Personal tools

Coexpression cluster:C2109

From FANTOM5_SSTAR

Revision as of 12:04, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2109_spleen_uterus_iPS_thyroid_diaphragm_bile_adipose



Phase1 CAGE Peaks

Hg19::chr11:128457446..128457461,-p4@ETS1
Hg19::chr11:128457478..128457485,-p26@ETS1
Hg19::chr11:128457492..128457506,-p6@ETS1
Hg19::chr1:159172206..159172217,-p3@LOC100131825


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:0045648positive regulation of erythrocyte differentiation0.00803602967149417
GO:0045646regulation of erythrocyte differentiation0.00803602967149417
GO:0045639positive regulation of myeloid cell differentiation0.00803602967149417
GO:0030218erythrocyte differentiation0.0126103850229601
GO:0045637regulation of myeloid cell differentiation0.0126103850229601
GO:0045597positive regulation of cell differentiation0.0145266690215472
GO:0051094positive regulation of developmental process0.0178492582126457
GO:0030099myeloid cell differentiation0.0178492582126457
GO:0045595regulation of cell differentiation0.0281261038502296
GO:0030097hemopoiesis0.0281261038502296
GO:0048534hemopoietic or lymphoid organ development0.0281261038502296
GO:0002520immune system development0.0281261038502296
GO:0008285negative regulation of cell proliferation0.031261038502296
GO:0050793regulation of developmental process0.031261038502296



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 organism9.19e-50114
anatomical cluster2.05e-14373
organ system subdivision1.93e-12223
anatomical conduit2.62e-12240
neural tube9.03e-1256
neural rod9.03e-1256
future spinal cord9.03e-1256
neural keel9.03e-1256
regional part of nervous system1.24e-1153
regional part of brain1.24e-1153
regional part of forebrain5.47e-1141
forebrain5.47e-1141
anterior neural tube5.47e-1141
future forebrain5.47e-1141
central nervous system7.94e-1081
male reproductive organ1.68e-0911
telencephalon2.22e-0934
multi-cellular organism2.37e-09656
brain grey matter2.72e-0934
gray matter2.72e-0934
brain9.14e-0968
future brain9.14e-0968
nervous system1.23e-0889
cerebral hemisphere4.36e-0832
regional part of telencephalon4.70e-0832
tube5.18e-08192
neural plate6.68e-0882
presumptive neural plate6.68e-0882
structure with developmental contribution from neural crest9.30e-08132
embryo1.21e-07592
multi-tissue structure1.97e-07342
anatomical system2.51e-07624
anatomical group2.89e-07625
neurectoderm3.46e-0786
regional part of cerebral cortex9.08e-0722


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.