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Coexpression cluster:C2186: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.11e-51!115;UBERON:0001049!7.59e-19!57;UBERON:0005068!7.59e-19!57;UBERON:0006241!7.59e-19!57;UBERON:0007135!7.59e-19!57;UBERON:0002616!8.39e-15!59;UBERON:0000062!1.13e-14!511;UBERON:0003075!3.34e-14!86;UBERON:0007284!3.34e-14!86;UBERON:0003080!8.05e-14!42;UBERON:0002780!3.76e-13!41;UBERON:0001890!3.76e-13!41;UBERON:0006240!3.76e-13!41;UBERON:0002346!1.20e-12!90;UBERON:0005743!1.36e-12!86;UBERON:0001017!3.46e-12!82;UBERON:0000073!6.26e-12!94;UBERON:0001016!6.26e-12!94;UBERON:0000955!1.07e-11!69;UBERON:0006238!1.07e-11!69;UBERON:0002020!2.02e-11!34;UBERON:0003528!2.02e-11!34;UBERON:0001893!2.63e-11!34;UBERON:0000468!5.45e-11!659;UBERON:0002791!8.47e-11!33;UBERON:0000467!2.67e-10!625;UBERON:0001869!2.93e-10!32;UBERON:0000480!3.64e-10!626;UBERON:0003056!4.08e-09!61;UBERON:0002619!1.65e-08!22;UBERON:0000153!2.46e-08!129;UBERON:0007811!2.46e-08!129;UBERON:0000922!2.68e-08!612;UBERON:0000923!8.52e-08!604;UBERON:0005291!8.52e-08!604;UBERON:0006598!8.52e-08!604;UBERON:0002532!8.52e-08!604;UBERON:0000033!9.00e-08!123;UBERON:0000479!1.08e-07!787;UBERON:0002050!1.11e-07!605;UBERON:0005423!1.11e-07!605;UBERON:0001950!1.54e-07!20;UBERON:0004111!5.95e-07!241;UBERON:0002308!6.86e-07!9;UBERON:0000125!6.86e-07!9;UBERON:0004121!7.76e-07!169;UBERON:0002420!9.72e-07!9;UBERON:0007245!9.72e-07!9;UBERON:0010009!9.72e-07!9;UBERON:0010011!9.72e-07!9;UBERON:0000454!9.72e-07!9
|ontology_enrichment_uberon=UBERON:0007023!1.11e-51!115;UBERON:0001049!7.59e-19!57;UBERON:0005068!7.59e-19!57;UBERON:0006241!7.59e-19!57;UBERON:0007135!7.59e-19!57;UBERON:0002616!8.39e-15!59;UBERON:0000062!1.13e-14!511;UBERON:0003075!3.34e-14!86;UBERON:0007284!3.34e-14!86;UBERON:0003080!8.05e-14!42;UBERON:0002780!3.76e-13!41;UBERON:0001890!3.76e-13!41;UBERON:0006240!3.76e-13!41;UBERON:0002346!1.20e-12!90;UBERON:0005743!1.36e-12!86;UBERON:0001017!3.46e-12!82;UBERON:0000073!6.26e-12!94;UBERON:0001016!6.26e-12!94;UBERON:0000955!1.07e-11!69;UBERON:0006238!1.07e-11!69;UBERON:0002020!2.02e-11!34;UBERON:0003528!2.02e-11!34;UBERON:0001893!2.63e-11!34;UBERON:0000468!5.45e-11!659;UBERON:0002791!8.47e-11!33;UBERON:0000467!2.67e-10!625;UBERON:0001869!2.93e-10!32;UBERON:0000480!3.64e-10!626;UBERON:0003056!4.08e-09!61;UBERON:0002619!1.65e-08!22;UBERON:0000153!2.46e-08!129;UBERON:0007811!2.46e-08!129;UBERON:0000922!2.68e-08!612;UBERON:0000923!8.52e-08!604;UBERON:0005291!8.52e-08!604;UBERON:0006598!8.52e-08!604;UBERON:0002532!8.52e-08!604;UBERON:0000033!9.00e-08!123;UBERON:0000479!1.08e-07!787;UBERON:0002050!1.11e-07!605;UBERON:0005423!1.11e-07!605;UBERON:0001950!1.54e-07!20;UBERON:0004111!5.95e-07!241;UBERON:0002308!6.86e-07!9;UBERON:0000125!6.86e-07!9;UBERON:0004121!7.76e-07!169;UBERON:0002420!9.72e-07!9;UBERON:0007245!9.72e-07!9;UBERON:0010009!9.72e-07!9;UBERON:0010011!9.72e-07!9;UBERON:0000454!9.72e-07!9
|tf_chipseq_enrich=CEBPB#1051;3:5.97836071936861:0.00715383248472697:0.0297167731633283
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}}
}}

Revision as of 12:36, 5 September 2012


Full id: C2186_liver_Hepatocyte_mature_left_vagina_skeletal_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr12:112219753..112219770,+p@chr12:112219753..112219770
+
Hg19::chr19:35630316..35630339,+p9@FXYD1
Hg19::chr19:35630344..35630384,+p5@FXYD1
Hg19::chr19:35630385..35630392,+p17@FXYD1


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
fat cell2.08e-1015
Uber Anatomy
Ontology termp-valuen
adult organism1.11e-51115
neural tube7.59e-1957
neural rod7.59e-1957
future spinal cord7.59e-1957
neural keel7.59e-1957
regional part of brain8.39e-1559
organ1.13e-14511
neural plate3.34e-1486
presumptive neural plate3.34e-1486
anterior neural tube8.05e-1442
regional part of forebrain3.76e-1341
forebrain3.76e-1341
future forebrain3.76e-1341
neurectoderm1.20e-1290
central nervous system3.46e-1282
regional part of nervous system6.26e-1294
nervous system6.26e-1294
brain1.07e-1169
future brain1.07e-1169
gray matter2.02e-1134
brain grey matter2.02e-1134
telencephalon2.63e-1134
multi-cellular organism5.45e-11659
regional part of telencephalon8.47e-1133
anatomical system2.67e-10625
cerebral hemisphere2.93e-1032
anatomical group3.64e-10626
pre-chordal neural plate4.08e-0961
regional part of cerebral cortex1.65e-0822
anterior region of body2.46e-08129
craniocervical region2.46e-08129
embryo2.68e-08612
germ layer8.52e-08604
embryonic tissue8.52e-08604
presumptive structure8.52e-08604
epiblast (generic)8.52e-08604
head9.00e-08123
tissue1.08e-07787
embryonic structure1.11e-07605
developing anatomical structure1.11e-07605
neocortex1.54e-0720
anatomical conduit5.95e-07241
nucleus of brain6.86e-079
neural nucleus6.86e-079
ectoderm-derived structure7.76e-07169
basal ganglion9.72e-079
nuclear complex of neuraxis9.72e-079
aggregate regional part of brain9.72e-079
collection of basal ganglia9.72e-079
cerebral subcortex9.72e-079


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
CEBPB#105135.978360719368610.007153832484726970.0297167731633283



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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