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Coexpression cluster:C3515

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Full id: C3515_neuroblastoma_neuroectodermal_brain_pineal_Retinal_Mesothelial_amygdala



Phase1 CAGE Peaks

  Short description
Hg19::chr15:77363355..77363369,- p3@TSPAN3
Hg19::chr15:77363375..77363406,- p2@TSPAN3
Hg19::chr15:77363411..77363423,- p4@TSPAN3


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset


uberon_data


Uber Anatomy
Ontology termp-valuen
nervous system5.84e-2889
central nervous system7.61e-2681
brain2.73e-2368
future brain2.73e-2368
neural tube2.01e-2056
neural rod2.01e-2056
future spinal cord2.01e-2056
neural keel2.01e-2056
anatomical cluster4.75e-20373
neurectoderm8.31e-2086
regional part of nervous system5.57e-1953
regional part of brain5.57e-1953
neural plate5.66e-1982
presumptive neural plate5.66e-1982
ectoderm-derived structure2.57e-17171
ectoderm2.57e-17171
presumptive ectoderm2.57e-17171
structure with developmental contribution from neural crest1.41e-16132
regional part of forebrain3.22e-1641
forebrain3.22e-1641
anterior neural tube3.22e-1641
future forebrain3.22e-1641
pre-chordal neural plate1.06e-1561
ecto-epithelium6.89e-15104
cell layer2.01e-14309
tube2.13e-14192
epithelium2.73e-14306
telencephalon3.08e-1334
brain grey matter3.71e-1334
gray matter3.71e-1334
anatomical conduit7.10e-13240
cerebral hemisphere8.67e-1332
regional part of telencephalon2.09e-1232
organ system subdivision5.97e-12223
cerebral cortex1.00e-0925
pallium1.00e-0925
regional part of cerebral cortex2.89e-0922
multi-tissue structure1.83e-08342
neocortex1.91e-0820


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


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

TF#promotersEnrichmentp-valueq-value
E2F1#186934.907389214879320.008460985347239390.0324623213210512
E2F6#187635.017155731697390.00791769806886330.0321457187301358
EBF1#187938.9064668465690.00141523283560980.00914015843907318
HMGN3#932438.178547723350590.001827766942164210.0108552830066925
IRF1#365937.63716375356390.002244692747297240.0127847230100331
MAX#414936.452555509007120.003721913834265510.0186236565224634
MXI1#460139.96157162875930.001011470541259020.00719401878633553
NFYA#4800318.42558069983050.0001598135507814160.00199316544423935
NFYB#4801316.75979325353650.0002123649923296180.00245453601526262
NRF1#4899312.21027944771090.0005492172401020010.00470469974893478
RFX5#5993312.04791082719510.0005717246050312580.00483994050618947
SMARCB1#6598318.25271578115740.000164397760679890.00202805784640291
SP1#666735.69838137814090.005403962701712170.0246026355973896
SP2#6668326.15353049384465.58768218891694e-050.000939124461101216
TFAP2A#7020316.5186343730450.0002218033880766340.00247859234403334
TFAP2C#7022310.80922860986020.0007916746575753130.00614414130656967
USF1#739136.361499277207960.00388404057290560.0189980008146163
YY1#752834.911170749853860.008441455341808260.0328679549059804
ZBTB7A#5134137.35190930787590.002516255860282270.0139888877777078
ZNF263#1012738.221841637010680.001799043925565870.010918778971535



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.