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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2431_heart_thalamus_substantia_spinal_corpus_globus_ovary
|full_id=C2431_heart_thalamus_substantia_spinal_corpus_globus_ovary
|id=C2431
|id=C2431

Revision as of 15:10, 12 September 2012


Full id: C2431_heart_thalamus_substantia_spinal_corpus_globus_ovary



Phase1 CAGE Peaks

Hg19::chr17:66951400..66951411,-p4@ABCA8
Hg19::chr17:66951415..66951429,-p2@ABCA8
Hg19::chr17:66951430..66951441,-p3@ABCA8
Hg19::chr17:66951474..66951550,-p1@ABCA8


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>

Uber Anatomy
Ontology termp-valuen
adult organism1.14e-47115
neural tube6.84e-2757
neural rod6.84e-2757
future spinal cord6.84e-2757
neural keel6.84e-2757
regional part of brain8.61e-2759
anatomical cluster1.51e-26286
anatomical conduit1.57e-23241
tube2.49e-23194
multi-tissue structure7.77e-23347
brain2.65e-2269
future brain2.65e-2269
central nervous system6.43e-2282
neural plate2.00e-2186
presumptive neural plate2.00e-2186
neurectoderm9.32e-2190
anterior neural tube1.91e-2042
regional part of forebrain6.91e-2041
forebrain6.91e-2041
future forebrain6.91e-2041
cell layer1.97e-19312
organism subdivision5.27e-19365
epithelium5.98e-19309
regional part of nervous system1.18e-1794
nervous system1.18e-1794
anterior region of body4.15e-16129
craniocervical region4.15e-16129
head9.59e-16123
gray matter1.79e-1534
brain grey matter1.79e-1534
telencephalon2.08e-1534
regional part of telencephalon7.30e-1533
cerebral hemisphere5.30e-1432
pre-chordal neural plate2.48e-1361
multi-cellular organism1.88e-12659
muscle tissue7.07e-1263
musculature7.07e-1263
musculature of body7.07e-1263
splanchnic layer of lateral plate mesoderm7.33e-1284
regional part of cerebral cortex1.26e-1122
primary circulatory organ2.62e-1127
tissue3.03e-11787
skeletal muscle tissue4.96e-1161
striated muscle tissue4.96e-1161
myotome4.96e-1161
ectoderm-derived structure9.56e-11169
ectoderm1.21e-10173
presumptive ectoderm1.21e-10173
neocortex1.43e-1020
embryo3.65e-10612
embryonic structure3.66e-10605
developing anatomical structure3.66e-10605
cerebral cortex5.27e-1025
pallium5.27e-1025
germ layer6.61e-10604
embryonic tissue6.61e-10604
presumptive structure6.61e-10604
epiblast (generic)6.61e-10604
heart9.67e-1024
primitive heart tube9.67e-1024
primary heart field9.67e-1024
anterior lateral plate mesoderm9.67e-1024
heart tube9.67e-1024
heart primordium9.67e-1024
cardiac mesoderm9.67e-1024
cardiogenic plate9.67e-1024
heart rudiment9.67e-1024
dermomyotome1.31e-0970
anatomical system3.59e-09625
anatomical group5.31e-09626
somite5.74e-0983
paraxial mesoderm5.74e-0983
presomitic mesoderm5.74e-0983
presumptive segmental plate5.74e-0983
trunk paraxial mesoderm5.74e-0983
presumptive paraxial mesoderm5.74e-0983
posterior neural tube1.30e-0715
chordal neural plate1.30e-0715
organ2.47e-07511
nucleus of brain2.62e-079
neural nucleus2.62e-079
brainstem5.18e-078
blood vessel5.98e-0760
epithelial tube open at both ends5.98e-0760
blood vasculature5.98e-0760
vascular cord5.98e-0760
epithelial tube7.23e-07118
basal ganglion7.25e-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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
HEY1#2346244.040111043105710.00375304636917980.0185976660538418
SRF#6722413.79717826216782.75840773062708e-050.000584114649186863
TAF1#687243.343046285745290.008005664898701650.0322086226879118
TBP#690843.706770687096390.005296377814784350.0244107856398174



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.

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