Personal tools

Coexpression cluster:C2314: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C2314_salivary_pituitary_cerebellum_breast_small_occipital_brain |id=C2314 }}")
 
No edit summary
Line 2: Line 2:
|full_id=C2314_salivary_pituitary_cerebellum_breast_small_occipital_brain
|full_id=C2314_salivary_pituitary_cerebellum_breast_small_occipital_brain
|id=C2314
|id=C2314
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!1.36e-32!86;UBERON:0001017!1.66e-32!82;UBERON:0000073!3.11e-31!94;UBERON:0001016!3.11e-31!94;UBERON:0001049!1.54e-30!57;UBERON:0005068!1.54e-30!57;UBERON:0006241!1.54e-30!57;UBERON:0007135!1.54e-30!57;UBERON:0000955!1.57e-28!69;UBERON:0006238!1.57e-28!69;UBERON:0002616!5.40e-26!59;UBERON:0002780!1.44e-25!41;UBERON:0001890!1.44e-25!41;UBERON:0006240!1.44e-25!41;UBERON:0003075!4.83e-25!86;UBERON:0007284!4.83e-25!86;UBERON:0003080!2.04e-24!42;UBERON:0002346!1.22e-23!90;UBERON:0004121!2.10e-22!169;UBERON:0000924!1.09e-21!173;UBERON:0006601!1.09e-21!173;UBERON:0003056!3.34e-21!61;UBERON:0001893!5.53e-21!34;UBERON:0002020!5.80e-21!34;UBERON:0003528!5.80e-21!34;UBERON:0002791!3.15e-20!33;UBERON:0000153!3.37e-20!129;UBERON:0007811!3.37e-20!129;UBERON:0001869!5.05e-20!32;UBERON:0000033!6.28e-19!123;UBERON:0007023!5.38e-18!115;UBERON:0002619!1.16e-16!22;UBERON:0001950!1.07e-15!20;UBERON:0000956!1.47e-15!25;UBERON:0000203!1.47e-15!25;UBERON:0000062!3.86e-09!511;UBERON:0000064!4.81e-09!219;UBERON:0003076!2.39e-07!15;UBERON:0003057!2.39e-07!15;UBERON:0000922!3.11e-07!612;UBERON:0002308!7.19e-07!9;UBERON:0000125!7.19e-07!9;UBERON:0002420!7.24e-07!9;UBERON:0007245!7.24e-07!9;UBERON:0010009!7.24e-07!9;UBERON:0010011!7.24e-07!9;UBERON:0000454!7.24e-07!9
}}
}}

Revision as of 14:22, 21 May 2012


Full id: C2314_salivary_pituitary_cerebellum_breast_small_occipital_brain



Phase1 CAGE Peaks

Hg19::chr14:77648077..77648103,+p3@TMEM63C
Hg19::chr14:77648123..77648162,+p1@TMEM63C
Hg19::chr14:77648167..77648183,+p2@TMEM63C
Hg19::chr14:77648188..77648205,+p4@TMEM63C


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
central nervous system1.66e-3282
regional part of nervous system3.11e-3194
nervous system3.11e-3194
neural tube1.54e-3057
neural rod1.54e-3057
future spinal cord1.54e-3057
neural keel1.54e-3057
brain1.57e-2869
future brain1.57e-2869
regional part of brain5.40e-2659
regional part of forebrain1.44e-2541
forebrain1.44e-2541
future forebrain1.44e-2541
neural plate4.83e-2586
presumptive neural plate4.83e-2586
anterior neural tube2.04e-2442
neurectoderm1.22e-2390
ectoderm-derived structure2.10e-22169
ectoderm1.09e-21173
presumptive ectoderm1.09e-21173
pre-chordal neural plate3.34e-2161
telencephalon5.53e-2134
gray matter5.80e-2134
brain grey matter5.80e-2134
regional part of telencephalon3.15e-2033
anterior region of body3.37e-20129
craniocervical region3.37e-20129
cerebral hemisphere5.05e-2032
head6.28e-19123
adult organism5.38e-18115
regional part of cerebral cortex1.16e-1622
neocortex1.07e-1520
cerebral cortex1.47e-1525
pallium1.47e-1525
organ3.86e-09511
organ part4.81e-09219
posterior neural tube2.39e-0715
chordal neural plate2.39e-0715
embryo3.11e-07612
nucleus of brain7.19e-079
neural nucleus7.19e-079
basal ganglion7.24e-079
nuclear complex of neuraxis7.24e-079
aggregate regional part of brain7.24e-079
collection of basal ganglia7.24e-079
cerebral subcortex7.24e-079


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.