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Coexpression cluster:C2103

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Full id: C2103_Fibroblast_putamen_left_caudate_hippocampus_heart_amniotic



Phase1 CAGE Peaks

Hg19::chr11:12030131..12030183,-p1@DKK3
Hg19::chr11:12030588..12030599,-p9@DKK3
Hg19::chr11:12030633..12030644,-p8@DKK3
Hg19::chr11:12030834..12030845,-p7@DKK3


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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.29e-11180
embryonic cell1.04e-10248
mesodermal cell1.62e-07119
fibroblast1.71e-0775
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure1.89e-34169
ectoderm1.32e-32173
presumptive ectoderm1.32e-32173
head3.03e-32123
anterior region of body8.91e-30129
craniocervical region8.91e-30129
organism subdivision2.39e-29365
epithelium3.50e-28309
cell layer5.36e-28312
neural plate2.58e-2786
presumptive neural plate2.58e-2786
anatomical conduit2.91e-26241
neural tube1.67e-2557
neural rod1.67e-2557
future spinal cord1.67e-2557
neural keel1.67e-2557
anatomical cluster4.13e-25286
neurectoderm7.50e-2590
central nervous system7.75e-2582
brain1.47e-2469
future brain1.47e-2469
regional part of brain1.96e-2459
regional part of nervous system7.46e-2394
nervous system7.46e-2394
tube7.14e-22194
multi-cellular organism1.66e-21659
anatomical system4.87e-21625
anatomical group1.11e-20626
organ part1.79e-19219
pre-chordal neural plate2.74e-1961
multi-tissue structure3.26e-19347
regional part of forebrain2.46e-1841
forebrain2.46e-1841
future forebrain2.46e-1841
anterior neural tube7.55e-1842
gray matter1.15e-1734
brain grey matter1.15e-1734
telencephalon1.40e-1734
regional part of telencephalon4.78e-1733
cerebral hemisphere5.58e-1732
adult organism4.96e-14115
cerebral cortex8.18e-1325
pallium8.18e-1325
embryo1.51e-12612
embryonic structure2.73e-12605
developing anatomical structure2.73e-12605
germ layer3.87e-12604
embryonic tissue3.87e-12604
presumptive structure3.87e-12604
epiblast (generic)3.87e-12604
organ5.93e-12511
vasculature1.82e-1179
vascular system1.82e-1179
regional part of cerebral cortex1.88e-1122
splanchnic layer of lateral plate mesoderm4.13e-1184
neocortex3.22e-1020
vessel2.51e-0969
posterior neural tube6.63e-0915
chordal neural plate6.63e-0915
blood vessel7.45e-0960
epithelial tube open at both ends7.45e-0960
blood vasculature7.45e-0960
vascular cord7.45e-0960
circulatory system9.13e-09113
surface structure1.65e-0895
somite5.17e-0883
paraxial mesoderm5.17e-0883
presomitic mesoderm5.17e-0883
presumptive segmental plate5.17e-0883
trunk paraxial mesoderm5.17e-0883
presumptive paraxial mesoderm5.17e-0883
cardiovascular system8.94e-08110
segmental subdivision of hindbrain2.62e-0712
hindbrain2.62e-0712
presumptive hindbrain2.62e-0712
extraembryonic membrane4.98e-0714
membranous layer4.98e-0714
subdivision of head5.59e-0748
segmental subdivision of nervous system7.92e-0713


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.