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|full_id=C4215_retina_medulla_medulloblastoma_pancreas_Retinal_eye_retinoblastoma
|full_id=C4215_retina_medulla_medulloblastoma_pancreas_Retinal_eye_retinoblastoma
|id=C4215
|id=C4215
|ontology_enrichment_celltype=CL:0002586!3.59e-15!3;CL:0000149!1.70e-11!4
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000966!2.07e-24!5;UBERON:0005388!2.07e-24!5;UBERON:0001802!2.07e-24!5;UBERON:0002346!1.97e-17!90;UBERON:0003075!1.41e-16!86;UBERON:0007284!1.41e-16!86;UBERON:0005743!1.74e-16!86;UBERON:0001781!3.59e-15!3;UBERON:0001782!3.59e-15!3;UBERON:0005424!3.59e-15!3;UBERON:0000073!1.58e-14!94;UBERON:0001016!1.58e-14!94;UBERON:0000970!3.73e-14!20;UBERON:0002104!2.04e-13!21;UBERON:0007023!1.31e-12!115;UBERON:0000020!3.90e-12!23;UBERON:0001032!1.42e-11!24;UBERON:0004456!1.42e-11!24;UBERON:0000019!1.84e-11!19;UBERON:0000047!1.84e-11!19;UBERON:0004088!1.84e-11!19;UBERON:0003072!1.84e-11!19;UBERON:0003071!1.84e-11!19;UBERON:0004128!1.84e-11!19;UBERON:0000033!2.35e-11!123;UBERON:0003056!2.42e-11!61;UBERON:0000924!1.21e-10!173;UBERON:0006601!1.21e-10!173;UBERON:0000153!1.28e-10!129;UBERON:0007811!1.28e-10!129;UBERON:0007625!1.47e-10!11;UBERON:0001017!1.97e-10!82;UBERON:0001456!2.82e-10!21;UBERON:0004121!5.89e-10!169;UBERON:0001049!8.80e-09!57;UBERON:0005068!8.80e-09!57;UBERON:0006241!8.80e-09!57;UBERON:0007135!8.80e-09!57;UBERON:0000955!3.86e-08!69;UBERON:0006238!3.86e-08!69;UBERON:0003076!8.57e-08!15;UBERON:0003057!8.57e-08!15;UBERON:0001896!1.30e-07!3;UBERON:0005290!1.30e-07!3;UBERON:0010096!1.30e-07!3;UBERON:0005085!3.59e-07!29;UBERON:0006947!4.01e-07!3;UBERON:0004054!4.01e-07!3;UBERON:0002616!5.78e-07!59;UBERON:0005383!7.81e-07!3;UBERON:0005382!7.81e-07!3
}}
}}

Revision as of 14:46, 21 May 2012


Full id: C4215_retina_medulla_medulloblastoma_pancreas_Retinal_eye_retinoblastoma



Phase1 CAGE Peaks

Hg19::chr2:242871899..242871908,-p@chr2:242871899..242871908
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Hg19::chr2:242871926..242871938,-p@chr2:242871926..242871938
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Hg19::chr9:73408368..73408372,-p@chr9:73408368..73408372
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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
retinal pigment epithelial cell3.59e-153
visual pigment cell1.70e-114
Uber Anatomy
Ontology termp-valuen
retina2.07e-245
photoreceptor array2.07e-245
posterior segment of eyeball2.07e-245
neurectoderm1.97e-1790
neural plate1.41e-1686
presumptive neural plate1.41e-1686
layer of retina3.59e-153
pigmented layer of retina3.59e-153
presumptive retinal pigmented epithelium3.59e-153
regional part of nervous system1.58e-1494
nervous system1.58e-1494
eye3.73e-1420
visual system2.04e-1321
adult organism1.31e-12115
sense organ3.90e-1223
sensory system1.42e-1124
entire sense organ system1.42e-1124
camera-type eye1.84e-1119
simple eye1.84e-1119
ocular region1.84e-1119
optic cup1.84e-1119
eye primordium1.84e-1119
optic vesicle1.84e-1119
head2.35e-11123
pre-chordal neural plate2.42e-1161
ectoderm1.21e-10173
presumptive ectoderm1.21e-10173
anterior region of body1.28e-10129
craniocervical region1.28e-10129
pigment epithelium of eye1.47e-1011
central nervous system1.97e-1082
face2.82e-1021
ectoderm-derived structure5.89e-10169
neural tube8.80e-0957
neural rod8.80e-0957
future spinal cord8.80e-0957
neural keel8.80e-0957
brain3.86e-0869
future brain3.86e-0869
posterior neural tube8.57e-0815
chordal neural plate8.57e-0815
medulla oblongata1.30e-073
myelencephalon1.30e-073
future myelencephalon1.30e-073
ectodermal placode3.59e-0729
male genital duct4.01e-073
internal male genitalia4.01e-073
regional part of brain5.78e-0759
caudate-putamen7.81e-073
dorsal striatum7.81e-073


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.