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Coexpression cluster:C503

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Full id: C503_occipital_spinal_thalamus_locus_optic_globus_pineal



Phase1 CAGE Peaks

  Short description
Hg19::chr14:95623976..95624057,+ p1@DICER1-AS
Hg19::chr18:46065393..46065444,+ p1@CTIF
Hg19::chr1:10436775..10436792,+ p@chr1:10436775..10436792
+
Hg19::chr1:66999791..66999798,+ p3@SGIP1
Hg19::chr1:67125565..67125577,+ p@chr1:67125565..67125577
+
Hg19::chr1:6997068..6997095,+ p@chr1:6997068..6997095
+
Hg19::chr3:133380806..133380856,+ p1@TFP1
Hg19::chr3:185080917..185080987,+ p2@MAP3K13
Hg19::chr4:118006697..118006741,- p1@TRAM1L1
Hg19::chr4:134070293..134070304,- p2@ENST00000509715
Hg19::chr4:71587632..71587646,+ p3@RUFY3
Hg19::chr4:71587669..71587752,+ p1@RUFY3
Hg19::chr4:71588022..71588055,+ p12@RUFY3
Hg19::chr4:85887859..85888004,+ p1@WDFY3-AS2
Hg19::chr5:133706714..133706743,- p1@CDKL3
Hg19::chr5:81574463..81574494,+ +
p@chr5:81574463..81574494
Hg19::chr7:86781858..86781879,+ p3@DMTF1
Hg19::chrX:100740401..100740449,+ p1@ARMCX4
Hg19::chrX:102585134..102585176,+ p1@TCEAL7


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 system8.31e-4489
central nervous system1.28e-4181
adult organism1.33e-39114
neural tube2.95e-3656
neural rod2.95e-3656
future spinal cord2.95e-3656
neural keel2.95e-3656
neurectoderm5.94e-3586
brain8.57e-3568
future brain8.57e-3568
regional part of nervous system4.56e-3453
regional part of brain4.56e-3453
neural plate2.96e-3382
presumptive neural plate2.96e-3382
ectoderm-derived structure3.78e-31171
ectoderm3.78e-31171
presumptive ectoderm3.78e-31171
regional part of forebrain1.41e-2841
forebrain1.41e-2841
anterior neural tube1.41e-2841
future forebrain1.41e-2841
pre-chordal neural plate7.65e-2561
structure with developmental contribution from neural crest1.93e-24132
brain grey matter9.08e-2434
gray matter9.08e-2434
ecto-epithelium1.09e-23104
telencephalon1.16e-2334
cerebral hemisphere2.16e-2232
regional part of telencephalon2.34e-2232
organ system subdivision9.17e-20223
cerebral cortex1.18e-1725
pallium1.18e-1725
regional part of cerebral cortex7.50e-1722
neocortex2.05e-1520
multi-cellular organism9.72e-14656
anatomical cluster4.21e-12373
multi-tissue structure1.55e-11342
anatomical system6.37e-09624
posterior neural tube8.29e-0915
chordal neural plate8.29e-0915
anatomical group1.23e-08625
organ4.97e-08503
basal ganglion1.38e-079
nuclear complex of neuraxis1.38e-079
aggregate regional part of brain1.38e-079
collection of basal ganglia1.38e-079
cerebral subcortex1.38e-079
neural nucleus1.47e-079
nucleus of brain1.47e-079
embryo1.48e-07592
segmental subdivision of nervous system1.63e-0713
germ layer1.73e-07560
germ layer / neural crest1.73e-07560
embryonic tissue1.73e-07560
presumptive structure1.73e-07560
germ layer / neural crest derived structure1.73e-07560
epiblast (generic)1.73e-07560
embryonic structure2.58e-07564
organ part3.37e-07218
cell layer5.02e-07309
epithelium7.80e-07306
segmental subdivision of hindbrain8.09e-0712
hindbrain8.09e-0712
presumptive hindbrain8.09e-0712
developing anatomical structure9.99e-07581


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
POLR2A#5430151.69535777096690.004160730889787010.0198276406916621
SRF#672253.6308363847810.009828519324532970.036941041844564
TRIM28#1015554.892243432963820.002770097925405220.0151763236233224
USF1#7391124.017789017183973.83675826695491e-060.00012537772110216
USF2#739253.418999311860420.01257386612071660.0454709835104403
YY1#7528123.101792052539285.99478432712854e-050.000985967370615712



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.