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Coexpression cluster:C2413

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Full id: C2413_parietal_occipital_medial_spinal_thalamus_medulla_brain



Phase1 CAGE Peaks

Hg19::chr17:44910420..44910434,-p@chr17:44910420..44910434
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Hg19::chr17:44910446..44910473,-p@chr17:44910446..44910473
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Hg19::chr4:16675930..16675942,-p10@LDB2
Hg19::chr4:90692879..90692891,-p@chr4:90692879..90692891
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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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural tube1.88e-10056
neural rod1.88e-10056
future spinal cord1.88e-10056
neural keel1.88e-10056
regional part of nervous system8.74e-9653
regional part of brain8.74e-9653
brain7.28e-8068
future brain7.28e-8068
regional part of forebrain7.36e-7941
forebrain7.36e-7941
anterior neural tube7.36e-7941
future forebrain7.36e-7941
central nervous system1.06e-7681
telencephalon7.13e-7334
brain grey matter2.07e-7234
gray matter2.07e-7234
neural plate4.97e-6982
presumptive neural plate4.97e-6982
nervous system3.73e-6889
cerebral hemisphere1.30e-6632
regional part of telencephalon3.14e-6632
neurectoderm2.23e-6586
adult organism1.46e-63114
pre-chordal neural plate5.77e-5461
ecto-epithelium2.20e-52104
regional part of cerebral cortex5.97e-5222
neocortex3.92e-4620
cerebral cortex2.29e-4525
pallium2.29e-4525
structure with developmental contribution from neural crest2.41e-41132
ectoderm-derived structure1.30e-32171
ectoderm1.30e-32171
presumptive ectoderm1.30e-32171
neural nucleus2.71e-299
nucleus of brain2.71e-299
organ system subdivision3.65e-25223
tube7.66e-24192
telencephalic nucleus4.28e-237
basal ganglion8.02e-239
nuclear complex of neuraxis8.02e-239
aggregate regional part of brain8.02e-239
collection of basal ganglia8.02e-239
cerebral subcortex8.02e-239
gyrus3.11e-226
posterior neural tube1.12e-2115
chordal neural plate1.12e-2115
brainstem6.53e-216
parietal lobe1.83e-185
segmental subdivision of hindbrain1.98e-1712
hindbrain1.98e-1712
presumptive hindbrain1.98e-1712
anatomical conduit4.80e-17240
segmental subdivision of nervous system5.54e-1613
corpus striatum4.61e-144
striatum4.61e-144
ventral part of telencephalon4.61e-144
future corpus striatum4.61e-144
organ part6.96e-13218
frontal cortex5.28e-123
epithelium5.47e-12306
occipital lobe6.18e-125
cell layer8.96e-12309
medulla oblongata1.29e-113
myelencephalon1.29e-113
future myelencephalon1.29e-113
anatomical cluster1.69e-11373
pons4.90e-113
caudate-putamen5.63e-113
dorsal striatum5.63e-113
limbic system1.01e-105
multi-tissue structure1.64e-09342
regional part of metencephalon2.70e-099
metencephalon2.70e-099
future metencephalon2.70e-099
middle frontal gyrus1.38e-082
middle temporal gyrus1.66e-082
regional part of diencephalon2.00e-084
temporal lobe3.07e-086
diencephalon3.38e-087
future diencephalon3.38e-087
dorsal plus ventral thalamus3.41e-082
thalamic complex3.41e-082
caudate nucleus6.21e-082
future caudate nucleus6.21e-082
locus ceruleus6.66e-082
brainstem nucleus6.66e-082
hindbrain nucleus6.66e-082
globus pallidus9.10e-082
pallidum9.10e-082
Ammon's horn1.63e-072
lobe parts of cerebral cortex1.63e-072
hippocampal formation1.63e-072
limbic lobe1.63e-072


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
FOXA2#3170212.31523187633260.009361916285467240.0353424606881588



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.