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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0007023!1.38e-40!115;UBERON:0001049!1.07e-14!57;UBERON:0005068!1.07e-14!57;UBERON:0006241!1.07e-14!57;UBERON:0007135!1.07e-14!57;UBERON:0001017!1.54e-13!82;UBERON:0005743!1.07e-12!86;UBERON:0000955!3.72e-12!69;UBERON:0006238!3.72e-12!69;UBERON:0002616!3.40e-11!59;UBERON:0000073!1.54e-10!94;UBERON:0001016!1.54e-10!94;UBERON:0003080!2.39e-10!42;UBERON:0002780!1.02e-09!41;UBERON:0001890!1.02e-09!41;UBERON:0006240!1.02e-09!41;UBERON:0000062!1.23e-09!511;UBERON:0003075!4.62e-08!86;UBERON:0007284!4.62e-08!86;UBERON:0000153!5.40e-08!129;UBERON:0007811!5.40e-08!129;UBERON:0002346!5.56e-08!90;UBERON:0000468!1.03e-07!659;UBERON:0000467!4.56e-07!625;UBERON:0001893!5.00e-07!34;UBERON:0000033!5.54e-07!123;UBERON:0000480!5.93e-07!626;UBERON:0002020!7.25e-07!34;UBERON:0003528!7.25e-07!34;UBERON:0002791!9.11e-07!33
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}}
}}

Revision as of 17:07, 8 August 2012


Full id: C1297_trachea_salivary_seminal_ductus_eye_submaxillary_throat



Phase1 CAGE Peaks

Hg19::chr10:115511386..115511397,+p4@C10orf81
Hg19::chr10:115511412..115511428,+p3@C10orf81
Hg19::chr10:115511434..115511454,+p1@C10orf81
Hg19::chr11:34909948..34909959,-p@chr11:34909948..34909959
-
Hg19::chr13:24144796..24144809,+p6@TNFRSF19
Hg19::chr3:46506387..46506404,-p1@LTF


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


GO IDGO nameFDR corrected p-value
GO:0005031tumor necrosis factor receptor activity0.0166781938844186
GO:0043120tumor necrosis factor binding0.0166781938844186
GO:0005035death receptor activity0.0166781938844186
GO:0008199ferric iron binding0.0374900304819804
GO:0055072iron ion homeostasis0.0374900304819804
GO:0006879cellular iron ion homeostasis0.0374900304819804
GO:0006826iron ion transport0.0374900304819804
GO:0007254JNK cascade0.0374900304819804
GO:0031098stress-activated protein kinase signaling pathway0.0374900304819804
GO:0006959humoral immune response0.0374900304819804
GO:0042742defense response to bacterium0.037829791018342
GO:0019955cytokine binding0.037829791018342
GO:0000041transition metal ion transport0.037829791018342
GO:0009617response to bacterium0.037829791018342
GO:0000165MAPKKK cascade0.0475310480760905
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0475310480760905
GO:0055066di-, tri-valent inorganic cation homeostasis0.0475310480760905
GO:0030003cellular cation homeostasis0.0475310480760905
GO:0055080cation homeostasis0.0475310480760905
GO:0051707response to other organism0.0475310480760905
GO:0006917induction of apoptosis0.0475310480760905
GO:0012502induction of programmed cell death0.0475310480760905
GO:0055082cellular chemical homeostasis0.0475310480760905
GO:0006873cellular ion homeostasis0.0475310480760905
GO:0015674di-, tri-valent inorganic cation transport0.0475310480760905
GO:0043065positive regulation of apoptosis0.0475310480760905
GO:0043068positive regulation of programmed cell death0.0475310480760905
GO:0050801ion homeostasis0.0475310480760905
GO:0009607response to biotic stimulus0.0496572657893629



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
granulocyte4.87e-078
Uber Anatomy
Ontology termp-valuen
adult organism1.38e-40115
neural tube1.07e-1457
neural rod1.07e-1457
future spinal cord1.07e-1457
neural keel1.07e-1457
central nervous system1.54e-1382
brain3.72e-1269
future brain3.72e-1269
regional part of brain3.40e-1159
regional part of nervous system1.54e-1094
nervous system1.54e-1094
anterior neural tube2.39e-1042
regional part of forebrain1.02e-0941
forebrain1.02e-0941
future forebrain1.02e-0941
organ1.23e-09511
neural plate4.62e-0886
presumptive neural plate4.62e-0886
anterior region of body5.40e-08129
craniocervical region5.40e-08129
neurectoderm5.56e-0890
multi-cellular organism1.03e-07659
anatomical system4.56e-07625
telencephalon5.00e-0734
head5.54e-07123
anatomical group5.93e-07626
gray matter7.25e-0734
brain grey matter7.25e-0734
regional part of telencephalon9.11e-0733


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)

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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.