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Coexpression cluster:C3465: Difference between revisions

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|full_id=C3465_testis_ductus_liver_seminal_Hepatocyte_hepatocellular_spleen
|full_id=C3465_testis_ductus_liver_seminal_Hepatocyte_hepatocellular_spleen
|id=C3465
|id=C3465
|ontology_enrichment_celltype=CL:0000181!2.00e-08!12;CL:0000417!2.00e-08!12;CL:0000668!2.00e-08!12;CL:0000414!2.00e-08!12;CL:0000412!2.00e-08!12;CL:0000182!2.00e-08!12
|ontology_enrichment_celltype=CL:0000181!7.08e-09!12;CL:0000417!7.08e-09!12;CL:0000668!7.08e-09!12;CL:0000412!7.08e-09!12;CL:0000182!7.08e-09!12
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.26e-35!115;UBERON:0005743!1.29e-18!86;UBERON:0003075!8.60e-17!86;UBERON:0007284!8.60e-17!86;UBERON:0001017!1.12e-16!82;UBERON:0000477!1.36e-16!286;UBERON:0002346!1.44e-15!90;UBERON:0000073!3.67e-15!94;UBERON:0001016!3.67e-15!94;UBERON:0001049!2.24e-14!57;UBERON:0005068!2.24e-14!57;UBERON:0006241!2.24e-14!57;UBERON:0007135!2.24e-14!57;UBERON:0000033!2.65e-14!123;UBERON:0000153!2.74e-14!129;UBERON:0007811!2.74e-14!129;UBERON:0000481!3.27e-14!347;UBERON:0002616!7.05e-14!59;UBERON:0004111!7.34e-14!241;UBERON:0000955!1.95e-13!69;UBERON:0006238!1.95e-13!69;UBERON:0000468!3.40e-13!659;UBERON:0003056!3.45e-12!61;UBERON:0000025!6.06e-12!194;UBERON:0004121!8.28e-12!169;UBERON:0000475!9.63e-12!365;UBERON:0000924!3.14e-11!173;UBERON:0006601!3.14e-11!173;UBERON:0000922!1.14e-10!612;UBERON:0000119!1.68e-10!312;UBERON:0003080!1.84e-10!42;UBERON:0002780!7.67e-10!41;UBERON:0001890!7.67e-10!41;UBERON:0006240!7.67e-10!41;UBERON:0000483!1.26e-09!309;UBERON:0000062!1.53e-09!511;UBERON:0009854!2.18e-09!23;UBERON:0002050!3.61e-09!605;UBERON:0005423!3.61e-09!605;UBERON:0009497!4.06e-09!25;UBERON:0000015!4.06e-09!25;UBERON:0002423!4.06e-09!25;UBERON:0006235!4.06e-09!25;UBERON:0004161!4.06e-09!25;UBERON:0001048!4.92e-09!168;UBERON:0000923!8.11e-09!604;UBERON:0005291!8.11e-09!604;UBERON:0006598!8.11e-09!604;UBERON:0002532!8.11e-09!604;UBERON:0008835!8.79e-09!22;UBERON:0003894!8.79e-09!22;UBERON:0000467!1.31e-08!625;UBERON:0000480!1.73e-08!626;UBERON:0002107!2.58e-08!19;UBERON:0006925!2.58e-08!19;UBERON:0008836!2.58e-08!19;UBERON:0005057!3.33e-08!26;UBERON:0009856!4.02e-08!26;UBERON:0002368!4.80e-08!35;UBERON:0005172!1.21e-07!55;UBERON:0005173!1.21e-07!55;UBERON:0007499!1.47e-07!25;UBERON:0003103!1.76e-07!69;UBERON:0002020!7.74e-07!34;UBERON:0003528!7.74e-07!34;UBERON:0002417!8.36e-07!61;UBERON:0000916!8.36e-07!61;UBERON:0000949!9.67e-07!45
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}}
}}

Revision as of 15:07, 19 October 2012


Full id: C3465_testis_ductus_liver_seminal_Hepatocyte_hepatocellular_spleen



Phase1 CAGE Peaks

Hg19::chr14:95047725..95047742,+p3@SERPINA5
Hg19::chr14:95047744..95047805,+p1@SERPINA5
Hg19::chr14:95053862..95053873,+p6@SERPINA5


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
metabolising cell7.08e-0912
endopolyploid cell7.08e-0912
parenchymal cell7.08e-0912
polyploid cell7.08e-0912
hepatocyte7.08e-0912
Uber Anatomy
Ontology termp-valuen
adult organism4.57e-33114
anatomical cluster1.04e-13373
neural plate3.19e-1382
presumptive neural plate3.19e-1382
organ system subdivision3.39e-12223
neurectoderm4.58e-1286
neural tube1.65e-1156
neural rod1.65e-1156
future spinal cord1.65e-1156
neural keel1.65e-1156
central nervous system2.39e-1181
anatomical conduit6.58e-11240
brain9.03e-1168
future brain9.03e-1168
regional part of nervous system2.10e-1053
regional part of brain2.10e-1053
multi-tissue structure4.29e-10342
epithelium of foregut-midgut junction1.79e-0925
anatomical boundary1.79e-0925
hepatobiliary system1.79e-0925
foregut-midgut junction1.79e-0925
septum transversum1.79e-0925
ecto-epithelium2.47e-09104
digestive tract diverticulum3.20e-0923
nervous system3.46e-0989
tube4.29e-09192
organ8.77e-09503
liver9.08e-0919
digestive gland9.08e-0919
liver bud9.08e-0919
hepatic diverticulum1.52e-0822
liver primordium1.52e-0822
abdomen element4.41e-0854
abdominal segment element4.41e-0854
endocrine gland4.96e-0835
structure with developmental contribution from neural crest5.18e-08132
cell layer8.05e-08309
ectoderm-derived structure9.51e-08171
ectoderm9.51e-08171
presumptive ectoderm9.51e-08171
exocrine gland1.13e-0731
exocrine system1.13e-0731
sac1.14e-0726
endocrine system1.63e-0745
multi-cellular organism1.67e-07656
male reproductive organ1.82e-0711
pre-chordal neural plate2.50e-0761
gland2.84e-0759
regional part of forebrain3.23e-0741
forebrain3.23e-0741
anterior neural tube3.23e-0741
future forebrain3.23e-0741
primordium4.41e-07160
epithelial sac4.69e-0725
epithelium6.96e-07306


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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