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Coexpression cluster:C4193: Difference between revisions

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|full_id=C4193_gall_signet_Hepatocyte_Adipocyte_hepatocellular_mature_kidney
|full_id=C4193_gall_signet_Hepatocyte_Adipocyte_hepatocellular_mature_kidney
|id=C4193
|id=C4193
|ontology_enrichment_celltype=CL:0000136!9.63e-11!15
|ontology_enrichment_celltype=CL:0000136!9.15e-11!15;CL:0000181!3.64e-08!12;CL:0000417!3.64e-08!12;CL:0000668!3.64e-08!12;CL:0000412!3.64e-08!12;CL:0000182!3.64e-08!12
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.17e-38!115;UBERON:0001049!2.48e-18!57;UBERON:0005068!2.48e-18!57;UBERON:0006241!2.48e-18!57;UBERON:0007135!2.48e-18!57;UBERON:0005743!7.17e-17!86;UBERON:0001017!1.63e-15!82;UBERON:0003075!4.16e-15!86;UBERON:0007284!4.16e-15!86;UBERON:0000073!1.06e-14!94;UBERON:0001016!1.06e-14!94;UBERON:0002346!8.23e-14!90;UBERON:0002616!9.18e-14!59;UBERON:0001893!1.29e-13!34;UBERON:0002780!1.71e-13!41;UBERON:0001890!1.71e-13!41;UBERON:0006240!1.71e-13!41;UBERON:0002020!5.33e-13!34;UBERON:0003528!5.33e-13!34;UBERON:0003080!5.66e-13!42;UBERON:0002791!9.73e-13!33;UBERON:0000955!2.15e-12!69;UBERON:0006238!2.15e-12!69;UBERON:0001869!3.35e-12!32;UBERON:0003056!8.17e-11!61;UBERON:0000033!8.23e-11!123;UBERON:0000153!2.50e-10!129;UBERON:0007811!2.50e-10!129;UBERON:0000956!4.21e-10!25;UBERON:0000203!4.21e-10!25;UBERON:0002619!1.19e-09!22;UBERON:0001950!1.45e-09!20;UBERON:0004121!2.61e-09!169;UBERON:0000062!4.16e-09!511;UBERON:0000924!1.00e-08!173;UBERON:0006601!1.00e-08!173;UBERON:0004111!2.94e-08!241;UBERON:0000025!2.95e-08!194;UBERON:0000477!6.49e-08!286;UBERON:0000468!1.00e-07!659;UBERON:0000922!1.85e-07!612;UBERON:0000200!4.31e-07!6;UBERON:0000467!9.53e-07!625
|ontology_enrichment_uberon=UBERON:0007023!2.89e-24!114;UBERON:0001049!6.25e-15!56;UBERON:0005068!6.25e-15!56;UBERON:0006241!6.25e-15!56;UBERON:0007135!6.25e-15!56;UBERON:0002619!8.95e-15!22;UBERON:0000073!2.45e-14!53;UBERON:0002616!2.45e-14!53;UBERON:0002780!2.95e-14!41;UBERON:0001890!2.95e-14!41;UBERON:0003080!2.95e-14!41;UBERON:0006240!2.95e-14!41;UBERON:0001950!5.40e-14!20;UBERON:0001893!8.26e-14!34;UBERON:0001869!6.40e-13!32;UBERON:0000956!1.01e-12!25;UBERON:0000203!1.01e-12!25;UBERON:0001017!7.92e-12!81;UBERON:0003075!8.96e-12!82;UBERON:0007284!8.96e-12!82;UBERON:0002791!4.72e-11!32;UBERON:0002346!6.00e-11!86;UBERON:0000025!1.56e-10!192;UBERON:0003528!3.08e-10!34;UBERON:0002020!3.08e-10!34;UBERON:0000200!4.32e-10!6;UBERON:0001016!4.54e-10!89;UBERON:0000955!7.14e-10!68;UBERON:0006238!7.14e-10!68;UBERON:0003056!2.59e-09!61;UBERON:0010371!5.46e-09!104;UBERON:0011216!5.42e-08!223;UBERON:0004111!1.00e-07!240
|tf_chipseq_enrich=HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392215653763547!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123057097555832!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.00073896501526598!SREBF1#6720;3:47.0058494404883:9.62099323994382e-06:0.000255156656421151
|tf_chipseq_enrich=HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392215653763547!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123057097555832!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.00073896501526598!SREBF1#6720;3:47.0058494404883:9.62099323994382e-06:0.000255156656421151
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}}
}}

Revision as of 15:45, 19 October 2012


Full id: C4193_gall_signet_Hepatocyte_Adipocyte_hepatocellular_mature_kidney



Phase1 CAGE Peaks

Hg19::chr2:223536339..223536352,+p2@MOGAT1
Hg19::chr2:223536370..223536388,+p1@MOGAT1
Hg19::chr2:223536428..223536435,+p4@MOGAT1


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 cell9.15e-1115
metabolising cell3.64e-0812
endopolyploid cell3.64e-0812
parenchymal cell3.64e-0812
polyploid cell3.64e-0812
hepatocyte3.64e-0812
Uber Anatomy
Ontology termp-valuen
adult organism2.89e-24114
neural tube6.25e-1556
neural rod6.25e-1556
future spinal cord6.25e-1556
neural keel6.25e-1556
regional part of cerebral cortex8.95e-1522
regional part of nervous system2.45e-1453
regional part of brain2.45e-1453
regional part of forebrain2.95e-1441
forebrain2.95e-1441
anterior neural tube2.95e-1441
future forebrain2.95e-1441
neocortex5.40e-1420
telencephalon8.26e-1434
cerebral hemisphere6.40e-1332
cerebral cortex1.01e-1225
pallium1.01e-1225
central nervous system7.92e-1281
neural plate8.96e-1282
presumptive neural plate8.96e-1282
regional part of telencephalon4.72e-1132
neurectoderm6.00e-1186
tube1.56e-10192
brain grey matter3.08e-1034
gray matter3.08e-1034
gyrus4.32e-106
nervous system4.54e-1089
brain7.14e-1068
future brain7.14e-1068
pre-chordal neural plate2.59e-0961
ecto-epithelium5.46e-09104
organ system subdivision5.42e-08223
anatomical conduit1.00e-07240


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
HDAC2#3066313.41562023662630.0004140761399857210.00392215653763547
HNF4A#3172323.13229036295378.07584663437677e-050.00123057097555832
NANOG#79923329.24477848101273.99627955670032e-050.00073896501526598
SREBF1#6720347.00584944048839.62099323994382e-060.000255156656421151



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.