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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

cell_data
uberon_data


Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.10e-12180
neurectodermal cell1.17e-0759
Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.55e-4294
nervous system4.55e-4294
central nervous system6.58e-3982
adult organism3.80e-36115
ectoderm5.10e-34173
presumptive ectoderm5.10e-34173
neural tube7.51e-3457
neural rod7.51e-3457
future spinal cord7.51e-3457
neural keel7.51e-3457
neurectoderm1.13e-3390
brain2.51e-3369
future brain2.51e-3369
ectoderm-derived structure7.41e-33169
neural plate1.14e-3286
presumptive neural plate1.14e-3286
regional part of brain2.52e-3259
head8.72e-27123
anterior neural tube2.21e-2642
anterior region of body3.57e-26129
craniocervical region3.57e-26129
regional part of forebrain5.08e-2641
forebrain5.08e-2641
future forebrain5.08e-2641
pre-chordal neural plate2.59e-2461
organism subdivision1.20e-22365
gray matter1.06e-2134
brain grey matter1.06e-2134
telencephalon1.57e-2134
regional part of telencephalon5.91e-2133
cerebral hemisphere2.25e-2032
multi-cellular organism5.77e-18659
cerebral cortex4.50e-1625
pallium4.50e-1625
regional part of cerebral cortex1.84e-1522
neocortex3.59e-1420
multi-tissue structure2.12e-13347
anatomical system3.05e-12625
embryo3.52e-12612
anatomical group6.42e-12626
cell layer1.11e-11312
epithelium1.91e-11309
embryonic structure8.08e-11605
developing anatomical structure8.08e-11605
germ layer1.68e-10604
embryonic tissue1.68e-10604
presumptive structure1.68e-10604
epiblast (generic)1.68e-10604
tube4.32e-09194
anatomical conduit7.70e-09241
organ7.97e-09511
posterior neural tube1.44e-0815
chordal neural plate1.44e-0815
organ part1.87e-08219
anatomical cluster2.18e-08286
segmental subdivision of nervous system2.09e-0713
nucleus of brain4.31e-079
neural nucleus4.31e-079
basal ganglion4.48e-079
nuclear complex of neuraxis4.48e-079
aggregate regional part of brain4.48e-079
collection of basal ganglia4.48e-079
cerebral subcortex4.48e-079
segmental subdivision of hindbrain9.14e-0712
hindbrain9.14e-0712
presumptive hindbrain9.14e-0712


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


No analysis results for this cluster

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.