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Coexpression cluster:C4558: Difference between revisions

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}}
}}

Revision as of 16:49, 26 November 2012


Full id: C4558_mature_heart_mesodermal_lung_skin_diaphragm_eye



Phase1 CAGE Peaks

Hg19::chr6:131291472..131291492,-p2@EPB41L2
Hg19::chr6:131291507..131291537,-p6@EPB41L2
Hg19::chr9:95298256..95298282,-p1@ECM2


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:0008091spectrin0.0101237505259809
GO:0030866cortical actin cytoskeleton organization and biogenesis0.0101237505259809
GO:0030865cortical cytoskeleton organization and biogenesis0.0101237505259809
GO:0030864cortical actin cytoskeleton0.0101237505259809
GO:0030863cortical cytoskeleton0.012653011472308
GO:0005178integrin binding0.0162633670782013
GO:0044448cell cortex part0.0162633670782013
GO:0005938cell cortex0.0202331933385269
GO:0005200structural constituent of cytoskeleton0.0208036560891747
GO:0007160cell-matrix adhesion0.0208036560891747
GO:0032403protein complex binding0.0208036560891747
GO:0031589cell-substrate adhesion0.0208036560891747
GO:0019898extrinsic to membrane0.0208036560891747
GO:0030036actin cytoskeleton organization and biogenesis0.0437120020465577
GO:0030029actin filament-based process0.0437120020465577
GO:0015629actin cytoskeleton0.0466293410899719



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
fibroblast1.07e-1276
muscle precursor cell5.29e-0958
myoblast5.29e-0958
multi-potent skeletal muscle stem cell5.29e-0958
muscle cell5.61e-0855
contractile cell1.67e-0759
fat cell2.75e-0715
Uber Anatomy
Ontology termp-valuen
adult organism5.30e-31114
structure with developmental contribution from neural crest2.08e-15132
neural tube1.00e-1356
neural rod1.00e-1356
future spinal cord1.00e-1356
neural keel1.00e-1356
multi-tissue structure1.45e-13342
regional part of nervous system4.55e-1253
regional part of brain4.55e-1253
regional part of forebrain1.43e-1141
forebrain1.43e-1141
anterior neural tube1.43e-1141
future forebrain1.43e-1141
muscle tissue1.81e-1164
musculature1.81e-1164
musculature of body1.81e-1164
neurectoderm2.12e-1186
neural plate2.66e-1182
presumptive neural plate2.66e-1182
skeletal muscle tissue1.04e-1062
striated muscle tissue1.04e-1062
myotome1.04e-1062
anatomical cluster1.58e-10373
anatomical conduit1.61e-10240
multi-cellular organism2.14e-10656
brain2.47e-1068
future brain2.47e-1068
tube4.07e-10192
tissue5.71e-10773
primary circulatory organ5.81e-1027
central nervous system5.96e-1081
cell layer1.13e-09309
heart1.68e-0924
primitive heart tube1.68e-0924
primary heart field1.68e-0924
anterior lateral plate mesoderm1.68e-0924
heart tube1.68e-0924
heart primordium1.68e-0924
cardiac mesoderm1.68e-0924
cardiogenic plate1.68e-0924
heart rudiment1.68e-0924
dense mesenchyme tissue2.26e-0973
epithelium2.63e-09306
paraxial mesoderm2.73e-0972
presumptive paraxial mesoderm2.73e-0972
telencephalon3.91e-0934
nervous system4.34e-0989
somite6.05e-0971
presomitic mesoderm6.05e-0971
presumptive segmental plate6.05e-0971
dermomyotome6.05e-0971
trunk paraxial mesoderm6.05e-0971
brain grey matter6.23e-0934
gray matter6.23e-0934
regional part of telencephalon2.85e-0832
cerebral hemisphere4.31e-0832
anatomical system1.43e-07624
organ system subdivision1.61e-07223
anatomical group1.92e-07625
regional part of cerebral cortex2.85e-0722
pre-chordal neural plate4.70e-0761
ecto-epithelium4.90e-07104
trunk mesenchyme7.32e-07122
mesenchyme7.93e-07160
entire embryonic mesenchyme7.93e-07160
multilaminar epithelium8.68e-0783
epithelial vesicle9.00e-0778


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.