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|full_id=C2555_Mast_brain_Hepatic_thymus_optic_cervical_corpus
|full_id=C2555_Mast_brain_Hepatic_thymus_optic_cervical_corpus
|id=C2555
|id=C2555
|ontology_enrichment_celltype=CL:0002139!1.69e-07!24;CL:0000115!2.23e-07!35
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.57e-31!115;UBERON:0001049!2.58e-17!57;UBERON:0005068!2.58e-17!57;UBERON:0006241!2.58e-17!57;UBERON:0007135!2.58e-17!57;UBERON:0001017!4.58e-14!82;UBERON:0003080!6.22e-14!42;UBERON:0005743!1.19e-13!86;UBERON:0002780!1.81e-13!41;UBERON:0001890!1.81e-13!41;UBERON:0006240!1.81e-13!41;UBERON:0000073!9.33e-13!94;UBERON:0001016!9.33e-13!94;UBERON:0002616!1.05e-12!59;UBERON:0002346!1.64e-12!90;UBERON:0000955!1.68e-12!69;UBERON:0006238!1.68e-12!69;UBERON:0003075!3.45e-12!86;UBERON:0007284!3.45e-12!86;UBERON:0002020!5.08e-12!34;UBERON:0003528!5.08e-12!34;UBERON:0001893!6.51e-12!34;UBERON:0002791!1.49e-11!33;UBERON:0001869!1.03e-10!32;UBERON:0000064!4.20e-10!219;UBERON:0002619!9.93e-10!22;UBERON:0001950!4.61e-09!20;UBERON:0003056!2.13e-08!61;UBERON:0004921!2.78e-08!129;UBERON:0004185!2.78e-08!129;UBERON:0000956!5.57e-08!25;UBERON:0000203!5.57e-08!25;UBERON:0004111!5.72e-08!241;UBERON:0000477!9.98e-08!286;UBERON:0000025!3.12e-07!194;UBERON:0001041!7.87e-07!98;UBERON:0000077!8.53e-07!130
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Revision as of 14:25, 21 May 2012


Full id: C2555_Mast_brain_Hepatic_thymus_optic_cervical_corpus



Phase1 CAGE Peaks

Hg19::chr1:204463845..204463857,-p3@PIK3C2B
Hg19::chr1:204463865..204463876,-p4@PIK3C2B
Hg19::chr1:204463880..204463915,-p2@PIK3C2B
Hg19::chr1:204463918..204463963,-p1@PIK3C2B


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
endothelial cell of vascular tree1.69e-0724
endothelial cell2.23e-0735
Uber Anatomy
Ontology termp-valuen
adult organism1.57e-31115
neural tube2.58e-1757
neural rod2.58e-1757
future spinal cord2.58e-1757
neural keel2.58e-1757
central nervous system4.58e-1482
anterior neural tube6.22e-1442
regional part of forebrain1.81e-1341
forebrain1.81e-1341
future forebrain1.81e-1341
regional part of nervous system9.33e-1394
nervous system9.33e-1394
regional part of brain1.05e-1259
neurectoderm1.64e-1290
brain1.68e-1269
future brain1.68e-1269
neural plate3.45e-1286
presumptive neural plate3.45e-1286
gray matter5.08e-1234
brain grey matter5.08e-1234
telencephalon6.51e-1234
regional part of telencephalon1.49e-1133
cerebral hemisphere1.03e-1032
organ part4.20e-10219
regional part of cerebral cortex9.93e-1022
neocortex4.61e-0920
pre-chordal neural plate2.13e-0861
subdivision of digestive tract2.78e-08129
endodermal part of digestive tract2.78e-08129
cerebral cortex5.57e-0825
pallium5.57e-0825
anatomical conduit5.72e-08241
anatomical cluster9.98e-08286
tube3.12e-07194
foregut7.87e-0798
mixed endoderm/mesoderm-derived structure8.53e-07130


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.