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Coexpression cluster:C1706

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Full id: C1706_pineal_occipital_paracentral_postcentral_alveolar_parietal_medial



Phase1 CAGE Peaks

Hg19::chr13:36429731..36429762,-p4@DCLK1
Hg19::chr13:36429763..36429778,-p7@DCLK1
Hg19::chr13:36429819..36429826,-p12@DCLK1
Hg19::chr13:36429874..36429881,-p13@DCLK1
Hg19::chr19:12945329..12945340,-p5@RTBDN


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
embryonic stem cell6.24e-115
Uber Anatomy
Ontology termp-valuen
central nervous system1.32e-7681
neural tube1.29e-7056
neural rod1.29e-7056
future spinal cord1.29e-7056
neural keel1.29e-7056
nervous system8.90e-7089
regional part of nervous system1.91e-6553
regional part of brain1.91e-6553
brain4.56e-6368
future brain4.56e-6368
regional part of forebrain9.04e-5741
forebrain9.04e-5741
anterior neural tube9.04e-5741
future forebrain9.04e-5741
brain grey matter2.66e-4734
gray matter2.66e-4734
telencephalon5.29e-4734
neural plate6.12e-4682
presumptive neural plate6.12e-4682
adult organism1.55e-44114
cerebral hemisphere9.16e-4432
regional part of telencephalon2.55e-4332
neurectoderm3.69e-4386
pre-chordal neural plate8.30e-3761
regional part of cerebral cortex2.41e-3522
ecto-epithelium2.66e-33104
neocortex1.49e-3120
organ system subdivision3.03e-31223
ectoderm-derived structure4.88e-31171
ectoderm4.88e-31171
presumptive ectoderm4.88e-31171
cerebral cortex1.60e-3025
pallium1.60e-3025
structure with developmental contribution from neural crest5.68e-26132
neural nucleus1.15e-189
nucleus of brain1.15e-189
basal ganglion2.02e-189
nuclear complex of neuraxis2.02e-189
aggregate regional part of brain2.02e-189
collection of basal ganglia2.02e-189
cerebral subcortex2.02e-189
tube4.02e-17192
anatomical cluster3.18e-15373
posterior neural tube1.16e-1415
chordal neural plate1.16e-1415
telencephalic nucleus1.16e-147
gyrus5.39e-146
anatomical conduit1.26e-13240
brainstem6.33e-136
limbic system2.58e-115
parietal lobe2.80e-115
diencephalon6.31e-117
future diencephalon6.31e-117
segmental subdivision of hindbrain3.45e-1012
hindbrain3.45e-1012
presumptive hindbrain3.45e-1012
corpus striatum7.17e-104
striatum7.17e-104
ventral part of telencephalon7.17e-104
future corpus striatum7.17e-104
segmental subdivision of nervous system2.77e-0913
organ part9.74e-09218
multi-cellular organism4.75e-08656
occipital lobe4.78e-085
temporal lobe5.11e-086
caudate-putamen8.85e-083
dorsal striatum8.85e-083
frontal cortex9.04e-083
embryo1.75e-07592
pons2.07e-073
medulla oblongata3.59e-073
myelencephalon3.59e-073
future myelencephalon3.59e-073
epithelium3.77e-07306
cell layer5.86e-07309


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#1488450.17360027146253.18412825898083e-071.59571579289683e-05
CTCF#1066444.288205098460020.005152015588243280.0239281076186481
EP300#203345.419153380978560.00209386927943890.0121139825878196
FOS#235347.198364247115530.0006947858453382510.00559552274069105
JUN#3725410.01026335386910.0001908531347801070.00230460290707591
JUND#372745.595731153496820.001849593301755460.0109314512388681
NANOG#79923423.39582278481016.64263001833934e-060.000194436557310914
SP1#666744.558705102512720.00407573565781680.0194794872948347
STAT3#677448.415571997723390.0003771527211598630.0037421103026045
TCF7L2#693448.616141250509880.0003438969725982450.0034728539858043
TFAP2A#7020413.2149074984366.38708543065286e-050.00104130629923814
TFAP2C#7022510.80922860986026.77323239348459e-060.000197099364152448



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.