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Coexpression cluster:C3112

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Full id: C3112_rhabdomyosarcoma_retina_occipital_Fibroblast_skeletal_Melanocyte_insula



Phase1 CAGE Peaks

Hg19::chr11:125034586..125034604,+p3@PKNOX2
Hg19::chr11:125034605..125034636,+p2@PKNOX2
Hg19::chr11:125034640..125034655,+p1@PKNOX2


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
central nervous system3.48e-3782
regional part of nervous system3.59e-3794
nervous system3.59e-3794
adult organism5.01e-36115
brain7.24e-3369
future brain7.24e-3369
regional part of brain2.84e-3259
neural tube9.67e-3257
neural rod9.67e-3257
future spinal cord9.67e-3257
neural keel9.67e-3257
neurectoderm1.84e-2890
neural plate2.14e-2886
presumptive neural plate2.14e-2886
regional part of forebrain3.07e-2441
forebrain3.07e-2441
future forebrain3.07e-2441
anterior neural tube4.56e-2342
ectoderm9.73e-23173
presumptive ectoderm9.73e-23173
ectoderm-derived structure2.40e-22169
telencephalon4.48e-2234
gray matter5.92e-2234
brain grey matter5.92e-2234
cerebral hemisphere1.94e-2132
regional part of telencephalon2.37e-2133
cell layer4.22e-21312
epithelium1.32e-20309
anterior region of body1.64e-19129
craniocervical region1.64e-19129
head1.85e-19123
multi-tissue structure4.24e-19347
pre-chordal neural plate4.87e-1961
tube6.43e-19194
cerebral cortex1.41e-1725
pallium1.41e-1725
regional part of cerebral cortex7.04e-1722
organism subdivision1.58e-16365
neocortex7.62e-1620
anatomical cluster8.98e-16286
anatomical conduit4.07e-15241
muscle tissue7.60e-1263
musculature7.60e-1263
musculature of body7.60e-1263
embryo1.07e-11612
skeletal muscle tissue2.09e-1161
striated muscle tissue2.09e-1161
myotome2.09e-1161
embryonic structure3.49e-10605
developing anatomical structure3.49e-10605
germ layer6.42e-10604
embryonic tissue6.42e-10604
presumptive structure6.42e-10604
epiblast (generic)6.42e-10604
multi-cellular organism7.18e-10659
posterior neural tube9.55e-1015
chordal neural plate9.55e-1015
organ part7.16e-09219
dermomyotome1.22e-0870
segmental subdivision of nervous system2.18e-0813
segmental subdivision of hindbrain2.97e-0812
hindbrain2.97e-0812
presumptive hindbrain2.97e-0812
primary circulatory organ3.94e-0827
somite9.72e-0883
paraxial mesoderm9.72e-0883
presomitic mesoderm9.72e-0883
presumptive segmental plate9.72e-0883
trunk paraxial mesoderm9.72e-0883
presumptive paraxial mesoderm9.72e-0883
heart1.42e-0724
primitive heart tube1.42e-0724
primary heart field1.42e-0724
anterior lateral plate mesoderm1.42e-0724
heart tube1.42e-0724
heart primordium1.42e-0724
cardiac mesoderm1.42e-0724
cardiogenic plate1.42e-0724
heart rudiment1.42e-0724
anatomical system8.52e-07625


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
CTBP2#1488362.71700033932814.049570681927e-060.00012906106574604
CTCF#1066435.360256373075030.0064925092527670.0278320064790762
CTCFL#140690319.74647435897440.0001298372005551160.00171126544532759
PBX3#5090321.91451268674419.49854535978121e-050.00136023389391223
RAD21#5885310.35503389545630.0009004912073565420.00661879099198465
ZBTB7A#5134137.35190930787590.002516255860282270.0139606484164906



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.