!7.35e-08!41;UBERON:0001890!7.35e-08!41;UBERON:0003080!7.35e-08!41;UBERON:0006240!7.35e-08!41;UBERON:0003076!1.06e-07!15;UBERON:0003057!1.06e-07!15;UBERON:0004121!1.17e-07!171;UBERON:0000924!1.17e-07!171;UBERON:0006601!1.17e-07!171;UBERON:0002791!2.10e-07!32;UBERON:0001869!2.37e-07!32;UBERON:0004733!3.82e-07!12;UBERON:0002028!3.82e-07!12;UBERON:0007277!3.82e-07!12;UBERON:0003056!4.17e-07!61;UBERON:0000477!5.68e-07!373
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}}
}}

Revision as of 15:14, 19 October 2012


Full id: C3594_gall_Melanocyte_normal_smooth_Fibroblast_bladder_umbilical



Phase1 CAGE Peaks

Hg19::chr16:84328580..84328591,+p9@WFDC1
Hg19::chr16:84328606..84328621,+p7@WFDC1
Hg19::chr16:84328632..84328654,+p6@WFDC1


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
melanocyte4.80e-0710
melanoblast4.80e-0710
Uber Anatomy
Ontology termp-valuen
adult organism1.33e-33114
organ system subdivision1.15e-14223
neural tube1.65e-1356
neural rod1.65e-1356
future spinal cord1.65e-1356
neural keel1.65e-1356
regional part of nervous system8.46e-1353
regional part of brain8.46e-1353
neural plate3.98e-1282
presumptive neural plate3.98e-1282
brain8.63e-1268
future brain8.63e-1268
central nervous system2.72e-1181
neurectoderm4.83e-1186
ecto-epithelium4.57e-10104
larynx4.72e-109
structure with developmental contribution from neural crest1.23e-09132
organ part1.77e-09218
multi-tissue structure3.09e-09342
nervous system3.94e-0989
telencephalon1.63e-0834
brain grey matter2.51e-0834
gray matter2.51e-0834
organ3.16e-08503
regional part of forebrain7.35e-0841
forebrain7.35e-0841
anterior neural tube7.35e-0841
future forebrain7.35e-0841
posterior neural tube1.06e-0715
chordal neural plate1.06e-0715
ectoderm-derived structure1.17e-07171
ectoderm1.17e-07171
presumptive ectoderm1.17e-07171
regional part of telencephalon2.10e-0732
cerebral hemisphere2.37e-0732
segmental subdivision of hindbrain3.82e-0712
hindbrain3.82e-0712
presumptive hindbrain3.82e-0712
pre-chordal neural plate4.17e-0761
anatomical cluster5.68e-07373


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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