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|full_id=C4199_Hepatocyte_brain_liver_optic_small_mature_colon
|full_id=C4199_Hepatocyte_brain_liver_optic_small_mature_colon
|id=C4199
|id=C4199
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.04e-19!115;UBERON:0001896!8.55e-16!3;UBERON:0005290!8.55e-16!3;UBERON:0010096!8.55e-16!3;UBERON:0003714!1.38e-11!2;UBERON:0005162!2.20e-11!2;UBERON:0000122!2.20e-11!2;UBERON:0002298!4.02e-10!8;UBERON:0001049!8.76e-10!57;UBERON:0005068!8.76e-10!57;UBERON:0006241!8.76e-10!57;UBERON:0007135!8.76e-10!57;UBERON:0000073!1.11e-09!94;UBERON:0001016!1.11e-09!94;UBERON:0000349!1.56e-09!5;UBERON:0004732!1.66e-09!13;UBERON:0003075!4.02e-08!86;UBERON:0007284!4.02e-08!86;UBERON:0003076!4.02e-08!15;UBERON:0003057!4.02e-08!15;UBERON:0002616!8.84e-08!59;UBERON:0002346!1.21e-07!90;UBERON:0000955!1.25e-07!69;UBERON:0006238!1.25e-07!69;UBERON:0001017!2.73e-07!82;UBERON:0000153!3.07e-07!129;UBERON:0007811!3.07e-07!129;UBERON:0004121!3.61e-07!169;UBERON:0000924!6.52e-07!173;UBERON:0006601!6.52e-07!173;UBERON:0005743!7.57e-07!86;UBERON:0004733!8.94e-07!12;UBERON:0002028!8.94e-07!12;UBERON:0007277!8.94e-07!12
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Revision as of 14:45, 21 May 2012


Full id: C4199_Hepatocyte_brain_liver_optic_small_mature_colon



Phase1 CAGE Peaks

Hg19::chr2:234730831..234730880,+p@chr2:234730831..234730880
+
Hg19::chr7:44198877..44198886,-p4@GCK
Hg19::chr7:99620513..99620522,+p@chr7:99620513..99620522
+


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.04e-19115
medulla oblongata8.55e-163
myelencephalon8.55e-163
future myelencephalon8.55e-163
neural tissue1.38e-112
multi cell component structure2.20e-112
neuron projection bundle2.20e-112
brainstem4.02e-108
neural tube8.76e-1057
neural rod8.76e-1057
future spinal cord8.76e-1057
neural keel8.76e-1057
regional part of nervous system1.11e-0994
nervous system1.11e-0994
limbic system1.56e-095
segmental subdivision of nervous system1.66e-0913
neural plate4.02e-0886
presumptive neural plate4.02e-0886
posterior neural tube4.02e-0815
chordal neural plate4.02e-0815
regional part of brain8.84e-0859
neurectoderm1.21e-0790
brain1.25e-0769
future brain1.25e-0769
central nervous system2.73e-0782
anterior region of body3.07e-07129
craniocervical region3.07e-07129
ectoderm-derived structure3.61e-07169
ectoderm6.52e-07173
presumptive ectoderm6.52e-07173
segmental subdivision of hindbrain8.94e-0712
hindbrain8.94e-0712
presumptive hindbrain8.94e-0712


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.